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Nowomiejska K, Baltaziak K, Całka P, Ciesielka M, Teresiński G, Rejdak R. Identification of the RPGR Gene Pathogenic Variants in a Cohort of Polish Male Patients with Retinitis Pigmentosa Phenotype. Genes (Basel) 2023; 14:1950. [PMID: 37895299 PMCID: PMC10606843 DOI: 10.3390/genes14101950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 10/13/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023] Open
Abstract
The goal of the study was to explore the spectrum of pathogenic variants in the RPGR gene in a group of male Polish patients with a retinitis pigmentosa (RP) phenotype. A total of 45 male index patients, including twins, being members of 44 families, were screened for pathogenic variants in the RPGR gene via the direct sequencing of PCR-amplified genomic DNA and underwent a comprehensive ophthalmological examination in one center located in Poland. A total of two pathogenic and five likely pathogenic variants in eight patients (18%) were detected in the studied cohort. Of these, five variants were novel, and five disease-causing variants (71%) were identified within the ORF15 mutational hotspot of the RPGR gene. The median age of onset of the disease was 10 years (range 6-14 years), the median age during the examination was 30 years (range 20-47 years), and the median visual acuity was 0.4 (range 0.01-0.7). The majority of patients had middle constriction of the visual field and thinning of the central foveal thickness. Dizygotic twins bearing the same hemizygous mutation showed a different retinal phenotype in regard to the severity of the symptoms. This is the first RPGR mutation screening in Poland showing a prevalence of 18% of RPGR pathogenic mutations and likely pathogenic variants in the studied cohort of male patients with an RP phenotype.
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Affiliation(s)
- Katarzyna Nowomiejska
- Chair and Department of General and Pediatric Ophthalmology, Medical University of Lublin, 20-059 Lublin, Poland; (K.B.); (R.R.)
| | - Katarzyna Baltaziak
- Chair and Department of General and Pediatric Ophthalmology, Medical University of Lublin, 20-059 Lublin, Poland; (K.B.); (R.R.)
| | - Paulina Całka
- Department of Forensic Medicine, Medical University of Lublin, 20-059 Lublin, Poland; (P.C.); (M.C.); (G.T.)
| | - Marzanna Ciesielka
- Department of Forensic Medicine, Medical University of Lublin, 20-059 Lublin, Poland; (P.C.); (M.C.); (G.T.)
| | - Grzegorz Teresiński
- Department of Forensic Medicine, Medical University of Lublin, 20-059 Lublin, Poland; (P.C.); (M.C.); (G.T.)
| | - Robert Rejdak
- Chair and Department of General and Pediatric Ophthalmology, Medical University of Lublin, 20-059 Lublin, Poland; (K.B.); (R.R.)
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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] [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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Tran M, Kolesnikova M, Kim AH, Kowal T, Ning K, Mahajan VB, Tsang SH, Sun Y. Clinical characteristics of high myopia in female carriers of pathogenic RPGR mutations: a case series and review of the literature. Ophthalmic Genet 2023; 44:295-303. [PMID: 36017691 PMCID: PMC9968361 DOI: 10.1080/13816810.2022.2113544] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 07/24/2022] [Accepted: 08/01/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND RPGR mutations are the most common cause of X-linked retinitis pigmentosa (XLRP). High myopia has been described as a very frequent feature among affected female carriers of XLRP. However, the clinical phenotype of female patients presenting with X-linked RPGR-related high myopia has not been well described. MATERIALS AND METHODS Retrospective case series of four female patients with RPGR mutations and a diagnosis of high myopia, who presented to two academic eye centers. Clinical data, including age, family history, visual acuity, refractive error, dilated fundus exam, fundus photography, optical coherence tomography, electroretinography, and results of genetic testing, were collected. RESULTS Three RPGR variants identified in the present study have not been previously associated with myopia in female carriers. One variant (c.2405_2406delAG, p.Glu802Glyfs *32) has been previously associated with a myopic phenotype in a female patient. Patients became symptomatic between the first and sixth decades of life. Myopia-associated tilted optic discs and posterior staphyloma were present in all patients. Two patients presented with intraretinal migration of the retinal pigment epithelium. CONCLUSION RPGR-related high myopia has been associated with mutations in exons 1-14 and ORF15 in heterozygous females. There is a wide range of visual function among carriers. Although the exact mechanism of RPGR-related high myopia is still unclear, continued molecular diagnosis and description of phenotypes remain a crucial step in understanding the impact of RPGR mutations on visual function in female XLRP carriers.
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Affiliation(s)
- Matthew Tran
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
- University of Nevada, Reno School of Medicine, Reno, Nevada, USA
| | - Masha Kolesnikova
- Jonas Children’s Vision Care, Department of Ophthalmology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Angela H. Kim
- Jonas Children’s Vision Care, Department of Ophthalmology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tia Kowal
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
- Palo Alto Veterans Administration, Palo Alto, California, USA
| | - Ke Ning
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
| | - Vinit B. Mahajan
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
- Palo Alto Veterans Administration, Palo Alto, California, USA
| | - Stephen H. Tsang
- Jonas Children’s Vision Care, Department of Ophthalmology, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Edward S. Harkness Eye Institute, New York Presbyterian Hospital, New York, New York, USA
| | - Yang Sun
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, California, USA
- Palo Alto Veterans Administration, Palo Alto, California, USA
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Birch DG, Cheetham JK, Daiger SP, Hoyng C, Kay C, MacDonald IM, Pennesi ME, Sullivan LS. Overcoming the Challenges to Clinical Development of X-Linked Retinitis Pigmentosa Therapies: Proceedings of an Expert Panel. Transl Vis Sci Technol 2023; 12:5. [PMID: 37294701 PMCID: PMC10270308 DOI: 10.1167/tvst.12.6.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/24/2023] [Indexed: 06/11/2023] Open
Abstract
X-linked retinitis pigmentosa (XLRP) is a rare inherited retinal disease manifesting as impaired night vision and peripheral vision loss that progresses to legal blindness. Although several trials of ocular gene therapy for XLRP have been conducted or are in progress, there is currently no approved treatment. In July 2022, the Foundation Fighting Blindness convened an expert panel to examine relevant research and make recommendations for overcoming the challenges and capitalizing on the opportunities in conducting clinical trials of RPGR-targeted therapy for XLRP. Data presented concerned RPGR structure and mutation types known to cause XLRP, RPGR mutation-associated retinal phenotype diversity, patterns in genotype/phenotype relationships, disease onset and progression from natural history studies, and the various functional and structural tests used to monitor disease progression. Panel recommendations include considerations, such as genetic screening and other factors that can impact clinical trial inclusion criteria, the influence of age on defining and stratifying participant cohorts, the importance of conducting natural history studies early in clinical development programs, and the merits and drawbacks of available tests for measuring treatment outcomes. We recognize the need to work with regulators to adopt clinically meaningful end points that would best determine the efficacy of a trial. Given the promise of RPGR-targeted gene therapy for XLRP and the difficulties encountered in phase III clinical trials to date, we hope these recommendations will help speed progress to finding a cure. Translational Relevance Examination of relevant data and recommendations for the successful clinical development of gene therapies for RPGR-associated XLRP.
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Affiliation(s)
| | | | - Stephen P. Daiger
- Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
| | - Carel Hoyng
- Radboud University, Nijmegen, The Netherlands
| | | | | | - Mark E. Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland, OR, USA
| | - Lori S. Sullivan
- Human Genetics Center, School of Public Health, University of Texas Health Science Center, Houston, TX, USA
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Kuruvilla SE, Song E, Raoof N, van Bysterveldt K, Oliver VF, Hong SC, Al-Taie R, Wilson G, Vincent AL. Genotypic and phenotypic characterisation of RP2- and RPGR-associated X-linked inherited retinal dystrophy, including female manifestations. Clin Exp Ophthalmol 2023. [PMID: 36882936 DOI: 10.1111/ceo.14220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 02/24/2023] [Accepted: 02/28/2023] [Indexed: 03/09/2023]
Abstract
BACKGROUND With the promise of gene replacement therapy, eligible males and females with X-linked inherited retinal dystrophy (XL-IRD) should be identified. METHODS Retrospective observational cohort study to establish the phenotypic and genotypic spectrum of XL-IRD within New Zealand (NZ). Thirty-two probands, including 9 females, with molecularly proven XL-IRD due to RP2 or RPGR mutations, and 72 family members, of which 43 were affected, were identified from the NZ IRD Database. Comprehensive ophthalmic phenotyping, familial cosegregation, genotyping, and bioinformatics were undertaken. Main outcome measures were: RP2 and RPGR pathogenic variant spectrum, phenotype in males and females (symptoms, age of onset, visual acuity, refraction, electrophysiology, autofluorescence, retinal appearance), and genotype-phenotype correlation. RESULTS For 32 families, 26 unique pathogenic variants were identified; in RP2 (n = 6, 21.9% of all families), RPGR exons 1-14 (n = 10, 43.75%), and RPGR-ORF15 (n = 10, 34.3%). Three RP2 and 8 RPGR exons 1-14 variants are novel, rare, and cosegregate. Thirty-one percent of carrier females were significantly affected, with 18.5% of families initially classified as autosomal dominant. Of five Polynesian families, 80% had novel disease-causing variants. One Māori family showed keratoconus segregating with an ORF15 variant. CONCLUSIONS Significant disease was present in 31% of genetically proven female carriers, often leading to an erroneous presumption of the inheritance pattern. Pathogenic variants in 44% of the families were in exon 1-14 of RPGR, more frequent than usually described, which may inform the gene testing algorithm. Proving cosegregation in families for novel variants and identifying affected females and males translates to optimised clinical care and potential for gene therapy.
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Affiliation(s)
- Shilpa E Kuruvilla
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand.,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Eileen Song
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Naz Raoof
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand.,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Katherine van Bysterveldt
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Verity F Oliver
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
| | - Sheng Chiong Hong
- Eye Department - Gisborne Hospital, Hauora Tairawhiti, Gisborne, New Zealand
| | - Rasha Al-Taie
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand.,Department of Ophthalmology, Manukau Super Clinic, Counties Manukau District Health Board, Manukau, New Zealand
| | - Graham Wilson
- Eye Department - Gisborne Hospital, Hauora Tairawhiti, Gisborne, New Zealand
| | - Andrea L Vincent
- Department of Ophthalmology, Faculty of Medical and Health Sciences, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand.,Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
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Genetic characteristics of suspected retinitis pigmentosa in a cohort of Chinese patients. Gene 2023; 853:147087. [PMID: 36464167 DOI: 10.1016/j.gene.2022.147087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The study aimed to screen for the causative variants in Chinese patients with suspected retinitis pigmentosa (RP). A cohort of 75 unrelated Chinese patients with a clinical diagnosis of RP and their available family members were enrolled in this study. Genomic DNA of all subjects was extracted and whole-exome sequencing (WES) was applied. Candidate variants were identified, and minigene assays were conducted to evaluate the pathogenicity of novel splicing variants. Totally, the diagnostic yield was 44 % (33/75) and 16 novel variants that had not been reported previously were found. Among the genetically solved 33 cases, 31 patients were identified as carrying causative variants of RP and 2 patients carried pathogenic variants implicated in other retinal diseases. USH2A, CYP4V2, and RPGR were the most common causative genes, accounting for about half of the genetically solved cases. Moreover, minigene assays validated that the novel splicing variants were detrimental. Additionally, 9 patients carried a single deleterious heterozygous variant in 6 genes with autosomal recessive hereditary patterns, and no corresponding copy number variants (CNVs) was detected. The findings of this study revealed the genetic landscape of RP in China and provided guidance for clinicians.
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7
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Hadalin V, Buscarino M, Sajovic J, Meglič A, Jarc-Vidmar M, Hawlina M, Volk M, Fakin A. Genetic Characteristics and Long-Term Follow-Up of Slovenian Patients with RPGR Retinal Dystrophy. Int J Mol Sci 2023; 24:ijms24043840. [PMID: 36835250 PMCID: PMC9958649 DOI: 10.3390/ijms24043840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/17/2023] Open
Abstract
Genetic characteristics and a long-term clinical follow-up of 18 Slovenian retinitis pigmentosa GTPase regulator (RPGR) patients from 10 families with retinitis pigmentosa (RP) or cone/cone-rod dystrophy (COD/CORD) are reported. RP (eight families) was associated with two already known (p.(Ser407Ilefs*46) and p.(Glu746Argfs*23)) and five novel variants (c.1245+704_1415-2286del, p.(Glu660*), p.(Ala153Thr), c.1506+1G>T, and p.(Arg780Serfs*54)). COD (two families) was associated with p.(Ter1153Lysext*38). The median age of onset in males with RP (N = 9) was 6 years. At the first examination (median age of 32 years), the median best corrected visual acuity (BCVA) was 0.30 logMAR, and all patients had a hyperautofluorescent ring on fundus autofluorescence (FAF) encircling preserved photoreceptors. At the last follow-up (median age of 39 years), the median BCVA was 0.48 logMAR, and FAF showed ring constriction transitioning to patch in 2/9. Among females (N = 6; median age of 40 years), two had normal/near-normal FAF, one had unilateral RP (male pattern), and three had a radial and/or focal pattern of retinal degeneration. After a median of 4 years (4-21) of follow-up, 2/6 exhibited disease progression. The median age of onset in males with COD was 25 years. At first examination (median age of 35 years), the median BCVA was 1.00 logMAR, and all patients had a hyperautofluorescent FAF ring encircling foveal photoreceptor loss. At the last follow-up (median age of 42 years), the median BCVA was 1.30 logMAR, and FAF showed ring enlargement. The majority of the identified variants (75%; 6/8) had not been previously reported in other RPGR cohorts, which suggested the presence of distinct RPGR alleles in the Slovenian population.
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Affiliation(s)
- Vlasta Hadalin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Maša Buscarino
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Andrej Meglič
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Martina Jarc-Vidmar
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Marko Hawlina
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
| | - Marija Volk
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Šlajmerjeva 4, 1000 Ljubljana, Slovenia
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, Grablovičeva 46, 1000 Ljubljana, Slovenia
- Correspondence:
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Lynn J, Raney A, Britton N, Ramoin J, Yang RW, Radojevic B, McClard CK, Kingsley R, Coussa RG, Bennett LD. Genetic Diagnosis for 64 Patients with Inherited Retinal Disease. Genes (Basel) 2022; 14:74. [PMID: 36672815 PMCID: PMC9859429 DOI: 10.3390/genes14010074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/07/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
The overlapping genetic and clinical spectrum in inherited retinal degeneration (IRD) creates challenges for accurate diagnoses. The goal of this work was to determine the genetic diagnosis and clinical features for patients diagnosed with an IRD. After signing informed consent, peripheral blood or saliva was collected from 64 patients diagnosed with an IRD. Genetic testing was performed on each patient in a Clinical Laboratory Improvement Amendments of 1988 (CLIA) certified laboratory. Mutations were verified with Sanger sequencing and segregation analysis when possible. Visual acuity was measured with a traditional Snellen chart and converted to a logarithm of minimal angle of resolution (logMAR). Fundus images of dilated eyes were acquired with the Optos® camera (Dunfermline, UK). Horizontal line scans were obtained with spectral-domain optical coherence tomography (SDOCT; Spectralis, Heidelberg, Germany). Genetic testing combined with segregation analysis resolved molecular and clinical diagnoses for 75% of patients. Ten novel mutations were found and unique genotype phenotype associations were made for the genes RP2 and CEP83. Collective knowledge is thereby expanded of the genetic basis and phenotypic correlation in IRD.
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Affiliation(s)
- Jacob Lynn
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Austin Raney
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Nathaniel Britton
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Josh Ramoin
- College of Osteopathic Medicine, Oklahoma State University, Stillwater, OK 74078, USA
| | - Ryan W. Yang
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Bojana Radojevic
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Cynthia K. McClard
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Ronald Kingsley
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Razek Georges Coussa
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
| | - Lea D. Bennett
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- College of Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Dean McGee Eye Institute, Oklahoma City, OK 73104, USA
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9
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Liu X, Jia R, Meng X, Wang L, Yang L. Analysis of RPGR gene mutations in 41 Chinese families affected by X-linked inherited retinal dystrophy. Front Genet 2022; 13:999695. [PMID: 36276946 PMCID: PMC9582779 DOI: 10.3389/fgene.2022.999695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Background: This study analyzed the phenotypes and genotypes of 41 Chinese families with inherited retinal dystrophy (IRD) and RPGR gene mutations.Methods: This retrospective analysis evaluated a cohort of 41 patients who were subjected to a specific Hereditary Eye Disease Enrichment Panel (HEDEP) analysis. All (likely) pathogenic variants were determined by Sanger sequencing, and co-segregation analyses were performed on the available family members. All cases were subjected to Sanger sequencing for RPGR open reading frame 15 (ORF15) mutations.Results: A total of 41 probands from different families with a clinical diagnosis of retinitis pigmentosa (RP; 34 cases) and cone-rod dystrophy (CORD; 7 cases) were included in this cohort. According to clinical information, 2, 18, and 21 cases were first assigned as autosomal dominant (AD), sporadic, and X-linked (XL) inheritance, respectively. Several cases of affected females who presented with a male phenotype have been described, posing challenges at diagnosis related to the apparent family history of AD. Mutations were located in RPGR exons or introns 1–14 and in ORF15 of 12 of 41 (29.3%) and 29 of 41 (70.7%) subjects, respectively. Thirty-four (likely) pathogenic mutations were identified. Frameshifts were the most frequently observed variants, followed by nonsense, splice, and missense mutations. Herein, a detailed description of four RP patients carrying RPGR intronic mutations is reported, and in vitro splice assays were performed to confirm the pathogenicity of these intronic mutations.Conclusion: Our findings provide useful insights for the genetic and clinical counseling of patients with XL IRD, which will be useful for ongoing and future gene therapy trials.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Likun Wang
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Peking-Tsinghua Center of Life Sciences, Peking University Health Science Center, Beijing, China
- *Correspondence: Likun Wang, ; Liping Yang,
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
- *Correspondence: Likun Wang, ; Liping Yang,
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Vinikoor-Imler LC, Simpson C, Narayanan D, Abbasi S, Lally C. Prevalence of RPGR-mutated X-linked retinitis pigmentosa among males. Ophthalmic Genet 2022; 43:581-588. [PMID: 36004681 DOI: 10.1080/13816810.2022.2109686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
BACKGROUND X-linked retinitis pigmentosa (XLRP) is a rare inherited retinal disease predominantly affecting males. MATERIALS AND METHODS A comprehensive literature review was conducted to determine the prevalence of retinitis pigmentosa GTPase regulator (RPGR)-mutated XLRP. Identified studies were used to estimate four components among males: the prevalence of retinitis pigmentosa (RP), the proportion of RP that was X-linked, the proportion of misclassified inheritance type among RP cases, and the proportion of XLRP that was RPGR-mutated. Studies providing a direct estimate of XLRP prevalence were also included. The components' sample size-weighted averages were combined to determine an overall prevalence estimate. RESULTS The prevalence of XLRP was estimated to be between 2.7-3.5 per 100,000 males in the US, Europe, and Australia. After correction for misclassification, the prevalence increased to 4.0-5.2 per 100,000 males. Finally, the proportion of XLRP cases due to RPGR mutations was applied, resulting in an RPGR-mutated XLRP estimate of 3.4-4.4 per 100,000 males. Studies from other countries were consistent with the results for the overall XLRP prevalence but were not included in the final calculation because of regional variations and lack of detailed information. CONCLUSIONS These findings address an important gap in the understanding of RPGR-mutated XLRP by summarizing the global burden of this condition.
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Affiliation(s)
| | | | - Divya Narayanan
- Global Medical Affairs, Biogen, Cambridge, Massachusetts, USA
| | - Saad Abbasi
- Global Medical Affairs, Biogen, Cambridge, Massachusetts, USA
| | - Cathy Lally
- Epidemiologic Research & Methods, LLC, Atlanta, Georgia, USA
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Nassisi M, De Bartolo G, Mohand-Said S, Condroyer C, Antonio A, Lancelot ME, Bujakowska K, Smirnov V, Pugliese T, Neidhardt J, Sahel JA, Zeitz C, Audo I. Retrospective Natural History Study of RPGR-Related Cone- and Cone-Rod Dystrophies While Expanding the Mutation Spectrum of the Disease. Int J Mol Sci 2022; 23:7189. [PMID: 35806195 PMCID: PMC9266815 DOI: 10.3390/ijms23137189] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 06/24/2022] [Accepted: 06/24/2022] [Indexed: 01/06/2023] Open
Abstract
Variants in the X-linked retinitis pigmentosa GTPase regulator gene (RPGR) and, specifically, in its retinal opening reading frame-15 isoform (RPGRORF15) may cause rod-cone (RCD), cone, and cone-rod dystrophies (CDs and CRDs). While RPGR-related RCDs have been frequently evaluated, the characteristics and progression of RPGR-related CD/CRDs are largely unknown. Therefore, the goal of our work was to perform genotype-phenotype correlations specifically in RPGRORF15-related CD/CRDs. This retrospective longitudinal study included 34 index patients and two affected relatives with a molecular diagnosis of RPGR-related CD/CRDs. Patients were recruited at the "Quinze-Vingts" Hospital, Paris, France and screened for mutations in RPGRORF15 at the Institut de la Vision, Paris, France. We identified 29 distinct variants, of which 27 were truncating. All were located in the 3' half of the RPGRORF15 transcript. Twenty of them were novel. Fifteen subjects were affected by CD, the remaining had CRD. When analyzing the longitudinal data, a progressive decline in visual acuity (VA) was noted, with more than 60% of the patients reaching VA ≥ 1 LogMar in the best eye after the fifth decade of life. To our knowledge, this is the largest described study of a cohort of CD/CRD patients affected by RPGRORF15 variants. Longitudinal data showed a rapidly progressive disease, possibly locating an optimal window of intervention for future therapies in younger ages.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
- Department of Clinical Sciences and Community Health, University of Milan, 20122 Milan, Italy
- Ophthalmology Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico di Milano, 20122 Milan, Italy
| | - Giuseppe De Bartolo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Saddek Mohand-Said
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Christel Condroyer
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - Marie-Elise Lancelot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Kinga Bujakowska
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA 02114, USA
| | - Vasily Smirnov
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Exploration de la Vision et Neuro-Ophthalmologie, Centre Hospitalier Universitaire de Lille, 59000 Lille, France
- Faculté de Médecine, Université de Lille, 59000 Lille, France
| | - Thomas Pugliese
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
| | - John Neidhardt
- Human Genetics, Faculty VI, School of Medicine and Health Sciences, University of Oldenburg, 26129 Oldenburg, Germany;
- Research Center Neurosensory Science, University Oldenburg, 26129 Oldenburg, Germany
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
- Department of Ophthalmology, University of Pittsburgh Medical School, Pittsburgh, PA 15213, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75012 Paris, France; (M.N.); (G.D.B.); (S.M.-S.); (C.C.); (A.A.); (M.-E.L.); (K.B.); (V.S.); (T.P.); (J.-A.S.)
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, National Rare Disease Center REFERET and INSERM-DGOS CIC 1423, 75012 Paris, France
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Pulido JS, Procopio R, Davila HJ, Bello N, Ku C, Pennesi ME, Yang P, Nagiel A, Mahroo OA, Aleman TS, Salido EM, Reynolds M. Inherited Retinal Disease Panels-Caveat Emptor-Truly Know Your Inherited Retinal Disease Panel. Retina 2022; 42:1-3. [PMID: 34690342 PMCID: PMC8702468 DOI: 10.1097/iae.0000000000003319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jose S Pulido
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
- Department of Ophthalmology, Mayo Clinic, Rochester, Minnesota
- Department of Molecular Medicine, Mayo Clinic, Rochester, Minnesota
| | - Rebecca Procopio
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Hiram J Davila
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Nicholas Bello
- Department of Ophthalmology, Wills Eye Hospital, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Cristy Ku
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute, Oregon Health & Science University, Portland, Oregon
| | - Aaron Nagiel
- The Vision Center, Children's Hospital Los Angeles, USC Roski Eye Institute, Keck School of Medicine University of Southern California, Los Angeles, California
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, University College London, London, United Kingdom
- Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom
- Department of Ophthalmology, Guy's and St Thomas' NHS Foundation Trust, London, United Kingdom
- Section of Ophthalmology, King's College London, London, United Kingdom
- Physiology, Development, and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Tomas S Aleman
- Department of Ophthalmology, Scheie Eye Institute at the Perelman Center for Advance Medicine and the Center for Advanced Retinal and Ocular Therapeutics (CAROT), University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
- The Children's Hospital of Philadelphia (CHOP), Philadelphia, Pennsylvania
| | - Ezequiel M Salido
- Department of Biochemistry, Ophthalmology, and Visual Sciences, West Virginia University, Morgantown, West Virginia; and
| | - Margaret Reynolds
- Department of Ophthalmology and Visual Sciences, Washington University in St. Louis, St. Louis, Missouri
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Yang J, Zhou L, Ouyang J, Xiao X, Sun W, Li S, Zhang Q. Genotype-Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review. Front Genet 2021; 12:600210. [PMID: 34745198 PMCID: PMC8565807 DOI: 10.3389/fgene.2021.600210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/27/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose RPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies. Methods Variants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed. Results A total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants. Conclusion Most pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR.
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Affiliation(s)
- Junxing Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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Rodríguez-Muñoz A, García-Bohórquez B, Udaondo P, Hervás-Ontiveros A, Salom D, Aller E, Jaijo T, García-García G, Millán J. CONCOMITANT MUTATIONS IN INHERITED RETINAL DYSTROPHIES: Why the Reproductive and Therapeutic Counseling Should Be Addressed Cautiously. Retina 2021; 41:1966-1975. [PMID: 33411470 DOI: 10.1097/iae.0000000000003103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
PURPOSE To highlight the challenge of correct reproductive and therapeutic counseling in complex pedigrees with different inherited retinal dystrophies (IRD). METHODS Two hundred eight patients diagnosed with nonsyndromic IRD underwent full ophthalmologic examination and molecular analysis using targeted next-generation sequencing. RESULTS Five families (4%) carried mutations in more than one gene that contribute to different IRD. Family fRPN-NB had a dominant mutation in SNRNP200, which was present in nine affected individuals and four unaffected, and a mutation in RP2 among 11 family members. Family fRPN-142 carried a mutation in RPGR that cosegregated with the disease in all affected individuals. In addition, the proband also harbored two disease-causing mutations in the genes BEST1 and SNRNP200. Family fRPN-169 beared compound heterozygous mutations in USH2A and a dominant mutation in RP1. Genetic testing of fRPN-194 determined compound heterozygous mutations in CNGA3 and a dominant mutation in PRPF8 only in the proband. Finally, fRPN-219 carried compound heterozygous mutations in the genes ABCA4 and TYR. CONCLUSION These findings reinforce the complexity of IRD and underscore the need for the combination of high-throughput genetic testing and clinical characterization. Because of these features, the reproductive and therapeutic counseling for IRD must be approached with caution.
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Affiliation(s)
- Ana Rodríguez-Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - Belén García-Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
| | - Patricia Udaondo
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Ana Hervás-Ontiveros
- Department of Ophthalmology, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - David Salom
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Department of Ophthalmology Hospital de Manises, Valencia, Spain; and
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
- Unit of Genetics, University and Polytechnic Hospital La Fe, Valencia, Spain
| | - Gema García-García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
| | - José Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- Joint Unit of Rare Diseases IIS La Fe-CIPF, Valencia, Spain
- Biomedical Research Network of Rare Diseases (CIBERER), Spain
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Analysis of imaging biomarkers and retinal nerve fiber layer thickness in RPGR-associated retinitis pigmentosa. Graefes Arch Clin Exp Ophthalmol 2021; 259:3597-3604. [PMID: 34287692 PMCID: PMC8589744 DOI: 10.1007/s00417-021-05233-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 03/22/2021] [Accepted: 05/03/2021] [Indexed: 01/23/2023] Open
Abstract
Purpose To investigate multimodal retinal imaging characteristics including the retinal nerve fiber layer (RNFL) thickness in patients with RPGR-associated retinitis pigmentosa (RP). Methods This cross-sectional case–control study included 17 consecutive patients (median age, 21 years) with RPGR-associated RP who underwent retinal imaging including optical coherence tomography (OCT), short-wavelength fundus autofluorescence (AF) imaging, and RNFL scans centered on the optic disc. RNFL thickness was manually segmented and compared to clinical and imaging parameters including the transfoveal ellipsoid zone (EZ) width, the horizontal diameter of the macular hyperautofluorescent ring. RNFL thickness was compared to 17 age- and sex-matched controls. Results In patients with RPGR-associated RP, the EZ width (R2 = 0.65), the central hyperautofluorescent ring on AF images (R2 = 0.72), and visual acuity (R2 = 0.68) were negatively correlated with age. In comparison to controls, a significantly (p < 0.0001) increased global RNFL thickness was identified in RPGR-associated RP, which was, however, less pronounced in progressed disease as indicated by the EZ width or the diameter of the central hyperautofluorescent ring. Conclusions This study describes retinal characteristics in patients with RPGR-associated RP including a pronounced peripapillary RNFL thickness compared to healthy controls. These results contribute to the knowledge about imaging biomarkers in RP, which might be of interest for therapeutic approaches such as gene replacement therapies.
![]() Supplementary Information The online version contains supplementary material available at 10.1007/s00417-021-05233-w.
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Chivers M, Li N, Pan F, Wieffer H, Slowik R, Leartsakulpanitch J. The Burden of X-Linked Retinitis Pigmentosa on Patients and Society: A Narrative Literature Review. CLINICOECONOMICS AND OUTCOMES RESEARCH 2021; 13:565-572. [PMID: 34188501 PMCID: PMC8236258 DOI: 10.2147/ceor.s297287] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/10/2021] [Indexed: 01/18/2023] Open
Abstract
X-linked retinitis pigmentosa (XLRP) is a severe form of retinitis pigmentosa (RP), a rare, inherited retinal degenerative disorder, that causes blindness. The aim of this literature review was to identify what is currently known about the burden of XLRP. Literature databases were searched for articles describing the clinical, humanistic, or economic burden of XLRP or RP in the US, Japan, France, Germany, Italy, Spain, and the UK, published in English between 2014 and 2019; gray literature and cited references were reviewed. Literature describing XLRP is limited as this is an ultra-rare condition; findings relating to burden of RP have been reported with interpretation of how burden differs for XLRP. In XLRP, night blindness usually presents in the first decade of life, followed by loss of peripheral and then central vision; legal blindness is reported at a median of 45 years in affected males (vs median 70 years for RP). There is limited evidence of humanistic or economic burden specific to XLRP; one study identified greater vision-related activity limitations in patients with XLRP compared with the wider RP population. Qualitative studies describe increased humanistic burden for people living with RP; difficulty undertaking everyday tasks (driving, hobbies, reading), psychosocial burden and barriers to work and career. People described the emotional impact of dealing with progression of RP, ongoing social and physical challenges, and the impact of RP on relationships. The economic burden of RP is associated with lost productivity, greater healthcare costs and increasing requirement for formal and informal care. In summary, XLRP remains an untreatable condition that can impact people from childhood. The humanistic burden of RP has been shown to increase as the disease progresses; hence, in XLRP the earlier onset and earlier progression to blindness during prime working years may mean a comparatively greater lifetime burden of disease.
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Affiliation(s)
| | - Nan Li
- Janssen Global Services,LLC, Raritan, NJ, 08869, USA
| | - Feng Pan
- Janssen Global Services,LLC, Raritan, NJ, 08869, USA
| | | | - Rafal Slowik
- Janssen Global Services,LLC, Raritan, NJ, 08869, USA
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A novel mutation of the RPGR gene in a Chinese X-linked retinitis pigmentosa family and possible involvement of X-chromosome inactivation. Eye (Lond) 2021; 35:1688-1696. [PMID: 32839555 PMCID: PMC8169654 DOI: 10.1038/s41433-020-01150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/14/2020] [Accepted: 08/13/2020] [Indexed: 01/30/2023] Open
Abstract
OBJECTIVES The objective of this study is to investigate the molecular mechanisms and genotype-phenotype correlations of a Chinese family with X-linked retinitis pigmentosa (XLRP). METHODS A four-generation family with a total of 41 individuals including 7 affected males was recruited. All subjects in this pedigree underwent a complete ophthalmic examination. Targeted capture and next-generation sequencing were performed on the proband using a multigene panel containing 57 known causative genes of retinitis pigmentosa (RP), including RP1, RP2, RPGR, RHO, PRPH2, CRB1 among others. All variants were verified in the remaining family members by polymerase chain reaction amplification and Sanger sequencing. Blood DNA was used for X-chromosome inactivation analysis in female carriers. RESULTS All the affected individuals were diagnosed with RP. The affected males showed symptoms from the first decade, while the female carriers had onset in the second decade or later. A frameshift mutation c.345_348delTGAA in the RPGR gene was identified in all affected males and female carriers. By XCI analysis, we found that there was little correlation between their phenotype and the methylation status of their X chromosomes. CONCLUSIONS A novel mutation c.345_348delTGAA of the RPGR gene was identified, expanding the spectrum of RPGR mutations causing XLRP. In this pedigree, the phenotype extended to female carriers, in whom RP was milder and its onset delayed compared to hemizygous males. Although lack of strong correlation between X-inactivation and the severity of the disease, the milder, variable effects in female carriers still could reflect X-inactivation patterns in the retina of each individual.
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Mahroo OA, Arno G, Ba-Abbad R, Downes SM, Bird A, Webster AR. Reanalysis of Association of Pro50Leu Substitution in Guanylate Cyclase Activating Protein-1 With Dominant Retinal Dystrophy. JAMA Ophthalmol 2020; 138:200-203. [PMID: 31804667 PMCID: PMC6902164 DOI: 10.1001/jamaophthalmol.2019.4959] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Question Is there evidence that the Pro50Leu substitution in guanylate cyclase activating protein-1 (encoded by the gene GUCA1A) is associated with a dominant retinal dystrophy? Findings In this cross-sectional study reevaluating the original published study of a family after examination of another family member and further genetic testing, a pathogenic variant in the X chromosome–linked RPGR gene was found. Also, publicly available genomic data show that the variant in GUCA1A is too common to cause a dominant retinal dystrophy. Meaning The p.(Pro50Leu) variant in GUCA1A should not be considered a pathogenic variant. Importance As genetic and genomic screening is becoming more widely accessed, correctly distinguishing pathogenic from nonpathogenic variants is of increasing relevance. Objective To reevaluate a previously reported family in whom the p.(Pro50Leu) variant in the gene GUCA1A was associated with a dominant retinal dystrophy, in light of new examination findings in the proband’s daughter. Design, Setting, and Participants A genetic study relating to a family with an inherited retinal dystrophy was performed at the retinal genetics service of Moorfields Eye Hospital from October 27, 2009, to May 23, 2019, after the proband’s daughter underwent fundus examination. Main Outcomes and Measures Results of sequencing of X chromosome–linked retinitis pigmentosa genes in the proband and specific analysis of the repetitive ORF15 region of the RPGR gene. Results A frame-shifting single-nucleotide deletion was found in the ORF15 exon of RPGR (GRCh37 [hg19] x:38145160delT; NM_001034853.1: c.3092delA p.[Glu1031Glyfs*58]), which may be associated with the loss of 121 amino acid residues at the carboxyl terminus of the protein. The p.(Pro50Leu) variant in GUCA1A was also found to be too common in a publicly available genome database to be a fully penetrant cause of a dominant retinal dystrophy. Conclusions and Relevance The phenotype in the family is now associated with the variant in RPGR. The findings suggest that the p.(Pro50Leu) variant in GUCA1A should not be regarded as pathogenic. This report also highlights the relevance of examining relatives, of reevaluating diagnoses in light of new data, and of considering X chromosome–linked inheritance in apparently autosomal dominant pedigrees unless there is clear male-to-male transmission.
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Affiliation(s)
- Omar A Mahroo
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom.,Institute of Ophthalmology, University College London, United Kingdom.,Section of Ophthalmology, King's College London, St Thomas' Hospital Campus, London, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, United Kingdom
| | - Gavin Arno
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom.,Institute of Ophthalmology, University College London, United Kingdom
| | - Rola Ba-Abbad
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom.,Institute of Ophthalmology, University College London, United Kingdom
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals National Health Service Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Alan Bird
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom.,Institute of Ophthalmology, University College London, United Kingdom
| | - Andrew R Webster
- Genetics Service, Moorfields Eye Hospital, London, United Kingdom.,Institute of Ophthalmology, University College London, United Kingdom
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19
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Translational Read-Through Therapy of RPGR Nonsense Mutations. Int J Mol Sci 2020; 21:ijms21228418. [PMID: 33182541 PMCID: PMC7697989 DOI: 10.3390/ijms21228418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 10/28/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022] Open
Abstract
X-chromosomal retinitis pigmentosa (RP) frequently is caused by mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. We evaluated the potential of PTC124 (Ataluren, TranslamaTM) treatment to promote ribosomal read-through of premature termination codons (PTC) in RPGR. Expression constructs in HEK293T cells showed that the efficacy of read-through reagents is higher for UGA than UAA PTCs. We identified the novel hemizygous nonsense mutation c.1154T > A, p.Leu385* (NM_000328.3) causing a UAA PTC in RPGR and generated patient-derived fibroblasts. Immunocytochemistry of serum-starved control fibroblasts showed the RPGR protein in a dot-like expression pattern along the primary cilium. In contrast, RPGR was no longer detectable at the primary cilium in patient-derived cells. Applying PTC124 restored RPGR at the cilium in approximately 8% of patient-derived cells. RT-PCR and Western blot assays verified the pathogenic mechanisms underlying the nonsense variant. Immunofluorescence stainings confirmed the successful PTC124 treatment. Our results showed for the first time that PTC124 induces read-through of PTCs in RPGR and restores the localization of the RPGR protein at the primary cilium in patient-derived cells. These results may provide a promising new treatment option for patients suffering from nonsense mutations in RPGR or other genetic diseases.
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20
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Liu X, Tao T, Zhao L, Li G, Yang L. Molecular diagnosis based on comprehensive genetic testing in 800 Chinese families with non-syndromic inherited retinal dystrophies. Clin Exp Ophthalmol 2020; 49:46-59. [PMID: 33090715 DOI: 10.1111/ceo.13875] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 09/23/2020] [Accepted: 10/05/2020] [Indexed: 12/16/2022]
Abstract
IMPORTANCE Inherited retinal dystrophies (IRDs) are a group of monogenic diseases, one of the leading causes of blindness. BACKGROUND Introducing a comprehensive genetic testing strategy by combining single gene Sanger sequencing, next-generation sequencing (NGS) including whole exome sequencing (WES), and a specific hereditary eye disease enrichment panel (HEDEP) sequencing, to identify the disease-causing variants of 800 Chinese probands affected with non-syndromic IRDs. DESIGN Retrospective analysis. PARTICIPANTS Eight hundred Chinese non-syndromic IRDs probands and their families. METHODS A total of 149 patients were subjected to Sanger sequencing. Of the 651 patients subjected to NGS, 86 patients underwent WES and 565 underwent HEDEP. Patients that likely carried copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA) or quantitative fluorescence PCR (QF-PCR). MAIN OUTCOME MEASURES The diagnostic rate. RESULTS (Likely) pathogenic variants were determined in 481 cases (60.13% detection rate). The detection rates of single gene Sanger sequencing, WES and HEDEP were 86.58%, 31.40% and 56.99%, respectively. Approximately 11.64% of 481 cases carried autosomal dominant variants, 72.97% carried AR variants and 15.39% were found to be X-linked. CNVs were confirmed by MLPA or QF-PCR in 17 families. Fourteen genes that each caused disease in 1% or more of the cohort were detected, and these genes were collectively responsible for disease in almost one half (46.38%) of the families. CONCLUSIONS AND RELEVANCE Sanger sequencing is ideal to detect pathogenic variants of clinical homogeneous diseases, whereas NGS is more appropriate for patients without an explicit clinical diagnosis.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Lin Zhao
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, China.,Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, China
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21
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Cehajic-Kapetanovic J, McClements ME, Whitfield J, Shanks M, Clouston P, MacLaren RE. Association of a Novel Intronic Variant in RPGR With Hypomorphic Phenotype of X-Linked Retinitis Pigmentosa. JAMA Ophthalmol 2020; 138:1151-1158. [PMID: 32970112 PMCID: PMC7516822 DOI: 10.1001/jamaophthalmol.2020.3634] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Importance Pathogenic variants in retinitis pigmentosa GTPase regulator (RPGR) gene typically lead to a severe form of X-linked retinitis pigmentosa, which is associated with early severe vision loss. Objective To investigate an X-linked retinal degeneration family with atypical preservation of visual acuity in the presence of a novel deep intronic splice site RPGR c.779-5T>G variant. Design, Setting, and Participants In this case series, 3 members of an X-linked retinal degeneration family were studied by in-depth phenotyping and genetic screening at a single center. Data were collected and analyzed from November 2018 to March 2020. Main Outcomes and Measures Data were collected on full ophthalmic history, examination, and retinal imaging. A full retinitis pigmentosa gene panel was analyzed by next-generation sequencing. The pathogenicity of the RPGR c.779-5T>G variant was assessed by in silico splice prediction tools and by purpose-designed in vitro splicing assay. Results An 84-year-old man was referred with clinical diagnosis of choroideremia and possible inclusion into a gene therapy trial. He presented with late-stage retinal degeneration and unusually preserved visual acuity (78 and 68 ETRDS letters) that clinically resembled choroideremia. His 23-year-old grandson was still in early stages of degeneration but showed a very different clinical picture, typical of retinitis pigmentosa. Next-generation sequencing identified a sole RPGR c.779-5T>G variant of undetermined pathogenicity in both cases. The daughter of the proband showed an RPGR carrier phenotype and was confirmed to carry the same variant. The molecular analysis confirmed that the RPGR c.779-5T>G variation reduced the efficiency of intron splicing compared with wild type, leading to a population of mutant and normal transcripts. The predicted consequences of the pathogenic variant are potential use of an alternative splice acceptor site or complete skipping of exon 8, resulting in truncated forms of the RPGR protein with different levels of glutamylation. Conclusions and Relevance These results support the importance of careful interpretation of inconsistent clinical phenotypes between family members. Using a molecular splicing assay, a new pathogenic variant in a noncoding region of RPGR was associated with a proportion of normal and hypomorphic RPGR, where cones are likely to survive longer than expected, potentially accounting for the preserved visual acuity observed in this family.
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Affiliation(s)
- Jasmina Cehajic-Kapetanovic
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Michelle E. McClements
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Jennifer Whitfield
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Morag Shanks
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Penny Clouston
- Genetics Laboratories, Churchill Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, England
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, England
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22
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柳 小, 李 莹, 杨 丽. [Comparison study of whole exome sequencing and targeted panel sequencing in molecular diagnosis of inherited retinal dystrophies]. BEIJING DA XUE XUE BAO. YI XUE BAN = JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2020; 52:836-844. [PMID: 33047716 PMCID: PMC7653409 DOI: 10.19723/j.issn.1671-167x.2020.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To evaluate and compare whole exome sequencing (WES) and targeted panel sequencing in the clinical molecular diagnosis of the Chinese families affected with inherited retinal dystrophies (IRDs). METHODS The clinical information of 182 probands affected with IRDs was collected, including their family history and the ophthalmic examination results. Blood samples of all probands and their relatives were collected and genomic DNA was extracted by standard protocols. The first 91 cases were subjected to the WES and the other 91 cases were subjected to a specific hereditary eye disease enrichment panel (HEDEP) designed by us. All likely pathogenic and pathogenic variants in the candidate genes were determined by Sanger sequencing and co-segregation analyses were performed in available family members. Copy number variations (CNVs) detected by HEDEP were further validated by multiplex ligation-dependent probe amplification (MLPA). As PRGR ORF15 was difficult to capture by next generation sequencing (NGS), all the samples were subjected to Sanger sequencing for this region. All sequence changes identified by NGS were classified according to the American College of Medical Gene-tics and Genomics and the Association for Molecular Pathology (ACMG/AMP) variant interpretation guidelines. In this study, only variants identified as pathogenic or likely pathogenic were included, while those variants of uncertain significance, likely benign or benign were not included. RESULTS In 91 cases with WES, pathogenic or likely pathogenic variants were determined in 30 cases, obtaining a detection rate of 33.00% (30/91); While in 91 cases with HEDEP sequencing, pathogenic or likely pathogenic variants were determined in 51 cases, achieving the diagnostic rate of 56.04% (51/91), and totally, the diagnostic rate was 44.51%. HEDEP had better sequencing coverage and read depth than WES, therefore HEDEP had higher detection rate. In addition, HEDEP could detect CNVs. In this study, we detected disease-causing variants in 29 distinct IRD-associated genes, USH2A, ABCA4 and RPGR were the three most common disease-causing genes, and the frequency of these genes in Chinese IRDs population was 11.54% (21/182), 6.59% (12/182) and 3.85% (7/182), respectively. We found 43 novel variants and 6 cases carried variants in RPGR ORF15. CONCLUSION NGS in conjunction with Sanger sequencing offers a reliable and effective approach for the genetic diagnosis of IRDs, and after evaluating the pros and cons of the two sequencing methods, we conclude that HEDEP should be used as a first-tier test for IRDs patients, WES can be used as a supplementary molecular diagnostic method due to its merit of detecting novel IRD-associated genes if HEDEP or other methods could not detect disease-causing va-riants in reported genes. In addition, our results enriched the mutational spectra of IRDs genes, and our methods paves the way of genetic counselling, family planning and up-coming gene-based therapies for these families.
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Affiliation(s)
- 小珍 柳
- />北京大学第三医院眼科,北京 100191Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China
| | - 莹莹 李
- />北京大学第三医院眼科,北京 100191Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China
| | - 丽萍 杨
- />北京大学第三医院眼科,北京 100191Department of Ophthalmology, Peking University Third Hospital, Beijing 100191, China
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23
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Zou X, Fang S, Wu S, Li H, Sun Z, Zhu T, Wei X, Sui R. Detailed comparison of phenotype between male patients carrying variants in exons 1-14 and ORF15 of RPGR. Exp Eye Res 2020; 198:108147. [PMID: 32702353 DOI: 10.1016/j.exer.2020.108147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/05/2020] [Accepted: 07/08/2020] [Indexed: 12/19/2022]
Abstract
PURPOSE To compare disease severity in detail between patients carrying variants in exons 1-14 and ORF15 of retinitis pigmentosa GTPase regulator (RPGR). METHODS Systematic next-generation sequencing data analysis, Sanger sequencing validation and segregation analysis were utilised to identify the pathogenic variants. Detailed ophthalmic examinations, including electroretinograms, fundus photography, fundus autofluorescence and optical coherence tomography were performed. Statistical analysis, including age adjustment and comparison, were performed based on cross-sectional level to compare disease severity between variants in the two RPGR variant groups. RESULTS Sixty-two variants were identified in RPGR in 86 patients from 77 unrelated families. Twenty-nine (37.7%) had variants in RPGR-exons 1-14 (group 1) and 48 (62.3%) in RPGR-ORF15 (group 2). Eighty-four patients were diagnosed with X-linked retinitis pigmentosa and only two patients with cone-rod dystrophy. LogMAR visual acuity increased 0.035 and 0.022 each year on average in group 1 and group 2, respectively. Group 2 patients had better visual acuity with a mean logMAR difference of 0.4378, which is significant after age adjustment (P < 0.01). Neither the value of log (ellipsoid zone width) nor central retinal thickness was significantly correlated with variant grouping after considering the effect of the age variable (P = 0.56 and 0.40, respectively). Spherical refractive error did not differ significantly between the two variant groups (P = 0.17). Patterns of autofluorescence included a hyperfluorescent ring at the posterior pole, diffuse hyperfluorescence in the macular area, and dark macular autofluorescence with or without fovea hyperfluorescence. The age and proportion of fundus autofluorescence patterns between the two variant groups were significantly different (P < 0.01). CONCLUSIONS Patients with variants in exons 1-14 retained less visual acuity than patients with ORF15 variants and deteriorated faster. However, the ellipsoid zone widths, central retinal thickness and refractions were comparable between the two groups. Autofluorescence pattern relates to the age and the variant grouping.
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Affiliation(s)
- Xuan Zou
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Sha Fang
- School of Statistics, Capital University of Economics and Business, Beijing, 100070, China
| | - Shijing Wu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Hui Li
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Tian Zhu
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Xing Wei
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, China.
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24
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Dufour VL, Cideciyan AV, Ye GJ, Song C, Timmers A, Habecker PL, Pan W, Weinstein NM, Swider M, Durham AC, Ying GS, Robinson PM, Jacobson SG, Knop DR, Chulay JD, Shearman MS, Aguirre GD, Beltran WA. Toxicity and Efficacy Evaluation of an Adeno-Associated Virus Vector Expressing Codon-Optimized RPGR Delivered by Subretinal Injection in a Canine Model of X-linked Retinitis Pigmentosa. Hum Gene Ther 2020; 31:253-267. [PMID: 31910043 DOI: 10.1089/hum.2019.297] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Applied Genetic Technologies Corporation (AGTC) is developing a recombinant adeno-associated virus (rAAV) vector AGTC-501, also designated rAAV2tYF-GRK1-hRPGRco, to treat X-linked retinitis pigmentosa (XLRP) in patients with mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene. The vector contains a codon-optimized human RPGR cDNA (hRPGRco) driven by a photoreceptor-specific promoter (G protein-coupled receptor kinase 1 [GRK1]), and is packaged in an AAV2 capsid variant with three surface tyrosine residues changed to phenylalanine (AAV2tYF). We conducted a toxicity and efficacy study of this vector administered by subretinal injection in the naturally occurring RPGR mutant (X-linked progressive retinal atrophy 2 [XLPRA2]) dog model. Sixteen RPGR mutant dogs divided into four groups of three to five animals each received either a subretinal injection of 0.07 mL of AGTC-501 at low (1.2 × 1011 vector genome [vg]/mL), mid (6 × 1011 vg/mL), or high dose (3 × 1012 vg/mL), or of vehicle control in the right eye at early-stage disease. The left eye remained untreated. Subretinal injections were well tolerated and were not associated with systemic toxicity. Electroretinography, in vivo retinal imaging, and histological analysis showed rescue of photoreceptor function and structure in the absence of ocular toxicity in the low- and mid-dose treatment groups when compared with the vehicle-treated group. The high-dose group showed evidence of both photoreceptor rescue and posterior segment toxicity. These results support the use of AGTC-501 in clinical studies with patients affected with XLRP caused by RPGR mutations and define the no-observed-adverse-effect level at 6 × 1011 vg/mL.
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Affiliation(s)
- Valérie L Dufour
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Artur V Cideciyan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Guo-Jie Ye
- Applied Genetic Technologies Corporation, Alachua, Florida
| | - Chunjuan Song
- Applied Genetic Technologies Corporation, Alachua, Florida
| | - Adrian Timmers
- Applied Genetic Technologies Corporation, Alachua, Florida
| | - Perry L Habecker
- Department of Pathobiology, New Bolton Center, School of Veterinary Medicine, University of Pennsylvania, Kennett Square, Pennsylvania
| | - Wei Pan
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nicole M Weinstein
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Malgorzata Swider
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amy C Durham
- Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Gui-Shuang Ying
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Samuel G Jacobson
- Department of Ophthalmology, Scheie Eye Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - David R Knop
- Applied Genetic Technologies Corporation, Alachua, Florida
| | | | | | - Gustavo D Aguirre
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - William A Beltran
- Division of Experimental Retinal Therapies, Department of Clinical Sciences & Advanced Medicine, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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25
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RPGR-Associated Dystrophies: Clinical, Genetic, and Histopathological Features. Int J Mol Sci 2020; 21:ijms21030835. [PMID: 32012938 PMCID: PMC7038140 DOI: 10.3390/ijms21030835] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/21/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022] Open
Abstract
This study describes the clinical, genetic, and histopathological features in patients with RPGR-associated retinal dystrophies. Nine male patients from eight unrelated families underwent a comprehensive ophthalmic examination. Additionally, the histopathology of the right eye from a patient with an end-stage cone-rod-dystrophy (CRD)/sector retinitis pigmentosa (RP) phenotype was examined. All RPGR mutations causing a CRD phenotype were situated in exon ORF15. The mean best-corrected visual acuity (BCVA, decimals) was 0.58 (standard deviation (SD)): 0.34; range: 0.05-1.13); and the mean spherical refractive error was -4.1 D (SD: 2.11; range: -1.38 to -8.19). Hyperautofluorescent rings were observed in six patients. Full-field electroretinography responses were absent in all patients. The visual field defects ranged from peripheral constriction to central islands. The mean macular sensitivity on microperimetry was 11.6 dB (SD: 7.8; range: 1.6-24.4) and correlated significantly with BCVA (r = 0.907; p = 0.001). A histological examination of the donor eye showed disruption of retinal topology and stratification, with a more severe loss found in the peripheral regions. Reactive gliosis was seen in the inner layers of all regions. Our study demonstrates the highly variable phenotype found in RPGR-associated retinal dystrophies. Therapies should be applied at the earliest signs of photoreceptor degeneration, prior to the remodeling of the inner retina.
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26
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Fahim AT, Sullivan LS, Bowne SJ, Jones KD, Wheaton DKH, Khan NW, Heckenlively JR, Jayasundera KT, Branham KH, Andrews CA, Othman MI, Karoukis AJ, Birch DG, Daiger SP. X-Chromosome Inactivation Is a Biomarker of Clinical Severity in Female Carriers of RPGR-Associated X-Linked Retinitis Pigmentosa. Ophthalmol Retina 2019; 4:510-520. [PMID: 31953110 DOI: 10.1016/j.oret.2019.11.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE X-linked retinitis pigmentosa can manifest in female carriers with widely variable severity, whereas others remain unaffected. The contribution of X-chromosome inactivation (XCI) to phenotypic variation has been postulated but not demonstrated. Furthermore, the impact of genotype and genetic modifiers has been demonstrated in affected males but has not been well established in female carriers. The purpose of this study was to describe the scope of clinical phenotype in female carriers with mutations in RPGR and quantify the contribution of genotype, genetic modifiers, and XCI to phenotypic severity. DESIGN Cohort study. PARTICIPANTS Seventy-seven female carriers with RPGR mutations from 41 pedigrees. METHODS Coding single nucleotide polymorphisms were sequenced in candidate genetic modifier genes encoding known RPGR-interacting proteins. X-chromosome inactivation ratios were determined in genomic DNA isolated from blood (n = 42) and saliva (n = 20) using methylation status of X-linked polymorphic repeats. These genetic data were compared with disease severity based on quantitative clinical parameters. MAIN OUTCOME MEASURES Visual acuity, Humphrey visual field (HVF) results, full-field electroretinography results, and dark adaptation. RESULTS Most individuals at all ages were mildly affected or unaffected, whereas those who progressed to moderate or severe vision loss were older than 30 years. RPGR genotype was not associated with clinical severity. The D1264N variant in RPGRIP1L was associated with more severe disease. Skewed XCI toward inactivation of the normal RPGR allele was associated with more severe disease. The XCI ratio in both blood and saliva was a predictor of visual function as measured by HVF diameter, rod amplitude, flicker amplitude, and flicker implicit time. For carriers with extreme XCI skewing of 80:20 or more, 57% were affected severely compared with 8% for those with XCI of less than 80:20 (P = 0.002). CONCLUSIONS Female carriers with mutations in RPGR demonstrate widely variable clinical severity. X-chromosome inactivation ratios correlate with clinical severity and may serve as a predictor of clinically significant disease. Because RPGR gene therapy trials are underway, a future imperative exists to determine which carriers require intervention and when to intervene. X-chromosome inactivation analysis may be useful for identifying candidates for early intervention.
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Affiliation(s)
- Abigail T Fahim
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan.
| | - Lori S Sullivan
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
| | - Sara J Bowne
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
| | | | | | - Naheed W Khan
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - K Thiran Jayasundera
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Kari H Branham
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Chris A Andrews
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Mohammad I Othman
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | - Athanasios J Karoukis
- Department of Ophthalmology and Visual Sciences, University of Michigan, Ann Arbor, Michigan
| | | | - Stephen P Daiger
- Department of Genetics, University of Texas Health Science Center, Houston, Texas
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27
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Mawatari G, Fujinami K, Liu X, Yang L, Yokokawa YF, Komori S, Ueno S, Terasaki H, Katagiri S, Hayashi T, Kuniyoshi K, Miyake Y, Tsunoda K, Yoshitake K, Iwata T, Nao-i N. Clinical and genetic characteristics of 14 patients from 13 Japanese families with RPGR-associated retinal disorder: report of eight novel variants. Hum Genome Var 2019; 6:34. [PMID: 31645972 PMCID: PMC6804603 DOI: 10.1038/s41439-019-0065-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/21/2019] [Accepted: 06/30/2019] [Indexed: 01/08/2023] Open
Abstract
Variants in the retinitis pigmentosa GTPase regulator (RPGR) gene are a major cause of X-linked inherited retinal disorder (IRD). We herein describe the clinical and genetic features of 14 patients from 13 Japanese families harboring RPGR variants in a nationwide cohort. Comprehensive ophthalmological examinations were performed to classify the patients into one of the phenotype subgroups: retinitis pigmentosa (RP) and cone rod dystrophy (CORD). The mean age of onset/at examination was 13.8/38.1 years (range, 0-50/11-72), respectively. The mean visual acuity in the right/left eye was 0.43/0.43 (range, 0.1-1.7/-0.08-1.52) LogMAR unit. Eight patients had RP, and six had CORD. Whole-exome sequencing with target analyses identified 13 RPGR variants in 730 families with IRD, including 8 novel variants. An association between the phenotype subgroup and the position of variants (cutoff of amino acid 950) was revealed. To conclude, the clinical and genetic spectrum of RPGR-associated retinal disorder was first illustrated in a Japanese population, with a high proportion of novel variants. These results suggest the distinct genetic background of RPGR in the Japanese population, in which the genotype-phenotype association was affirmed. This evidence should be helpful monitoring and counseling patients and in selecting patients for future therapeutic trials.
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Affiliation(s)
- Go Mawatari
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan
| | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | - Xiao Liu
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China
| | - Lizhu Yang
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Yu-Fujinami Yokokawa
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Graduate School of Health Management, Keio University, Tokyo, Japan
- Division of Public Health, Yokokawa Clinic, Suita, Osaka, Japan
| | - Shiori Komori
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Aichi Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Aichi Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Aichi Japan
| | - Satoshi Katagiri
- Department of Ophthalmology, The Jikei University School of Medicine, Nishi-Shimbashi, Minato-ku, Tokyo, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Nishi-Shimbashi, Minato-ku, Tokyo, Japan
| | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kinki University Faculty of Medicine, Osaka-Sayama City, Osaka, Japan
| | - Yozo Miyake
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Kobe Eye Center, Next Vision, Kobe, Hyogo, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
| | - Nobuhisa Nao-i
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan
| | - on behalf of the JEGC study group
- Department of Ophthalmology, Faculty of Medicine, University of Miyazaki, Kiyotake, Miyazaki, Japan
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University, Chongqing, China
- Graduate School of Health Management, Keio University, Tokyo, Japan
- Division of Public Health, Yokokawa Clinic, Suita, Osaka, Japan
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Showa-ku, Nagoya, Aichi Japan
- Department of Ophthalmology, The Jikei University School of Medicine, Nishi-Shimbashi, Minato-ku, Tokyo, Japan
- Department of Ophthalmology, Kinki University Faculty of Medicine, Osaka-Sayama City, Osaka, Japan
- Kobe Eye Center, Next Vision, Kobe, Hyogo, Japan
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Meguro-ku, Tokyo, Japan
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Sanchez Tocino H, Diez Montero C, Villanueva Gómez A, Lobo Valentin R, Montero-Moreno JA. Phenotypic high myopia in X-linked retinitis pigmentosa secondary to a novel mutation in the RPGR gene. Ophthalmic Genet 2019; 40:170-176. [DOI: 10.1080/13816810.2019.1605385] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | | | - Ana Villanueva Gómez
- Pediatric Ophthalmology Unit, Rio Hortega University Hospital, Valladolid, Spain
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Chiang JPW, Lamey TM, Wang NK, Duan J, Zhou W, McLaren TL, Thompson JA, Ruddle J, De Roach JN. Development of High-Throughput Clinical Testing of RPGR ORF15 Using a Large Inherited Retinal Dystrophy Cohort. Invest Ophthalmol Vis Sci 2019; 59:4434-4440. [PMID: 30193314 DOI: 10.1167/iovs.18-24555] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Mutations in the ORF15 region of RPGR account for approximately half of all X-linked retinitis pigmentosa cases. However, a robust high-throughput method for the detection of ORF15 mutations has yet to be validated. We set out to develop the first clinically validated next-generation sequencing (NGS) method for the detection of mutations in this difficult-to-sequence region, including test accuracy and coverage data. Methods As part of a blind-test, 145 research samples, previously tested by Sanger sequencing, and 81 clinical samples were evaluated using NGS of long-range PCR products fragmented with Illumina's Nextera library preparation kit (method 1), or with Centrillion's OneTube technology, supplemented with duplication analysis using an ORF15-specific in-silico array (method 2). DNA fragments were analyzed using Agilent's DNA 1000 assay, and sequencing was done on Illumina's MiSeq 2×150 or HiSeq2500 2×100. NextGENe by SoftGenetics was used for data analysis and variant calling. Results The Nextera library preparation method produced 24 cases of discordance due to (in order of decreasing occurrence) false-negatives, incorrectly called variants, and a false-positive. Subsequent use of a new, OneTube NGS library preparation method, supplemented with duplication analyses, resolved discordance between Sanger and NGS data in all cases. This improvement in variant detection accuracy was largely attributed to improvement in random fragmentation offered by the enzymatic OneTube method, resulting in more complete coverage of the highly repetitive ORF15 region. Minimum coverage was roughly 320 reads for Nextera and 6800 reads for OneTube (normalized for total read counts). Conclusions This paper documents the first clinically validated NGS method for reliable, high-throughput sequencing of RPGR ORF15. Sensitivity and specificity of the new method were 100%, with the caveat of unclear zygosity calling for one large duplication case. These findings demonstrate a reliable and practical implementation for NGS-based diagnosis of RPGR ORF15 mutations. They also provide the foundation for targeted, high-coverage sequencing of any other repetitive regions within the genome.
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Affiliation(s)
- John P W Chiang
- Molecular Vision Laboratory, Hillsboro, Oregon, United States
| | - Tina M Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Nicholas K Wang
- Molecular Vision Laboratory, Hillsboro, Oregon, United States
| | - Jie Duan
- Molecular Vision Laboratory, Hillsboro, Oregon, United States
| | - Wei Zhou
- Centrillion Technologies, Palo Alto, California, United States
| | - Terri L McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | | | - John N De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
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Application of Whole Exome and Targeted Panel Sequencing in the Clinical Molecular Diagnosis of 319 Chinese Families with Inherited Retinal Dystrophy and Comparison Study. Genes (Basel) 2018; 9:genes9070360. [PMID: 30029497 PMCID: PMC6071067 DOI: 10.3390/genes9070360] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/11/2018] [Accepted: 07/12/2018] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of clinically and genetically heterogeneous diseases involving more than 280 genes and no less than 20 different clinical phenotypes. In this study, our aims were to identify the disease-causing gene variants of 319 Chinese patients with IRD, and compare the pros and cons of targeted panel sequencing and whole exome sequencing (WES). Patients were assigned for analysis with a hereditary eye disease enrichment panel (HEDEP) or WES examination based on time of recruitment. This HEDEP was able to capture 441 hereditary eye disease genes, which included 291 genes related to IRD. As RPGR ORF15 was difficult to capture, all samples were subjected to Sanger sequencing for this region. Among the 163 disease-causing variants identified in this study, 73 had been previously reported, and the other 90 were novel. Genes most commonly implicated in different inheritances of IRDs in this cohort were presented. HEDEP and WES achieved diagnostic yield with 41.2% and 33.0%, respectively. In addition, nine patients were found to carry pathogenic mutations in the RPGR ORF15 region with Sanger sequencing. Our study demonstrates that HEDEP can be used as a first-tier test for patients with IRDs.
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Nanda A, Salvetti AP, Martinez-Fernandez de la Camara C, MacLaren RE. Misdiagnosis of X-linked retinitis pigmentosa in a choroideremia patient with heavily pigmented fundi. Ophthalmic Genet 2018; 39:380-383. [PMID: 29377744 DOI: 10.1080/13816810.2018.1430242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Inherited retinal diseases are thought to be the leading cause of sight loss in the working age population. Mutations found in the RPGR and CHM genes cause retinitis pigmentosa (RP) and choroideremia, respectively. In the first instance, an X-linked family history of visual field loss commonly raises the suspicion of one of these two genes. In choroideremia, the classic description of a white fundal reflex secondary to the widespread chorioretinal degeneration was made over a hundred years ago in Caucasians. But, it is not so obvious in heavily pigmented fundi. Hence, the clinical diagnosis of CHM in non-Caucasian patients may be challenging in the first stages of the disease. Here we report a case of a Southeast Asian gentleman who has a family history of X-linked retinal degeneration and was found to have a confirmed in-frame deletion of 12 DNA nucleotides in exon 15 of the RPGR gene. Later in life, however, his fundal appearance showed unusual areas of circular pigment hypertrophy and clumping. He was therefore tested for carrying a disease-causing mutation in the CHM gene and a null mutation was found. Since gene therapy trials are ongoing for both of these conditions, it has now become critically important to establish the correct genetic diagnosis in order to recruit suitable candidates. Moreover, this case demonstrates the necessity to remain vigilant in the interpretation of genetic results which are inconsistent with clinical features.
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Affiliation(s)
- A Nanda
- a Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital , Oxford , United Kingdom
| | - A P Salvetti
- a Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital , Oxford , United Kingdom.,b Eye 5 Clinic, Sacco Hospital, University of Milan , Milano , Italy
| | | | - R E MacLaren
- a Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital , Oxford , United Kingdom.,c Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences , University of Oxford , Oxford , United Kingdom
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Liu F, Qin Y, Yu S, Soares DC, Yang L, Weng J, Li C, Gao M, Lu Z, Hu X, Liu X, Jiang T, Liu JY, Shu X, Tang Z, Liu M. Pathogenic mutations in retinitis pigmentosa 2 predominantly result in loss of RP2 protein stability in humans and zebrafish. J Biol Chem 2017; 292:6225-6239. [PMID: 28209709 PMCID: PMC5391753 DOI: 10.1074/jbc.m116.760314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Mutations in retinitis pigmentosa 2 (RP2) account for 10-20% of X-linked retinitis pigmentosa (RP) cases. The encoded RP2 protein is implicated in ciliary trafficking of myristoylated and prenylated proteins in photoreceptor cells. To date >70 mutations in RP2 have been identified. How these mutations disrupt the function of RP2 is not fully understood. Here we report a novel in-frame 12-bp deletion (c.357_368del, p.Pro120_Gly123del) in zebrafish rp2 The mutant zebrafish shows reduced rod phototransduction proteins and progressive retinal degeneration. Interestingly, the protein level of mutant Rp2 is almost undetectable, whereas its mRNA level is near normal, indicating a possible post-translational effect of the mutation. Consistent with this hypothesis, the equivalent 12-bp deletion in human RP2 markedly impairs RP2 protein stability and reduces its protein level. Furthermore, we found that a majority of the RP2 pathogenic mutations (including missense, single-residue deletion, and C-terminal truncation mutations) severely destabilize the RP2 protein. The destabilized RP2 mutant proteins are degraded via the proteasome pathway, resulting in dramatically decreased protein levels. The remaining non-destabilizing mutations T87I, R118H/R118G/R118L/R118C, E138G, and R211H/R211L are suggested to impair the interaction between RP2 and its protein partners (such as ARL3) or with as yet unknown partners. By utilizing a combination of in silico, in vitro, and in vivo approaches, our work comprehensively indicates that loss of RP2 protein structural stability is the predominating pathogenic consequence for most RP2 mutations. Our study also reveals a role of the C-terminal domain of RP2 in maintaining the overall protein stability.
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Affiliation(s)
- Fei Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yayun Qin
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shanshan Yu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dinesh C Soares
- MRC Human Genetics Unit/Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom, and
| | - Lifang Yang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Weng
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chang Li
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Meng Gao
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhaojing Lu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xuebin Hu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiliang Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tao Jiang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jing Yu Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Zhaohui Tang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Mugen Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China,
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Na KH, Kim HJ, Kim KH, Han S, Kim P, Hann HJ, Ahn HS. Prevalence, Age at Diagnosis, Mortality, and Cause of Death in Retinitis Pigmentosa in Korea-A Nationwide Population-based Study. Am J Ophthalmol 2017; 176:157-165. [PMID: 28130043 DOI: 10.1016/j.ajo.2017.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 11/18/2022]
Abstract
PURPOSE To determine the prevalence and mortality of retinitis pigmentosa (RP) patients in Korea. DESIGN Population-based retrospective cohort study. METHODS We used data covering the 2011-2014 period from the Rare Intractable Disease (RID) registry and Health Insurance Review and Assessment (HIRA) service, which include information on all patients diagnosed with RP based on predefined diagnostic criteria. Using the HIRA-RID database, we evaluated the prevalence and age at diagnosis of RP patients across the entire Korean population. We further linked the data from Statistics Korea to the HIRA-RID database to confirm mortality and causes of death. RESULTS The prevalence in the total population across all ages was 11.09 per 105 people, and the prevalence in those over the age of 40 was 16.16 per 105 people. The age at diagnosis ranged from 0 to 95 and, on average, was 44.8. The standardized mortality ratio (SMR) was 1.56 for all ages, peaking at 2.61 in men aged 40-59, which was attributed to 6.6-fold higher suicide rates than the same age group in the general male population. CONCLUSIONS This is the first nationwide epidemiologic study of RP patients covering the entire population of all ages. The results suggest that the prevalence of RP in Korea is about 1 in 9000 for all ages and 1 in 6000 for those over 40 years of age. The higher mortality of RP patients than that of the general population is attributable to a high suicide rate in male RP patients of working ages, which necessitates a careful attention to their mental health.
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Affiliation(s)
- Kun-Hoo Na
- Department of Ophthalmology, Korea University College of Medicine, Seoul, South Korea
| | - Hyun Jung Kim
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, South Korea
| | - Kyoung Hoon Kim
- Department of Public Health, Graduate School, Korea University, Seoul, South Korea
| | - Seungjin Han
- Department of Public Health, Graduate School, Korea University, Seoul, South Korea
| | - Patrick Kim
- Department of Ophthalmology, Soonchunhyang University College of Medicine, Soonchunhyang University Cheonan Hospital, Chungcheongnam-do, South Korea
| | - Hoo Jae Hann
- Medical Research Institute and Department of Anatomy, College of Medicine, Ewha Womans University, Seoul, South Korea
| | - Hyeong Sik Ahn
- Department of Preventive Medicine, Korea University College of Medicine, Seoul, South Korea.
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Novel variants of RPGR in X-linked retinitis pigmentosa families and genotype-phenotype correlation. Eur J Ophthalmol 2017; 27:240-248. [PMID: 27768226 DOI: 10.5301/ejo.5000879] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2016] [Indexed: 11/20/2022]
Abstract
PURPOSE To identify novel mutations in the retinitis pigmentosa GTPase regulator (RPGR) gene and retinitis pigmentosa 2 (RP2) gene underlying X-linked retinitis pigmentosa (XLRP) and assess genotype-phenotype correlations. METHODS The patient cohort, consisting of 13 individuals from 3 unrelated XLRP families, underwent comprehensive ophthalmologic examination. The open reading frames of RPGR and RP2 were analyzed with Sanger sequencing in each patient. The identified genetic variants were defined as mutations or polymorphisms on the basis of their pathological effect. RESULTS We found 3 genetic variants: a novel mutation c.1591G>T in exon 14 and a novel polymorphism c.1105C>T in exon 10, resulting in p.Glu531* and p.Arg369Cys of RPGR gene, respectively, and one already known mutation c.413A>G in exon 2, resulting in a p.Glu138Gly of RP2 gene. Considering our XLRP probands, RPGR-related phenotypic damages were similar and less severe than those of the patient with the RP2 mutation. On the other hand, the female carriers of XLRP variants showed different RPGR-related consequences, ranging from rods hypofunctionality in c.1591G>T nonsense heterozygosity to no retinal changes in c.1105C>T polymorphic heterozygosity. CONCLUSIONS These findings broaden the spectrum of RPGR mutations and phenotypic variability of the disease, which will be useful for genetic consultation and diagnosis in the future.
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Unravelling the genetic basis of simplex Retinitis Pigmentosa cases. Sci Rep 2017; 7:41937. [PMID: 28157192 PMCID: PMC5291209 DOI: 10.1038/srep41937] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 01/04/2017] [Indexed: 12/20/2022] Open
Abstract
Retinitis Pigmentosa (RP) is the most common form of inherited retinal dystrophy (IRD) characterized ultimately by photoreceptors degeneration. Exhibiting great clinical and genetic heterogeneity, RP can be inherited as an autosomal dominant (ad), autosomal recessive (ar) and X-linked (xl) disorder. Although the relative prevalence of each form varies somewhat between populations, a major proportion (41% in Spain) of patients represent simplex cases (sRP) in which the mode of inheritance is unknown. Molecular genetic diagnostic is crucial, but also challenging, for sRP patients because any of the 81 RP genes identified to date may be causative. Herein, we report the use of a customized targeted gene panel consisting of 68 IRD genes for the molecular characterization of 106 sRP cases. The diagnostic rate was 62.26% (66 of 106) with a proportion of clinical refinements of 30.3%, demonstrating the high efficiency of this genomic approach even for clinically ambiguous cases. The high number of patients diagnosed here has allowed us to study in detail the genetic basis of the sRP. The solved sRP cohort is composed of 62.1% of arRP cases, 24.2% of adRP and 13.6% of xlRP, which implies consequences for counselling of patients and families.
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Identification of novel X-linked gain-of-function RPGR-ORF15 mutation in Italian family with retinitis pigmentosa and pathologic myopia. Sci Rep 2016; 6:39179. [PMID: 27995965 PMCID: PMC5171904 DOI: 10.1038/srep39179] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 11/18/2016] [Indexed: 11/09/2022] Open
Abstract
The aim of this study was to describe a new pathogenic variant in the mutational hot spot exon ORF15 of retinitis pigmentosa GTPase regulator (RPGR) gene within an Italian family with X-linked retinitis pigmentosa (RP), detailing its distinctive genotype-phenotype correlation with pathologic myopia (PM). All members of this RP-PM family underwent a complete ophthalmic examination. The entire open reading frames of RPGR and retinitis pigmentosa 2 genes were analyzed by Sanger sequencing. A novel frame-shift mutation in exon ORF15 of RPGR gene (c.2091_2092insA; p.A697fs) was identified as hemizygous variant in the male proband with RP, and as heterozygous variant in the females of this pedigree who invariably exhibited symmetrical PM in both eyes. The c.2091_2092insA mutation coherently co-segregated with the observed phenotypes. These findings expand the spectrum of X-linked RP variants. Interestingly, focusing on Caucasian ethnicity, just three RPGR mutations are hitherto reported in RP-PM families: one of these is located in exon ORF15, but none appears to be characterized by a high penetrance of PM trait as observed in the present, relatively small, pedigree. The geno-phenotypic attributes of this heterozygosity suggest that gain-of-function mechanism could give rise to PM via a degenerative cell-cell remodeling of the retinal structures.
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Charng J, Cideciyan AV, Jacobson SG, Sumaroka A, Schwartz SB, Swider M, Roman AJ, Sheplock R, Anand M, Peden MC, Khanna H, Heon E, Wright AF, Swaroop A. Variegated yet non-random rod and cone photoreceptor disease patterns in RPGR-ORF15-associated retinal degeneration. Hum Mol Genet 2016; 25:5444-5459. [PMID: 27798110 PMCID: PMC6078602 DOI: 10.1093/hmg/ddw361] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 12/13/2022] Open
Abstract
Mutations in the ORF15 exon of the RPGR gene cause a common form of X-linked retinitis pigmentosa, which often results in severe loss of vision. In dogs and mice, gene augmentation therapy has been shown to arrest the progressive degeneration of rod and cone photoreceptors. However, the distribution of potentially treatable photoreceptors across the human retinas and the rate of degeneration are not known. Here, we have defined structural and functional features of the disease in 70 individuals with ORF15 mutations. We also correlated the features observed in patients with those of three Rpgr-mutant (Rpgr-ko, Rd9, and Rpgr-cko) mice. In patients, there was pronounced macular disease. Across the retina, rod and cone dysfunction showed a range of patterns and a spectrum of severity between individuals, but a high symmetry was observed between eyes of each individual. Genotype was not related to disease expression. In the Rpgr-ko mice, there were intra-retinal differences in rhodopsin and cone opsin trafficking. In Rd9 and Rpgr-cko mice, retinal degeneration showed inter-ocular symmetry. Longitudinal results in patients revealed localized rod and cone dysfunction with progression rates of 0.8 to 1.3 log per decade in sensitivity loss. Relatively retained rod and cone photoreceptors in mid- and far-peripheral temporal-inferior and nasal-inferior visual field regions should be good targets for future localized gene therapies in patients.
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Affiliation(s)
- Jason Charng
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Artur V. Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Samuel G. Jacobson
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Alexander Sumaroka
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Sharon B. Schwartz
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Malgorzata Swider
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Alejandro J. Roman
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Rebecca Sheplock
- Scheie Eye Institute, Department of Ophthalmology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, PA, USA
| | - Manisha Anand
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, USA
| | - Marc C. Peden
- Retina Associates of Florida, Tampa, Florida, FL, USA
| | - Hemant Khanna
- Department of Ophthalmology, University of Massachusetts Medical School, Worcester, Massachusetts, MA, USA
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, The Hospital for Sick Children, University of Toronto, Toronto, Canada
| | - Alan F. Wright
- MRC Human Genetics Unit, MRC IGMM, University of Edinburgh, Edinburgh, Scotland, UK
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland, MD, USA
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Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM. Molecular findings from 537 individuals with inherited retinal disease. J Med Genet 2016; 53:761-767. [PMID: 27208204 PMCID: PMC5106339 DOI: 10.1136/jmedgenet-2016-103837] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/14/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. METHODS We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). RESULTS Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. CONCLUSIONS Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.
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Affiliation(s)
- Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Sanjeev Bhaskar
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - James O'Sullivan
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Simon G Williams
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Janine A Lamb
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Panagiotis I Sergouniotis
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Rachel L Gillespie
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephen P Daiger
- School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - Georgina Hall
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - I Christopher Lloyd
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Paul N Bishop
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Graeme C M Black
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
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Lim H, Park YM, Lee JK, Taek Lim H. Single-Exome sequencing identified a novel RP2 mutation in a child with X-linked retinitis pigmentosa. CANADIAN JOURNAL OF OPHTHALMOLOGY 2016; 51:326-330. [DOI: 10.1016/j.jcjo.2016.03.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Revised: 12/08/2015] [Accepted: 03/25/2016] [Indexed: 10/21/2022]
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Improved Diagnosis of Inherited Retinal Dystrophies by High-Fidelity PCR of ORF15 followed by Next-Generation Sequencing. J Mol Diagn 2016; 18:817-824. [PMID: 27620828 DOI: 10.1016/j.jmoldx.2016.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 06/10/2016] [Accepted: 06/16/2016] [Indexed: 11/21/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of retinal dystrophy. The disease is characterized by the progressive degeneration of photoreceptors, ultimately leading to blindness. The exon ORF15 of RP GTPase regulator (RPGR) is a mutation hot spot for X-linked RP and one form of cone dystrophy. However, accurate molecular testing of ORF15 is challenging because of a large segment of highly repetitive purine-rich sequence in this exon. ORF15 performs poorly in next-generation sequencing-based panels or whole exome sequencing analysis, whereas Sanger sequencing of ORF15 requires special reagents and PCR conditions with multiple pairs of overlapping primers that often do not provide a clean sequence. Because of these technical difficulties, molecular analysis of ORF15 is performed mostly in research laboratories without validation for clinical application. Herein, we report the development of a single step of high-fidelity PCR followed by next-generation sequencing for accurate mutation detection, which is easily integrated into routine clinical practice. Our approach has improved coverage depth of ORF15 with the ability to detect single-nucleotide variants and deletions/duplications. Using this method, we were able to identify ORF15 pathogenic variants in approximately 31% of undiagnosed RP patients. Our results underline the clinical importance of complete and accurate sequence analysis of ORF15 for patients with retinal dystrophies.
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Kropatsch R, Akkad DA, Frank M, Rosenhagen C, Altmüller J, Nürnberg P, Epplen JT, Dekomien G. A large deletion in RPGR causes XLPRA in Weimaraner dogs. Canine Genet Epidemiol 2016; 3:7. [PMID: 27398221 PMCID: PMC4938961 DOI: 10.1186/s40575-016-0037-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 06/21/2016] [Indexed: 11/20/2022] Open
Abstract
Background Progressive retinal atrophy (PRA) belongs to a group of inherited retinal disorders associated with gradual vision impairment due to degeneration of retinal photoreceptors in various dog breeds. PRA is highly heterogeneous, with autosomal dominant, recessive or X-linked modes of inheritance. In this study we used exome sequencing to investigate the molecular genetic basis of a new type of PRA, which occurred spontaneously in a litter of German short-hair Weimaraner dogs. Results Whole exome sequencing in two PRA-affected Weimaraner dogs identified a large deletion comprising the first four exons of the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene known to be involved in human retinitis pigmentosa and canine PRA. Screening of 16 individuals in the corresponding pedigree of short-hair Weimaraners by qPCR, verified the deletion in hemizygous or heterozygous state in one male and six female dogs, respectively. The mutation was absent in 88 additional unrelated Weimaraners. The deletion was not detectable in the parents of one older female which transmitted the mutation to her offspring, indicating that the RPGR deletion represents a de novo mutation concerning only recent generations of the Weimaraner breed in Germany. Conclusion Our results demonstrate the value of an existing DNA biobank combined with exome sequencing to identify the underlying genetic cause of a spontaneously occurring inherited disease. Identification of the genetic cause has allowed the development of a diagnostic test, which should help to eradicate the PRA causing mutation from the respective canine line. Thus, planning of future pairings is facilitated and manifestation of this type of PRA can be prevented. Electronic supplementary material The online version of this article (doi:10.1186/s40575-016-0037-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Regina Kropatsch
- Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Denis A Akkad
- Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
| | - Matthias Frank
- Kleintierklinik Frank, Mooswaldallee 10 i, 79108 Freiburg, Germany
| | - Carsten Rosenhagen
- Tierärztliche Überweisungspraxis, Lortzingstraße 12, 28209 Bremen, Germany
| | - Janine Altmüller
- Cologne Center for Genomics, University of Cologne, Weyertal 115 b, 50931 Cologne, Germany ; Institute of Human Genetics, University of Cologne, Kerpener Str. 34, 50931 Cologne, Germany
| | - Peter Nürnberg
- Cologne Center for Genomics, University of Cologne, Weyertal 115 b, 50931 Cologne, Germany ; Center for Molecular Medicine Cologne (CMMC), University of Cologne, Robert-Koch Str. 21, 50931 Cologne, Germany ; Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph-Stelzmann-Str. 26, 50931 Cologne, Germany
| | - Jörg T Epplen
- Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany ; Faculty of Health, University Witten-Herdecke, Alfred-Herrhausen-Strasse 50, 58448 Witten, Germany
| | - Gabriele Dekomien
- Department of Human Genetics, Ruhr-University, Universitätsstraße 150, 44801 Bochum, Germany
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Loss of RPGR glutamylation underlies the pathogenic mechanism of retinal dystrophy caused by TTLL5 mutations. Proc Natl Acad Sci U S A 2016; 113:E2925-34. [PMID: 27162334 DOI: 10.1073/pnas.1523201113] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mutations in the X-linked retinitis pigmentosa GTPase regulator (RPGR) gene are a major cause of retinitis pigmentosa, a blinding retinal disease resulting from photoreceptor degeneration. A photoreceptor specific ORF15 variant of RPGR (RPGR(ORF15)), carrying multiple Glu-Gly tandem repeats and a C-terminal basic domain of unknown function, localizes to the connecting cilium where it is thought to regulate cargo trafficking. Here we show that tubulin tyrosine ligase like-5 (TTLL5) glutamylates RPGR(ORF15) in its Glu-Gly-rich repetitive region containing motifs homologous to the α-tubulin C-terminal tail. The RPGR(ORF15) C-terminal basic domain binds to the noncatalytic cofactor interaction domain unique to TTLL5 among TTLL family glutamylases and targets TTLL5 to glutamylate RPGR. Only TTLL5 and not other TTLL family glutamylases interacts with RPGR(ORF15) when expressed transiently in cells. Consistent with this, a Ttll5 mutant mouse displays a complete loss of RPGR glutamylation without marked changes in tubulin glutamylation levels. The Ttll5 mutant mouse develops slow photoreceptor degeneration with early mislocalization of cone opsins, features resembling those of Rpgr-null mice. Moreover TTLL5 disease mutants that cause human retinal dystrophy show impaired glutamylation of RPGR(ORF15) Thus, RPGR(ORF15) is a novel glutamylation substrate, and this posttranslational modification is critical for its function in photoreceptors. Our study uncovers the pathogenic mechanism whereby absence of RPGR(ORF15) glutamylation leads to retinal pathology in patients with TTLL5 gene mutations and connects these two genes into a common disease pathway.
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Photoreceptor rescue by an abbreviated human RPGR gene in a murine model of X-linked retinitis pigmentosa. Gene Ther 2015; 23:196-204. [PMID: 26348595 PMCID: PMC4863462 DOI: 10.1038/gt.2015.93] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 07/05/2015] [Accepted: 08/21/2015] [Indexed: 11/08/2022]
Abstract
The X-linked RP3 gene codes for the ciliary protein RPGR and accounts for over 10% of inherited retinal degenerations. The critical RPGR-ORF15 splice variant contains a highly repetitive purine-rich linker region that renders it unstable and difficult to adapt for gene therapy. To test the hypothesis that the precise length of the linker region is not critical for function, we evaluated whether AAV-mediated replacement gene therapy with a human ORF15 variant containing in-frame shortening of the linker region could reconstitute RPGR function in vivo. We delivered human RPGR-ORF15 replacement genes with deletion of most (314-codons, “short form”) or 1/3 (126-codons, “long form”) of the linker region to Rpgr null mice. Human RPGR-ORF15 expression was detected post-treatment with both forms of ORF15 transgenes. However, only the long form correctly localized to the connecting cilia and led to significant functional and morphological rescue of rods and cones. Thus the highly repetitive region of RPGR is functionally important but that moderate shortening of its length, which confers the advantage of added stability, preserves its function. These findings provide a theoretical basis for optimizing replacement gene design in clinical trials for X-linked RP3.
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Deng WT, Dyka FM, Dinculescu A, Li J, Zhu P, Chiodo VA, Boye SL, Conlon TJ, Erger K, Cossette T, Hauswirth WW. Stability and Safety of an AAV Vector for Treating RPGR-ORF15 X-Linked Retinitis Pigmentosa. Hum Gene Ther 2015; 26:593-602. [PMID: 26076799 DOI: 10.1089/hum.2015.035] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Our collaborative successful gene replacement therapy using AAV vectors expressing a variant of human RPGR-ORF15 in two canine models provided therapeutic proof of concept for translation into human treatment. The ORF15 sequence contained within this AAV vector, however, has ORF15 DNA sequence variations compared to the published sequence that are likely due to its unusual composition of repetitive purine nucleotides. This mutability is a concern for AAV vector production and safety when contemplating a human trial. In this study, we establish the safety profile of AAV-hIRBP-hRPGR and AAV-hGRK1-hRPGR vectors used in the initial canine proof-of-principle experiments by demonstrating hRPGR-ORF15 sequence stability during all phases of manipulation, from plasmid propagation to vector production to its stability in vivo after subretinal administration to animals. We also evaluate potential toxicity in vivo by investigating protein expression, retinal structure and function, and vector biodistribution. Expression of hRPGR is detected in the inner segments and synaptic terminals of photoreceptors and is restricted to the connecting cilium when the vector is further diluted. Treated eyes exhibit no toxicity as assessed by retinal histopathology, immunocytochemistry, optical coherence tomography, fundoscopy, electroretinogram, and vector biodistribution. Therefore, the hRPGR-ORF15 variant in our AAV vectors appears to be a more stable form than the endogenous hRPGR cDNA when propagated in vitro. Its safety profile presented here in combination with its proven efficacy supports future gene therapy clinical trials.
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Affiliation(s)
- Wen-Tao Deng
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Frank M Dyka
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Astra Dinculescu
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Jie Li
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Ping Zhu
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Vince A Chiodo
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Sanford L Boye
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
| | - Thomas J Conlon
- 2 Powell Gene Therapy Center, Department of Pediatrics, University of Florida , Gainesville, Florida
| | - Kirsten Erger
- 2 Powell Gene Therapy Center, Department of Pediatrics, University of Florida , Gainesville, Florida
| | - Travis Cossette
- 2 Powell Gene Therapy Center, Department of Pediatrics, University of Florida , Gainesville, Florida
| | - William W Hauswirth
- 1 Department of Ophthalmology, College of Medicine, University of Florida , Gainesville, Florida
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Schwarz N, Carr AJ, Lane A, Moeller F, Chen LL, Aguilà M, Nommiste B, Muthiah MN, Kanuga N, Wolfrum U, Nagel-Wolfrum K, da Cruz L, Coffey PJ, Cheetham ME, Hardcastle AJ. Translational read-through of the RP2 Arg120stop mutation in patient iPSC-derived retinal pigment epithelium cells. Hum Mol Genet 2015; 24:972-86. [PMID: 25292197 PMCID: PMC4986549 DOI: 10.1093/hmg/ddu509] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/29/2014] [Indexed: 01/08/2023] Open
Abstract
Mutations in the RP2 gene lead to a severe form of X-linked retinitis pigmentosa. RP2 patients frequently present with nonsense mutations and no treatments are currently available to restore RP2 function. In this study, we reprogrammed fibroblasts from an RP2 patient carrying the nonsense mutation c.519C>T (p.R120X) into induced pluripotent stem cells (iPSC), and differentiated these cells into retinal pigment epithelial cells (RPE) to study the mechanisms of disease and test potential therapies. RP2 protein was undetectable in the RP2 R120X patient cells, suggesting a disease mechanism caused by complete lack of RP2 protein. The RP2 patient fibroblasts and iPSC-derived RPE cells showed phenotypic defects in IFT20 localization, Golgi cohesion and Gβ1 trafficking. These phenotypes were corrected by over-expressing GFP-tagged RP2. Using the translational read-through inducing drugs (TRIDs) G418 and PTC124 (Ataluren), we were able to restore up to 20% of endogenous, full-length RP2 protein in R120X cells. This level of restored RP2 was sufficient to reverse the cellular phenotypic defects observed in both the R120X patient fibroblasts and iPSC-RPE cells. This is the first proof-of-concept study to demonstrate successful read-through and restoration of RP2 function for the R120X nonsense mutation. The ability of the restored RP2 protein level to reverse the observed cellular phenotypes in cells lacking RP2 indicates that translational read-through could be clinically beneficial for patients.
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Affiliation(s)
- Nele Schwarz
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Amanda-Jayne Carr
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Amelia Lane
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Fabian Moeller
- Johannes Gutenberg-University Muellerweg 6, 55099 Mainz, Germany and
| | - Li Li Chen
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Mònica Aguilà
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Britta Nommiste
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Manickam N Muthiah
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK, Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Naheed Kanuga
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
| | - Uwe Wolfrum
- Johannes Gutenberg-University Muellerweg 6, 55099 Mainz, Germany and
| | | | - Lyndon da Cruz
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK, Moorfields Eye Hospital, 162 City Road, London EC1V 2PD, UK
| | - Peter J Coffey
- UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1V 9EL, UK
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Zhao L, Wang F, Wang H, Li Y, Alexander S, Wang K, Willoughby CE, Zaneveld JE, Jiang L, Soens ZT, Earle P, Simpson D, Silvestri G, Chen R. Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet 2014; 134:217-30. [PMID: 25472526 DOI: 10.1007/s00439-014-1512-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 11/20/2014] [Indexed: 11/24/2022]
Abstract
Retinitis pigmentosa (RP) is a group of inherited retinal disorders characterized by progressive photoreceptor degeneration. An accurate molecular diagnosis is essential for disease characterization and clinical prognoses. A retinal capture panel that enriches 186 known retinal disease genes, including 55 known RP genes, was developed. Targeted next-generation sequencing was performed for a cohort of 82 unrelated RP cases from Northern Ireland, including 46 simplex cases and 36 familial cases. Disease-causing mutations were identified in 49 probands, including 28 simplex cases and 21 familial cases, achieving a solving rate of 60 %. In total, 65 pathogenic mutations were found, and 29 of these were novel. Interestingly, the molecular information of 12 probands was neither consistent with their initial inheritance pattern nor clinical diagnosis. Further clinical reassessment resulted in a refinement of the clinical diagnosis in 11 patients. This is the first study to apply next-generation sequencing-based, comprehensive molecular diagnoses to a large number of RP probands from Northern Ireland. Our study shows that molecular information can aid clinical diagnosis, potentially changing treatment options, current family counseling and management.
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Affiliation(s)
- Li Zhao
- Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, 77030, USA
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Beltran WA, Cideciyan AV, Lewin AS, Hauswirth WW, Jacobson SG, Aguirre GD. Gene augmentation for X-linked retinitis pigmentosa caused by mutations in RPGR. Cold Spring Harb Perspect Med 2014; 5:a017392. [PMID: 25301933 DOI: 10.1101/cshperspect.a017392] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
X-linked retinitis pigmentosa (XLRP) caused by mutations in the RPGR gene is a severe and early onset form of retinal degeneration, and no treatment is currently available. Recent evidence in two clinically relevant canine models shows that adeno-associated viral (AAV)-mediated RPGR gene transfer to rods and cones can prevent disease onset and rescue photoreceptors at early- and mid-stages of degeneration. There is thus a strong incentive for conducting long-term, preclinical efficacy and safety studies, while concomitantly pursuing the detailed phenotypic characterization of XLRP disease in patients that may benefit from such corrective therapy.
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Affiliation(s)
- William A Beltran
- Section of Ophthalmology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Artur V Cideciyan
- Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Alfred S Lewin
- Department of Molecular Genetics & Microbiology, University of Florida, Gainesville, Florida 32610
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida, Gainesville, Florida 32610
| | - Samuel G Jacobson
- Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104
| | - Gustavo D Aguirre
- Section of Ophthalmology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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48
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Mutations of 60 known causative genes in 157 families with retinitis pigmentosa based on exome sequencing. Hum Genet 2014; 133:1255-71. [DOI: 10.1007/s00439-014-1460-2] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 06/03/2014] [Indexed: 12/01/2022]
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Siemiatkowska AM, Collin RWJ, den Hollander AI, Cremers FPM. Genomic approaches for the discovery of genes mutated in inherited retinal degeneration. Cold Spring Harb Perspect Med 2014; 4:a017137. [PMID: 24939053 PMCID: PMC4109577 DOI: 10.1101/cshperspect.a017137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In view of their high degree of genetic heterogeneity, inherited retinal diseases (IRDs) pose a significant challenge for identifying novel genetic causes. Thus far, more than 200 genes have been found to be mutated in IRDs, which together contain causal variants in >80% of the cases. Accurate genetic diagnostics is particularly important for isolated cases, in which X-linked and de novo autosomal dominant variants are not uncommon. In addition, new gene- or mutation-specific therapies are emerging, underlining the importance of identifying causative mutations in each individual. Sanger sequencing of selected genes followed by cost-effective targeted next-generation sequencing (NGS) can identify defects in known IRD-associated genes in the majority of the cases. Exome NGS in combination with genetic linkage or homozygosity mapping studies can aid the identification of the remaining causal genes. As these are thought to be mutated in <1% of the cases, validation through functional modeling in, for example, zebrafish and/or replication through the genotyping of large patient cohorts is required. In the near future, whole genome NGS in combination with transcriptome NGS may reveal mutations that are currently hidden in the noncoding regions of the human genome.
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Affiliation(s)
- Anna M Siemiatkowska
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
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50
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Yang L, Yin X, Feng L, You D, Wu L, Chen N, Li A, Li G, Ma Z. Novel mutations of RPGR in Chinese retinitis pigmentosa patients and the genotype-phenotype correlation. PLoS One 2014; 9:e85752. [PMID: 24454928 PMCID: PMC3893273 DOI: 10.1371/journal.pone.0085752] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 11/30/2013] [Indexed: 11/19/2022] Open
Abstract
X-linked Retinitis Pigmentosa (XLRP) accounts for 10–20% of all RP cases, and represents the most severe subtype of this disease. Mutations in the Retinitis Pigmentosa GTPase Regulator (RPGR) gene are the most common causes of XLRP, accounting for over 70–75% of all XLRP cases. In this work, we analyzed all the exons of RPGR gene with Sanger sequencing in seven Chinese XLRP families, two of these with a provisional diagnosis of adRP but without male-to-male transmission. Three novel deletions (c.2233_34delAG; c.2236_37delGA and c.2403_04delAG) and two known nonsense mutations (c.851C→G and c.2260G→T) were identified in five families. Two novel deletions (c.2233_34delAG and c.2236_37delGA) resulted in the same frame shift (p.E746RfsX22), created similar phenotype in Family 3 and 4. The novel deletion (c.2403_04delAG; p.E802GfsX31) resulted in both XLRP and x-linked cone-rod dystrophy within the male patients of family 5, which suggested the presence of either genetic or environmental modifiers, or both, play a substantial role in disease expression. Genotype-phenotype correlation analysis suggested that (1) both patients and female carriers with mutation in Exon 8 (Family 1) manifest more severe disease than did those with ORF15 mutations (Family 2&3&4); (2) mutation close to downstream of ORF15 (Family 5) demonstrate the early preferential loss of cone function with moderate loss of rod function.
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Affiliation(s)
- Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Xiaobei Yin
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
| | - Lina Feng
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Debo You
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Lemeng Wu
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Ningning Chen
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Aijun Li
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, P. R. China
- * E-mail: (GL); (ZM)
| | - Zhizhong Ma
- Department of Ophthalmology, Peking University Third Hospital, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Beijing, P. R. China
- * E-mail: (GL); (ZM)
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