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Koller S, Beltraminelli T, Maggi J, Wlodarczyk A, Feil S, Baehr L, Gerth-Kahlert C, Menghini M, Berger W. Functional Analysis of a Novel, Non-Canonical RPGR Splice Variant Causing X-Linked Retinitis Pigmentosa. Genes (Basel) 2023; 14:genes14040934. [PMID: 37107692 PMCID: PMC10137330 DOI: 10.3390/genes14040934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/05/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
X-linked retinitis pigmentosa (XLRP) caused by mutations in the RPGR gene is one of the most severe forms of RP due to its early onset and intractable progression. Most cases have been associated with genetic variants within the purine-rich exon ORF15 region of this gene. RPGR retinal gene therapy is currently being investigated in several clinical trials. Therefore, it is crucial to report and functionally characterize (all novel) potentially pathogenic DNA sequence variants. Whole-exome sequencing (WES) was performed for the index patient. The splicing effects of a non-canonical splice variant were tested on cDNA from whole blood and a minigene assay. WES revealed a rare, non-canonical splice site variant predicted to disrupt the wildtype splice acceptor and create a novel acceptor site 8 nucleotides upstream of RPGR exon 12. Reverse-transcription PCR analyses confirmed the disruption of the correct splicing pattern, leading to the insertion of eight additional nucleotides in the variant transcript. Transcript analyses with minigene assays and cDNA from peripheral blood are useful tools for the characterization of splicing defects due to variants in the RPGR and may increase the diagnostic yield in RP. The functional analysis of non-canonical splice variants is required to classify those variants as pathogenic according to the ACMG's criteria.
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Affiliation(s)
- Samuel Koller
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Tim Beltraminelli
- Department of Ophthalmology, Institute of Clinical Neurosciences of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6962 Lugano, Switzerland
| | - Jordi Maggi
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Agnès Wlodarczyk
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Silke Feil
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Luzy Baehr
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
| | - Christina Gerth-Kahlert
- Department of Ophthalmology, University Hospital, University of Zurich, 8091 Zurich, Switzerland
| | - Moreno Menghini
- Department of Ophthalmology, Institute of Clinical Neurosciences of Southern Switzerland, Ente Ospedaliero Cantonale (EOC), 6962 Lugano, Switzerland
- Department of Ophthalmology, University Hospital, University of Zurich, 8091 Zurich, Switzerland
| | - Wolfgang Berger
- Institute of Medical Molecular Genetics, University of Zurich, 8952 Schlieren, Switzerland
- Zurich Center for Integrative Human Physiology (ZIHP), University of Zurich, 8057 Zurich, Switzerland
- Neuroscience Center Zurich (ZNZ), University and ETH Zurich, 8057 Zurich, Switzerland
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Li W, Jiang XS, Han DM, Gao JY, Yang ZT, Jiang L, Zhang Q, Zhang SH, Gao Y, Wu JH, Li JK. Genetic Characteristics and Variation Spectrum of USH2A-Related Retinitis Pigmentosa and Usher Syndrome. Front Genet 2022; 13:900548. [PMID: 36110214 PMCID: PMC9468824 DOI: 10.3389/fgene.2022.900548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 06/10/2022] [Indexed: 11/13/2022] Open
Abstract
Purposes: We aimed to characterize the USH2A genotypic spectrum in a Chinese cohort and provide a detailed genetic profile for Chinese patients with USH2A-IRD.Methods: We designed a retrospective study wherein a total of 1,334 patients diagnosed with IRD were included as a study cohort, namely 1,278 RP and 56 USH patients, as well as other types of IEDs patients and healthy family members as a control cohort. The genotype-phenotype correlation of all participants with USH2A variant was evaluated.Results: Etiological mutations in USH2A, the most common cause of RP and USH, were found in 16.34% (n = 218) genetically solved IRD patients, with prevalences of 14.87% (190/1,278) and 50% (28/56). After bioinformatics and QC processing, 768 distinct USH2A variants were detected in all participants, including 136 disease-causing mutations present in 665 alleles, distributed in 5.81% of all participants. Of these 136 mutations, 43 were novel, nine were founder mutations, and two hot spot mutations with allele count ≥10. Furthermore, 38.5% (84/218) of genetically solved USH2A-IRD patients were caused by at least one of both c.2802T>G and c.8559–2 A>G mutations, and 36.9% and 69.6% of the alleles in the RP and USH groups were truncating, respectively.Conclusion: USH2A-related East Asian-specific founder and hot spot mutations were the major causes for Chinese RP and USH patients. Our study systematically delineated the genotype spectrum of USH2A-IRD, enabled accurate genetic diagnosis, and provided East Asian and other ethnicities with baseline data of a Chinese origin, which would better serve genetic counseling and therapeutic targets selection.
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Affiliation(s)
- Wei Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Xiao-Sen Jiang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Dong-Ming Han
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Jia-Yu Gao
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Zheng-Tao Yang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Li Jiang
- Department of Ophthalmology, Laizhou City People’s Hospital, Yantai, China
| | - Qian Zhang
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- BGI-Shenzhen, Shenzhen, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Ya Gao
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Ji-Hong Wu
- Eye Institute, Eye and ENT Hospital, College of Medicine, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
| | - Jian-Kang Li
- BGI-Shenzhen, Shenzhen, China
- *Correspondence: Wei Li, ; Ya Gao, ; Ji-Hong Wu, ; Jian-Kang Li,
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Griffith J, Sioufi K, Wilbanks L, Magrath GN, Say EAT, Lyons MJ, Wilkes M, Pai GS, Peterseim MMW. Inherited Retinal Dystrophy in Southeastern United States: Characterization of South Carolina Patients and Comparative Literature Review. Genes (Basel) 2022; 13:genes13081490. [PMID: 36011402 PMCID: PMC9407983 DOI: 10.3390/genes13081490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/16/2022] [Accepted: 08/18/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a group of rare diseases involving more than 340 genes and a variety of clinical phenotypes that lead to significant visual impairment. The aim of this study is to evaluate the rates and genetic characteristics of IRDs in the southeastern region of the United States (US). A retrospective chart review was performed on 325 patients with a clinical diagnosis of retinal dystrophy. Data including presenting symptoms, visual acuity, retinal exam findings, imaging findings, and genetic test results were compiled and compared to national and international IRD cohorts. The known ethnic groups included White (64%), African American or Black (30%), Hispanic (3%), and Asian (2%). The most prevalent dystrophies identified clinically were non-syndromic retinitis pigmentosa (29.8%), Stargardt disease (8.3%), Usher syndrome (8.3%), cone-rod dystrophy (8.0%), cone dystrophy (4.9%), and Leber congenital amaurosis (4.3%). Of the 101 patients (31.1%) with genetic testing, 54 (53.5%) had causative genetic variants identified. The most common pathogenic genetic variants were USH2A (n = 11), ABCA4 (n = 8), CLN3 (n = 7), and CEP290 (n = 3). Our study provides initial information characterizing IRDs within the diverse population of the southeastern US, which differs from national and international genetic and diagnostic trends with a relatively high proportion of retinitis pigmentosa in our African American or Black population and a relatively high frequency of USH2A pathogenic variants.
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Affiliation(s)
- Joseph Griffith
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Kareem Sioufi
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Laurie Wilbanks
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - George N. Magrath
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Emil A. T. Say
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
| | | | - Meg Wilkes
- Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Gurpur Shashidhar Pai
- Department of Genetics, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Mae Millicent Winfrey Peterseim
- Department of Ophthalmology, Medical University of South Carolina, Charleston, SC 29425, USA
- Correspondence: ; Tel.: +1-843-792-3758
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Sallum JMF, Kaur VP, Shaikh J, Banhazi J, Spera C, Aouadj C, Viriato D, Fischer MD. Epidemiology of Mutations in the 65-kDa Retinal Pigment Epithelium (RPE65) Gene-Mediated Inherited Retinal Dystrophies: A Systematic Literature Review. Adv Ther 2022; 39:1179-1198. [PMID: 35098484 PMCID: PMC8918161 DOI: 10.1007/s12325-021-02036-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 12/22/2021] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Inherited retinal dystrophies (IRDs) represent a genetically diverse group of progressive, visually debilitating diseases. Adult and paediatric patients with vision loss due to IRD caused by biallelic mutations in the 65-kDa retinal pigment epithelium (RPE65) gene are often clinically diagnosed as retinitis pigmentosa (RP), and Leber congenital amaurosis (LCA). This study aimed to understand the epidemiological landscape of RPE65 gene-mediated IRD through a systematic review of the literature, as the current evidence base for its epidemiology is very limited. METHODS Medline, Embase, and other databases were searched for articles on the epidemiology of RPE65 gene-mediated IRDs from inception until June 2021. Studies were included if they were original research articles reporting the epidemiology of RP and LCA and/or proportion of RPE65 gene mutations in these clinically diagnosed or molecularly confirmed IRDs patients. RESULTS A total of 100 studies with relevant data were included in this systematic review. The range for prevalence of LCA and RP in the literature was 1.20-2.37 and 11.09-26.43 per 100,000, respectively. The proportion of RPE65 mutations in clinically diagnosed patients with LCA was found to be between ~ 2-16% within the US and major European countries (France, Germany, Italy, Spain, and the UK). This range was also comparable to our findings in the Asian region for RPE65-LCA (1.26-16.67%). Similarly, for these European countries, RPE65-RP was estimated between 0.23 and 1.94%, and RPE65-IRD range was 1.2-14%. Further, in the Americas region, mutations in RPE65 were reported to cause 1-3% of RP and 0.8-3.7% of IRD cases. Lastly, the RPE65-IRD range was 4.81-8% in the Middle East region. CONCLUSIONS There are significant variations in reporting of RPE65 proportions within countries as well as regions. Generating robust epidemiological evidence on RPE65 gene-mediated IRDs would be fundamental to support rare disease awareness, timely therapeutic intervention, and public health decision-making.
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Affiliation(s)
- Juliana M F Sallum
- Department of Ophthalmology, Universidade Federal de São Paulo, São Paulo, Brazil
- Instituto de Genética Ocular, São Paulo, Brazil
| | | | | | | | | | | | | | - M Dominik Fischer
- Centre for Ophthalmology, University Eye Hospital, University Hospital Tübingen, Tübingen, Germany
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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