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Di Iorio E, Adamo GG, Sorrentino U, De Nadai K, Barbaro V, Mura M, Pellegrini M, Boaretto F, Tavolato M, Suppiej A, Nasini F, Salviati L, Parmeggiani F. Pseudodominant inheritance of retinitis pigmentosa in a family with mutations in the Eyes Shut Homolog (EYS) gene. Sci Rep 2024; 14:18580. [PMID: 39127808 PMCID: PMC11316741 DOI: 10.1038/s41598-024-69640-9] [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: 03/31/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024] Open
Abstract
Sequence variants in Eyes Shut Homolog (EYS) gene are one of the most frequent causes of autosomal recessive retinitis pigmentosa (RP). Herein, we describe an Italian RP family characterized by EYS-related pseudodominant inheritance. The female proband, her brother, and both her sons showed typical RP, with diminished or non-recordable full-field electroretinogram, narrowing of visual field, and variable losses of central vision. To investigate this apparently autosomal dominant pedigree, next generation sequencing (NGS) of a custom panel of RP-related genes was performed, further enhanced by bioinformatic detection of copy-number variations (CNVs). Unexpectedly, all patients had a compound heterozygosity involving two known pathogenic EYS variants i.e., the exon 33 frameshift mutation c.6714delT and the exon 29 deletion c.(5927þ1_5928-1)_(6078þ1_6079-1)del, with the exception of the youngest son who was homozygous for the above-detailed frameshift mutation. No pathologic eye conditions were instead observed in the proband's husband, who was a heterozygous healthy carrier of the same c.6714delT variant in exon 33 of EYS gene. These findings provide evidence that pseudodominant pattern of inheritance can hide an autosomal recessive RP partially or totally due to CNVs, recommending CNVs study in those pedigrees which remain genetically unsolved after the completion of NGS or whole exome sequencing analysis.
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Affiliation(s)
- Enzo Di Iorio
- Department of Molecular Medicine, University of Padova, 35121, Padova, Italy
- Clinical Genetics Unit, Azienda Ospedaliero Universitaria di Padova, 35121, Padova, Italy
| | - Ginevra Giovanna Adamo
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121, Ferrara, Italy
| | - Ugo Sorrentino
- Clinical Genetics Unit, Azienda Ospedaliero Universitaria di Padova, 35121, Padova, Italy
- Department of Women and Children's Health, University of Padova, 35121, Padova, Italy
| | - Katia De Nadai
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121, Ferrara, Italy
- ERN-EYE Network - Center for Retinitis Pigmentosa of Veneto Region, Camposampiero Hospital, Azienda ULSS 6 Euganea, 35012, Camposampiero, Padova, Italy
| | | | - Marco Mura
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121, Ferrara, Italy
- King Khaled Eye Specialist Hospital, 11462, Riyadh, Saudi Arabia
| | - Marco Pellegrini
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121, Ferrara, Italy
| | - Francesca Boaretto
- Clinical Genetics Unit, Azienda Ospedaliero Universitaria di Padova, 35121, Padova, Italy
| | - Marco Tavolato
- ERN-EYE Network - Center for Retinitis Pigmentosa of Veneto Region, Camposampiero Hospital, Azienda ULSS 6 Euganea, 35012, Camposampiero, Padova, Italy
| | - Agnese Suppiej
- ERN-EYE Network - Center for Retinitis Pigmentosa of Veneto Region, Camposampiero Hospital, Azienda ULSS 6 Euganea, 35012, Camposampiero, Padova, Italy
- Department of Medical Sciences, University of Ferrara, 44121, Ferrara, Italy
| | - Francesco Nasini
- Ophthalmic Unit, Azienda Ospedaliero Universitaria di Ferrara, 44124, Cona, Ferrara, Italy
| | - Leonardo Salviati
- Clinical Genetics Unit, Azienda Ospedaliero Universitaria di Padova, 35121, Padova, Italy
- Department of Women and Children's Health, University of Padova, 35121, Padova, Italy
| | - Francesco Parmeggiani
- Department of Translational Medicine and for Romagna, University of Ferrara, 44121, Ferrara, Italy.
- ERN-EYE Network - Center for Retinitis Pigmentosa of Veneto Region, Camposampiero Hospital, Azienda ULSS 6 Euganea, 35012, Camposampiero, Padova, Italy.
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Pungor K, Lee J, Denee T, Kambarov Y, Nissinen R, Ampeh K, Pellegrini M, Parmeggiani F. Impacts of X-linked Retinitis Pigmentosa and Patient Pathways in European Countries: Results from the Cross-sectional EXPLORE XLRP-1 Physician Survey. Adv Ther 2024; 41:3378-3395. [PMID: 38976125 PMCID: PMC11263408 DOI: 10.1007/s12325-024-02935-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/17/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION X-linked retinitis pigmentosa (XLRP) is a rare, incurable, vision-threatening, genetic disease. In this study, we aimed to reveal the real-world burden of this disease from the viewpoint of retina specialists and geneticists involved directly in XLRP care and to identify unique insights that may not otherwise be available through typical clinical studies or health economic research. METHODS In this exploratory, cross-sectional study (EXPLORE XLRP-1), retina specialists (n = 20) and geneticists (n = 5) in France, Germany, Italy, Spain, and the UK provided anonymized insights on their experiences managing patients with XLRP (n = 80) via an online survey and 60-min telephone interview. RESULTS Survey respondents reported that patient independence decreased over time, where 37% of patients were considered "completely autonomous" at diagnosis versus 23% at the last consultation. At their last visit, 45% of patients were active in the workforce; 67% (12/18) of "completely autonomous" patients had active working status compared with 13% (1/8) of "completely dependent" patients. The average time from onset of symptoms to diagnosis was 4 years and varied among countries. In 78% of patients, XLRP was confirmed by genetic testing, the rate of which varied among countries (range, 50-94%), taking up to 6 months to receive results. Specialists identified unmet needs in XLRP management including more standardized assessments of quality of life (QoL) as well as easier and earlier access to specialists, genetic testing, patient support programs, and effective treatment options. CONCLUSIONS The diagnosis, genetic testing, and management pathways among patients with XLRP can vary considerably. There is a need for more standardized diagnosis and management pathways, and QoL assessments, due to the major impact that XLRP has on patients' lives.
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Affiliation(s)
| | | | - Tom Denee
- Janssen-Cilag BV, Breda, Netherlands
| | | | | | | | - Marco Pellegrini
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- Department of Ophthalmology, Ospedali Privati Forlì "Villa Igea", Forlì, Italy
- Istituto Internazionale per la Ricerca e Formazione in Oftalmologia, Forlì, Italy
| | - Francesco Parmeggiani
- Department of Translational Medicine, University of Ferrara, Ferrara, Italy
- ERN-EYE Network - Center for Retinitis Pigmentosa of Veneto Region, Camposampiero Hospital, Padua, Italy
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Chan J, Holdstock J, Shovelton J, Reid J, Speight G, Molha D, Pullabhatla V, Carpenter S, Uddin E, Washio T, Sato H, Izumi Y, Watanabe R, Niiro H, Fukushima Y, Ashida N, Hirose T, Maeda A. Clinical and analytical validation of an 82-gene comprehensive genome-profiling panel for identifying and interpreting variants responsible for inherited retinal dystrophies. PLoS One 2024; 19:e0305422. [PMID: 38870140 PMCID: PMC11175448 DOI: 10.1371/journal.pone.0305422] [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] [Received: 02/20/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Inherited retinal dystrophies comprise a clinically complex and heterogenous group of diseases characterized by visual impairment due to pathogenic variants of over 300 different genes. Accurately identifying the causative gene and associated variant is crucial for the definitive diagnosis and subsequent selection of precise treatments. Consequently, well-validated genetic tests are required in the clinical practice. Here, we report the analytical and clinical validation of a next-generation sequencing targeted gene panel, the PrismGuide IRD Panel System. This system enables comprehensive genome profiling of 82 genes related to inherited retinal dystrophies. The PrismGuide IRD Panel System demonstrated 100% (n = 43) concordance with Sanger sequencing in detecting single-nucleotide variants, small insertions, and small deletions in the target genes and also in assessing their zygosity. It also identified copy-number loss in four out of five cases. When assessing precision, we evaluated the reproducibility of variant detection with 2,160 variants in 144 replicates and found 100% agreement in terms of single-nucleotide variants (n = 1,584) and small insertions and deletions (n = 576). Furthermore, the PrismGuide IRD Panel System generated sufficient read depth for variant calls across the purine-rich and highly repetitive open-reading frame 15 region of RPGR and detected all five variants tested. These results show that the PrismGuide IRD Panel System can accurately and consistently detect single-nucleotide variants and small insertions and deletions. Thus, the PrismGuide IRD Panel System could serve as useful tool that is applicable in clinical practice for identifying the causative genes based on the detection and interpretation of variants in patients with inherited retinal dystrophies and can contribute to a precise molecular diagnosis and targeted treatments.
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Affiliation(s)
- Jacqueline Chan
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Jolyon Holdstock
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - John Shovelton
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - James Reid
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Graham Speight
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Duarte Molha
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Venu Pullabhatla
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Stephanie Carpenter
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Ezam Uddin
- Oxford Gene Technology Operations Limited, Kidlington, Oxfordshire, United Kingdom
| | - Takanori Washio
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
- Division of Clinical Cancer Genomics, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Hiroko Sato
- Life Innovation Center, Riken Genesis Co. LTD, Kawasaki, Kanagawa, Japan
| | - Yuuki Izumi
- Technology Innovation, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Reiko Watanabe
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Hayato Niiro
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | | | - Naoko Ashida
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Takashi Hirose
- Medical & Scientific Affairs, Sysmex Corporation, Kobe, Hyogo, Japan
| | - Akiko Maeda
- Department of Ophthalmology, Kobe City Eye Hospital, Kobe, Hyogo, Japan
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Seliniotaki AK, Ververi A, Koukoula S, Efstathiou G, Gerou S, Ziakas N, Mataftsi A. Female carrier of RPGR mutation presenting with high myopia. Ophthalmic Genet 2024; 45:159-163. [PMID: 37489109 DOI: 10.1080/13816810.2023.2237571] [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: 01/28/2023] [Accepted: 07/12/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Inherited retinopathies can initially present with high refractive error in the first decade of life, before accompanying signs or symptoms are evident. CASE PRESENTATION A 4-year-old girl with high myopia (S-12.00 C-4.00 × 20 in the right and S-14.50 C-2.75 × 160 in the left eye), moderate visual acuity (0.3 logMAR in the right and 0.4 logMAR in the left eye), and left esotropia, presented with unremarkable past medical history and no family history of high refractive error or low vision. In optical coherence tomography imaging, macular thinning was evident, while morphology was normal. Full-field electroretinogram revealed normal implicit time recordings with reduced amplitudes in scotopic and photopic conditions. Fundus autofluorescence showed a radial pattern in both eyes. During a 5-year follow-up, significant myopia progression ensued (S-17.25 C-3.00 × 20 in the right and S-17.25 C-2.00 × 160 in the left eye), with a corresponding increase in axial length and an unchanged visual acuity. Whole-exome sequencing revealed a heterozygous termination codon variant c.212C>G (p.Ser71Ter) in RPGR, considered to be pathogenic. Segregation analysis precluded the variation in the mother and sister. A random pattern of X-chromosome inactivation was detected in the proband, without X-chromosome inactivation deviation. CONCLUSION This is the second report associating this specific RPGR mutation with high myopia and the first report to identify it in a female proband. This case provides additional evidence on the genotypic-phenotypic correlation between RPGR c.212C>G mutation and high myopia.
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Affiliation(s)
- Aikaterini K Seliniotaki
- 2nd Department of Ophthalmology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Athina Ververi
- Genetic Unit, 1st Gynecological & Obstetrics Department, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Georgios Efstathiou
- Analysi Biopathological Diagnostic Research Laboratories, Thessaloniki, Greece
| | - Spyridon Gerou
- Analysi Biopathological Diagnostic Research Laboratories, Thessaloniki, Greece
| | - Nikolaos Ziakas
- 2nd Department of Ophthalmology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Asimina Mataftsi
- 2nd Department of Ophthalmology, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
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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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Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies. Biomolecules 2023; 13:biom13020271. [PMID: 36830640 PMCID: PMC9953031 DOI: 10.3390/biom13020271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/23/2023] [Accepted: 01/27/2023] [Indexed: 02/04/2023] Open
Abstract
Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.
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Clinical and Genetic Re-Evaluation of Inherited Retinal Degeneration Pedigrees following Initial Negative Findings on Panel-Based Next Generation Sequencing. Int J Mol Sci 2022; 23:ijms23020995. [PMID: 35055178 PMCID: PMC8780304 DOI: 10.3390/ijms23020995] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/03/2022] [Accepted: 01/12/2022] [Indexed: 02/06/2023] Open
Abstract
Although rare, inherited retinal degenerations (IRDs) are the most common reason for blind registration in the working age population. They are highly genetically heterogeneous (>300 known genetic loci), and confirmation of a molecular diagnosis is a prerequisite for many therapeutic clinical trials and approved treatments. First-tier genetic testing of IRDs with panel-based next-generation sequencing (pNGS) has a diagnostic yield of ≈70-80%, leaving the remaining more challenging cases to be resolved by second-tier testing methods. This study describes the phenotypic reassessment of patients with a negative result from first-tier pNGS and the rationale, outcomes, and cost of second-tier genetic testing approaches. Removing non-IRD cases from consideration and utilizing case-appropriate second-tier genetic testing techniques, we genetically resolved 56% of previously unresolved pedigrees, bringing the overall resolve rate to 92% (388/423). At present, pNGS remains the most cost-effective first-tier approach for the molecular assessment of diverse IRD populations Second-tier genetic testing should be guided by clinical (i.e., reassessment, multimodal imaging, electrophysiology), and genetic (i.e., single alleles in autosomal recessive disease) indications to achieve a genetic diagnosis in the most cost-effective manner.
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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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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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Koyanagi Y, Ueno S, Ito Y, Kominami T, Komori S, Akiyama M, Murakami Y, Ikeda Y, Sonoda KH, Terasaki H. Relationship Between Macular Curvature and Common Causative Genes of Retinitis Pigmentosa in Japanese Patients. Invest Ophthalmol Vis Sci 2021; 61:6. [PMID: 32749464 PMCID: PMC7441377 DOI: 10.1167/iovs.61.10.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To determine the relationship between the macular curvature and the causative genes of retinitis pigmentosa (RP). Methods We examined the medical records of the right eyes of 65 cases with RP (31 men and 34 women; average age, 47.6 years). There were 31 cases with the EYS variants, 11 cases with the USH2A variants, six cases with the RPGR variants, 13 cases with the RP1 variants, and four cases with the RP1L1 variants. The mean curvature of Bruch's membrane was calculated within 6 mm of the fovea as the mean macular curvature index (MMCI, 1/µm). We used multiple linear regression analysis to determine the independence of the causative genes contributing to the MMCIs after adjustments for age, sex, axial length, and width of the ellipsoid zone. Results The median MMCI was −31.2 × 10−5/µm for the RPGR eyes, −16.5 × 10−5/µm for the RP1L1 eyes, −13.0 × 10−5/µm for the RP1 eyes, −9.8 × 10−5/µm for the EYS eyes, and −9.0 × 10−5/µm for the USH2A eyes. Compared with the EYS gene as the reference gene, the RPGR gene was significantly related to the MMCI values after adjusting for the other parameters (P = 5.30 × 10−6). In contrast, the effects of the other genes, USH2A, RP1, and RP1L1, were not significantly different from that of the EYS gene (P = 0.26, P = 0.49, and P = 0.92, respectively). Conclusions The RPGR gene had a stronger effect on the steep macular curvature than the other ciliopathy-related genes.
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Li HP, Yuan SQ, Wang XG, Sheng XL, Li XR. Myopia with X-linked retinitis pigmentosa results from a novel gross deletion of RPGR gene. Int J Ophthalmol 2020; 13:1306-1311. [PMID: 32821686 DOI: 10.18240/ijo.2020.08.18] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 06/29/2020] [Indexed: 12/31/2022] Open
Abstract
AIM To identify mutations with whole exome sequencing (WES) in a Chinese X-linked retinitis pigmentosa (XLRP) family. METHODS Patients received the comprehensive ophthalmic evaluation. Genomic DNA was extracted from peripheral blood and subjected to SureSelect Human All Exon 6+ UTR exon capture kit. The exons were sequenced as 100 base paired reads on Illumina HiSeq2500 system. Only mutations that resulted in a change in amino acid sequence were selected. A pattern of inheritance of the RP family was aligned to identified causal mutation. RESULTS We analysed the data of WES information from XLRP family. The analysis revealed a hemizygous large genomic deletion of RPGR c.29_113del was responsible for this XLRP. The gross deletion lead to a frame-shift mutation and generate stop codon at 7 animo acid behind Asp (D10Afs*7), which would serious truncate RPGR protein. The novel frame-shift mutation was found to segregate with retinitis pigmentosa (RP) phenotype in this family. Bilateral myopia was present on the male patients, but carrier female showed unilateral myopia without RP. CONCLUSION Our study identifies a novel frame-shift mutation of RPGR in a Chinese family, which would expand the spectrum of RPGR mutations. The geno-phenotypic analysis reveals a correlation between RP and myopia. Although exact mechanism of RP related myopia is still unknown, but the novel frame-shift mutation will give our hit on studying the molecular pathogenesis of RP and myopia.
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Affiliation(s)
- Hui-Ping Li
- Tianjin Medical University Eye Hospital, Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin 300384, China.,Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, Yinchuan 750002, Ningxia Hui Autonomous Region, China
| | - Shi-Qin Yuan
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, Yinchuan 750002, Ningxia Hui Autonomous Region, China
| | - Xiao-Guang Wang
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, Yinchuan 750002, Ningxia Hui Autonomous Region, China
| | - Xun-Lun Sheng
- Department of Ophthalmology, Ningxia Eye Hospital, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest University for Nationalities, Ningxia Clinical Research Center on Diseases of Blindness in Eye, Yinchuan 750002, Ningxia Hui Autonomous Region, China
| | - Xiao-Rong Li
- Tianjin Medical University Eye Hospital, Tianjin Key Laboratory of Retinal Functions and Diseases, Eye Institute and School of Optometry, Tianjin 300384, China
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Talib M, Boon CJF. Retinal Dystrophies and the Road to Treatment: Clinical Requirements and Considerations. Asia Pac J Ophthalmol (Phila) 2020; 9:159-179. [PMID: 32511120 PMCID: PMC7299224 DOI: 10.1097/apo.0000000000000290] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
: Retinal dystrophies (RDs) comprise relatively rare but devastating causes of progressive vision loss. They represent a spectrum of diseases with marked genetic and clinical heterogeneity. Mutations in the same gene may lead to different diagnoses, for example, retinitis pigmentosa or cone dystrophy. Conversely, mutations in different genes may lead to the same phenotype. The age at symptom onset, and the rate and characteristics of peripheral and central vision decline, may vary widely per disease group and even within families. For most RD cases, no effective treatment is currently available. However, preclinical studies and phase I/II/III gene therapy trials are ongoing for several RD subtypes, and recently the first retinal gene therapy has been approved by the US Food and Drug Administration for RPE65-associated RDs: voretigene neparvovec-rzyl (Luxturna). With the rapid advances in gene therapy studies, insight into the phenotypic spectrum and long-term disease course is crucial information for several RD types. The vast clinical heterogeneity presents another important challenge in the evaluation of potential efficacy in future treatment trials, and in establishing treatment candidacy criteria. This perspective describes these challenges, providing detailed clinical descriptions of several forms of RD that are caused by genes of interest for ongoing and future gene or cell-based therapy trials. Several ongoing and future treatment options will be described.
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Affiliation(s)
- Mays Talib
- Department of Ophthalmology, Leiden, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden, The Netherlands
- Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, University of Amsterdam. Amsterdam, The Netherlands
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Pasquini G, Cora V, Swiersy A, Achberger K, Antkowiak L, Müller B, Wimmer T, Fraschka SAK, Casadei N, Ueffing M, Liebau S, Stieger K, Busskamp V. Using Transcriptomic Analysis to Assess Double-Strand Break Repair Activity: Towards Precise in vivo Genome Editing. Int J Mol Sci 2020; 21:E1380. [PMID: 32085662 PMCID: PMC7073035 DOI: 10.3390/ijms21041380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/13/2020] [Accepted: 02/15/2020] [Indexed: 12/17/2022] Open
Abstract
Mutations in more than 200 retina-specific genes have been associated with inherited retinal diseases. Genome editing represents a promising emerging field in the treatment of monogenic disorders, as it aims to correct disease-causing mutations within the genome. Genome editing relies on highly specific endonucleases and the capacity of the cells to repair double-strand breaks (DSBs). As DSB pathways are cell-cycle dependent, their activity in postmitotic retinal neurons, with a focus on photoreceptors, needs to be assessed in order to develop therapeutic in vivo genome editing. Three DSB-repair pathways are found in mammalian cells: Non-homologous end joining (NHEJ); microhomology-mediated end joining (MMEJ); and homology-directed repair (HDR). While NHEJ can be used to knock out mutant alleles in dominant disorders, HDR and MMEJ are better suited for precise genome editing, or for replacing entire mutation hotspots in genomic regions. Here, we analyzed transcriptomic in vivo and in vitro data and revealed that HDR is indeed downregulated in postmitotic neurons, whereas MMEJ and NHEJ are active. Using single-cell RNA sequencing analysis, we characterized the dynamics of DSB repair pathways in the transition from dividing cells to postmitotic retinal cells. Time-course bulk RNA-seq data confirmed DSB repair gene expression in both in vivo and in vitro samples. Transcriptomic DSB repair pathway profiles are very similar in adult human, macaque, and mouse retinas, but not in ground squirrel retinas. Moreover, human-induced pluripotent stem-cell-derived neurons and retinal organoids can serve as well suited in vitro testbeds for developing genomic engineering approaches in photoreceptors. Our study provides additional support for designing precise in vivo genome-editing approaches via MMEJ, which is active in mature photoreceptors.
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Affiliation(s)
- Giovanni Pasquini
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Virginia Cora
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Anka Swiersy
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
| | - Kevin Achberger
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Lena Antkowiak
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Brigitte Müller
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Tobias Wimmer
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Sabine Anne-Kristin Fraschka
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, 72076 Tübingen, Germany
- DFG NGS Competence Center Tübingen, 72076 Tübingen, Germany
| | - Marius Ueffing
- Department of Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, 72076 Tübingen, Germany
| | - Stefan Liebau
- Institute of Neuroanatomy & Developmental Biology (INDB), Eberhard Karls University Tübingen, 72074 Tübingen, Germany
| | - Knut Stieger
- Department of Ophthalmology, Justus-Liebig-University, 35392 Giessen, Germany
| | - Volker Busskamp
- Center for Regenerative Therapies (CRTD), Technical University Dresden, 01307 Dresden, Germany
- Universitäts-Augenklinik Bonn, University of Bonn, Dept. of Ophthalmology, 53127 Bonn, Germany
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Zhang Z, Dai H, Wang L, Tao T, Xu J, Sun X, Yang L, Li G. Novel mutations of RPGR in Chinese families with X-linked retinitis pigmentosa. BMC Ophthalmol 2019; 19:240. [PMID: 31775781 PMCID: PMC6882249 DOI: 10.1186/s12886-019-1250-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 11/18/2019] [Indexed: 12/15/2022] Open
Abstract
Background RP (retinitis pigmentosa) is a group of hereditary retinal degenerative diseases. XLRP is a relatively severe subtype of RP. Thus, it is necessary to identify genes and mutations in patients who present with X-linked retinitis pigmentosa. Methods Genomic DNA was extracted from peripheral blood. The coding regions and intron-exon boundaries of the retinitis pigmentosa GTPase regulator (RPGR) and RP2 genes were amplified by PCR and then sequenced directly. Ophthalmic examinations were performed to identify affected individuals from two families and to characterize the phenotype of the disease. Results Mutation screening demonstrated two novel nonsense mutations (c.1541C > G; p.S514X and c.2833G > T; p.E945X) in the RPGR gene. The clinical manifestation of family 1 with mutations in exon 13 was mild. Genotype-phenotype correlation analysis suggested that patients with mutations close to the downstream region of ORF15 in family 2 manifested an early loss of cone function. Family 2 carried a nonsense mutation in ORF15 that appeared to have a semi-dominant pattern of inheritance. All male patients and two female carriers in family 2 manifested pathological myopia (PM), indicating that there may be a distinctive X-linked genotype-phenotype correlation between RP and PM. Conclusions We identified two novel mutations of the RPGR gene, which broadens the spectrum of RPGR mutations and the phenotypic spectrum of the disease in Chinese families.
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Affiliation(s)
- Zhimeng Zhang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Hehua Dai
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Lei Wang
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Tianchang Tao
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Jing Xu
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Xiaowei Sun
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China
| | - Liping Yang
- Department of Ophthalmology, Key Laboratory of Vision Loss and Restoration, Ministry of Education, Peking University Third Hospital, Beijing, People's Republic of China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University; Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, People's Republic of China.
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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: 33] [Impact Index Per Article: 6.6] [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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Abstract
Currently, myopic retinopathy is the most common irreversible blinding disease but its pathophysiology is not completely clear. A cross-sectional, observational study was conducted in a single center to analyze aqueous samples from highly myopic eyes (axial length >25 mm, n = 92) and ametropic or mild myopic eyes (n = 88) for inflammatory cytokines. Vascular endothelial growth factor (VEGF), Interleukin 6 (IL-6), and matrix metalloproteinase-2 (MMP-2) were measured using an enzyme-linked immunosorbent assay. IL-6 and MMP-2 were significantly higher in the highly myopic eyes than in the non-high myopic eyes (IL-6: 11.90 vs. 4.38 pg/mL, p < 0.0001; MMP-2: 13.10 vs. 8.82 ng/mL, p = 0.0003) while adjusting for age, gender, and intraocular pressure. There was a significant positive association between levels of IL-6 and MMP-2 in aqueous humor and the axial lengths of the eye globes (IL-6, β = 0.065, p < 0.0001, n = 134; MMP-2, β = 0.097, p < 0.0001, n = 131). Conversely, VEGF in aqueous humor was significantly lower in the highly myopic eyes than in the non-high myopic eyes (45.56 vs. 96.90 pg/mL, p < 0.0001, n = 153) while age, gender, and intraocular pressure were adjusted. The results suggest that low-grade intraocular inflammation may play an important role in the development and progression of high myopia and myopic retinopathy.
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Wan L, Deng B, Wu Z, Chen X. Exome sequencing study of 20 patients with high myopia. PeerJ 2018; 6:e5552. [PMID: 30245926 PMCID: PMC6148412 DOI: 10.7717/peerj.5552] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 08/07/2018] [Indexed: 02/05/2023] Open
Abstract
Background High myopia is a common ocular disease worldwide. To expand our current understanding of the genetic basis of high myopia, we carried out a whole exome sequencing (WES) study to identify potential causal gene mutations. Methods A total of 20 individuals with high myopia were exome sequenced. A novel filtering strategy combining phenotypes and functional impact of variants was applied to identify candidate genes by multi-step bioinformatics analyses. Network and enrichment analysis were employed to examine the biological pathways involved in the candidate genes. Results In 16 out of 20 patients, we identified 20 potential pathogenic gene variants for high myopia. A total of 18 variants were located in myopia-associated chromosomal regions. In addition to the novel mutations found in five known myopia genes (ADAMTS18, CSMD1, P3H2, RPGR, and SLC39A5), we also identified pathogenic variants in seven ocular disease genes (ABCA4, CEP290, HSPG2, PCDH15, SAG, SEMA4A, and USH2A) as novel candidate genes. The biological processes associated with vision were significantly enriched in our candidate genes, including visual perception, photoreceptor cell maintenance, retinoid metabolic process, and cellular response to zinc ion starvation. Discussion Systematic mutation analysis of candidate genes was performed using WES data, functional interaction (FI) network, Gene Ontology and pathway enrichment. FI network analysis revealed important network modules and regulator linker genes (EP300, CTNNB1) potentially related to high myopia development. Our study expanded the list of candidate genes associated with high myopia, which increased the genetic screening performance and provided implications for future studies on the molecular genetics of myopia.
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Affiliation(s)
- Ling Wan
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Boling Deng
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Zhengzheng Wu
- Department of Ophthalmology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital and Affiliated Hospital of University of Electronic Science and Technology, Chengdu, Sichuan, China
| | - Xiaoming Chen
- Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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