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Kondo H, Tsukahara-Kawamura T, Matsushita I, Nagata T, Hayashi T, Nishina S, Higasa K, Uchio E, Kondo M, Sakamoto T, Kusaka S. Familial Exudative Vitreoretinopathy With and Without Pathogenic Variants of Norrin/β-Catenin Signaling Genes. OPHTHALMOLOGY SCIENCE 2024; 4:100514. [PMID: 38881609 PMCID: PMC11179410 DOI: 10.1016/j.xops.2024.100514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 06/18/2024]
Abstract
Purpose To determine the clinical characteristics of familial exudative vitreoretinopathy (FEVR) associated with or without pathogenic variants of the Norrin/β-catenin genes. Design This was a multicenter, cross-sectional, observational, and genetic study. Subjects Two-hundred eighty-one probands with FEVR were studied. Methods Whole-exome sequence and/or Sanger sequence was performed for the Norrin/β-catenin genes, the FZD4, LRP5, TSPAN12, and NDP genes on blood collected from the probands. The clinical symptoms of the probands with or without the pathogenic variants were assessed as well as differences in the inter Norrin/β-catenin genes. Main Outcome Measures The phenotype associated with or without pathogenic variants of the Norrin/β-catenin genes. Results One-hundred eight probands (38.4%) had 88 different pathogenic or likely pathogenic variants in the genes: 24 with the FZD4, 42 with the LRP5, 10 with the TSPAN12, and 12 with the NDP gene. Compared with the 173 probands without pathogenic variants, the 108 variant-positive probands had characteristics of familial predisposition (63.9% vs. 37.6%, P < 0.0001), progression during infancy (75.0% vs. 53.8%, P = 0.0004), asymmetrical severity between the 2 eyes (50.0% vs. 37.6%, P = 0.0472), and nonsyndromic characteristics (10.2% vs. 17.3%, P = 0.1185). The most frequent stage at which the more severe eye conditions was present was at stage 4 in both groups (40.7% vs. 34.7%). However, the advanced stages of 3 to 5 in the more severe eye were found more frequently in probands with variants than in those without variants (83.3% vs. 58.4%, P < 0.0001). Patients with rhegmatogenous retinal detachments progressed from stage 1 or 2 were found less frequently in the variant-positive probands (8.3% vs. 17.3%, P = 0.0346). Nine probands with NDP variants had features different from probands with typical Norrin/β-catenin gene variants including the sporadic, symmetrical, and systemic characteristics consistent with Norrie disease. Conclusions The results showed that the clinical characteristics of FEVR of patients with variants in the Norrin/β-catenin genes are different from those with other etiologies. We recommend that clinicians who diagnose a child with FEVR perform genetic testing so that the parents can be informed on the prognosis of the vision and general health in the child. Financial Disclosures Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Affiliation(s)
- Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | | | - Itsuka Matsushita
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Tatsuo Nagata
- Department of Ophthalmology, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo, Japan
| | - Sachiko Nishina
- Division of Ophthalmology, National Center for Child Health and Development, Tokyo, Japan
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
| | - Eiichi Uchio
- Department of Ophthalmology, Fukuoka University, Fukuoka, Japan
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Faculty of Medicine, Tsu, Japan
| | - Taiji Sakamoto
- Department of Ophthalmology, Kagoshima University Faculty of Medicine, Kagoshima, Japan
| | - Shunji Kusaka
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osakasayama, Japan
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Dimopoulos IS, Huryn LA, Hufnagel RB, Ullah E, Agather AR, Blain D, Brooks BP, Cukras CA, Zein WM. OUTER RETINAL MICROCAVITATIONS IN RETINITIS PIGMENTOSA : A Novel Optical Coherence Tomography Finding Common in RP1 -Related Retinopathy. Retina 2024; 44:1260-1267. [PMID: 38478753 PMCID: PMC11189741 DOI: 10.1097/iae.0000000000004091] [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] [Indexed: 06/21/2024]
Abstract
PURPOSE To describe a novel optical coherence tomography (OCT) finding of outer retina microcavitations in RP1 -related retinopathy and other retinal degenerations. METHODS Medical charts and OCT images of 28 patients with either autosomal dominant retinitis pigmentosa or autosomal recessive retinitis pigmentosa RP1 -related retinopathy were reviewed. Outer retina microcavitations were defined as hyporeflective OCT structures of at least 30 µ m in diameter between the ellipsoid zone and retinal pigment epithelium. Comparison was made based on the following metrics: (1) functional measures including best-corrected visual acuity and color discrimination errors on D-15 test; and (2) structural measures, including central subfield, average macular thickness, and preserved transfoveal ellipsoid zone width. Mann-Whitney tests were used for comparisons with significance set at P < 0.05. The specificity of microcavitations for RP1 -related retinopathy was estimated against 26 patients with non- RP1 retinitis pigmentosa. RESULTS Among 15 included patients, microcavitations were found in at least one eye of all patients with arRP and 7/12 (58%) of patients with adRP. Patients with adRP and microcavitations were older at the time of examination (51 vs. 43 years of age; P = 0.04) and their eyes demonstrated worse best-corrected visual acuity (0.09 vs. 0 logMAR; P = 0.008), reduced central subfield (256 vs. 293 µ m; P = 0.01), average macular thickness (241 vs. 270 µ m; P = 0.02), and shorter transfoveal ellipsoid zone widths (1.67 vs. 4.98 mm; P < 0.0001). The finding of microcavitations showed a specificity of 0.92 for RP1 -related retinopathy. CONCLUSION A novel OCT finding of outer retina microcavitations was commonly observed in patients with RP1 -related retinopathy. Eyes with outer retinal OCT microcavitations had worse visual function and more affected central retinal structure.
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Affiliation(s)
- Ioannis S Dimopoulos
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
- Medical Genetics and Ophthalmic Genomics Unit, National Eye Institute, National Institutes of Health, Bethesda, Maryland; and
| | - Aime R Agather
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Delphine Blain
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Catherine A Cukras
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
- Unit on Clinical Investigation of Retinal Disease, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland
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Daich Varela M, Jeste M, de Guimaraes TAC, Mahroo OA, Arno G, Webster AR, Michaelides M. Clinical, Ophthalmic, and Genetic Characterization of RPGRIP1-Associated Leber Congenital Amaurosis/Early-Onset Severe Retinal Dystrophy. Am J Ophthalmol 2024; 266:255-263. [PMID: 38768745 DOI: 10.1016/j.ajo.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
PURPOSE To present the clinical characteristics, retinal features, natural history, and genetics of RPGRIP1-associated early-onset severe retinal dystrophy (EOSRD)/Leber congenital amaurosis (LCA). DESIGN Retrospective case series. METHODS Review of clinical notes, multimodal retinal imaging, and molecular diagnosis of 18 patients (17 families) with EOSRD/LCA and disease-causing variants in RPGRIP1. RESULTS The mean age of visual symptoms onset was 0.87 ± 1 year (birth to 3 years), and the mean age at baseline visit was 11.4 ± 10.2 years (1-39 years). At the baseline visit, 44% of patients were legally blind (range, 2-39 years), and there was no significant association found between age and best-corrected visual acuity (BCVA) in cross-sectional analysis. Retinal evaluation showed an abolished electroretinogram or a cone-rod dystrophy pattern, no or minimal pigment deposits, a hyperautofluorescent ring at the posterior pole, and a largely preserved central macular architecture, with retained outer nuclear layer and ellipsoid zone island into adulthood. Eleven variants (48%) were previously unreported, and 13 families (76%) had a double-null (DN) genotype. Twelve patients (67%) had follow-up assessments over a 15.7 ± 9.5-year period. The rate of BCVA decline was 0.02 logarithm of the minimum angle of resolution (1 letter)/year. CONCLUSIONS RPGRIP1 EOSRD/LCA often presents at birth or early infancy, with nystagmus, decreased visual acuity, hyperopia, and photophobia. Patients with a DN genotype may develop symptoms earlier and have worse vision. Multimodal imaging may show a hyperautofluorescent posterior pole ring and relatively preserved central macular architecture, suggesting that the condition is a promising candidate for gene supplementation.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Mrunmayi Jeste
- St Thomas' Hospital (M.J., O.A.M), London, United Kingdom
| | - Thales A C de Guimaraes
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; St Thomas' Hospital (M.J., O.A.M), London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom; UCL Institute of Ophthalmology, University College London (M.D.V., T.A.C.deG., O.A.M., G.A., A.R.W., M.M.), London, United Kingdom.
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D'haene E, López-Soriano V, Martínez-García PM, Kalayanamontri S, Rey AD, Sousa-Ortega A, Naranjo S, Van de Sompele S, Vantomme L, Mahieu Q, Vergult S, Neto A, Gómez-Skarmeta JL, Martínez-Morales JR, Bauwens M, Tena JJ, De Baere E. Comparative 3D genome analysis between neural retina and retinal pigment epithelium reveals differential cis-regulatory interactions at retinal disease loci. Genome Biol 2024; 25:123. [PMID: 38760655 PMCID: PMC11100165 DOI: 10.1186/s13059-024-03250-6] [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: 06/30/2023] [Accepted: 04/17/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Vision depends on the interplay between photoreceptor cells of the neural retina and the underlying retinal pigment epithelium (RPE). Most genes involved in inherited retinal diseases display specific spatiotemporal expression within these interconnected retinal components through the local recruitment of cis-regulatory elements (CREs) in 3D nuclear space. RESULTS To understand the role of differential chromatin architecture in establishing tissue-specific expression at inherited retinal disease loci, we mapped genome-wide chromatin interactions using in situ Hi-C and H3K4me3 HiChIP on neural retina and RPE/choroid from human adult donor eyes. We observed chromatin looping between active promoters and 32,425 and 8060 candidate CREs in the neural retina and RPE/choroid, respectively. A comparative 3D genome analysis between these two retinal tissues revealed that 56% of 290 known inherited retinal disease genes were marked by differential chromatin interactions. One of these was ABCA4, which is implicated in the most common autosomal recessive inherited retinal disease. We zoomed in on retina- and RPE-specific cis-regulatory interactions at the ABCA4 locus using high-resolution UMI-4C. Integration with bulk and single-cell epigenomic datasets and in vivo enhancer assays in zebrafish revealed tissue-specific CREs interacting with ABCA4. CONCLUSIONS Through comparative 3D genome mapping, based on genome-wide, promoter-centric, and locus-specific assays of human neural retina and RPE, we have shown that gene regulation at key inherited retinal disease loci is likely mediated by tissue-specific chromatin interactions. These findings do not only provide insight into tissue-specific regulatory landscapes at retinal disease loci, but also delineate the search space for non-coding genomic variation underlying unsolved inherited retinal diseases.
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Affiliation(s)
- Eva D'haene
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Víctor López-Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Pedro Manuel Martínez-García
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Soraya Kalayanamontri
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Sousa-Ortega
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Silvia Naranjo
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Stijn Van de Sompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Lies Vantomme
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Quinten Mahieu
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Sarah Vergult
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Ana Neto
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - José Luis Gómez-Skarmeta
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain
| | - Juan Ramón Martínez-Morales
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
| | - Juan Jesús Tena
- Centro Andaluz de Biología del Desarrollo, Consejo Superior de Investigaciones Científicas and Universidad Pablo de Olavide, Sevilla, Spain.
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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Shamsnajafabadi H, Kaukonen M, Bellingrath JS, MacLaren RE, Cehajic-Kapetanovic J. In Silico CRISPR-Cas-Mediated Base Editing Strategies for Early-Onset, Severe Cone-Rod Retinal Degeneration in Three Crumbs homolog 1 Patients, including the Novel Variant c.2833G>A. Genes (Basel) 2024; 15:625. [PMID: 38790254 PMCID: PMC11121323 DOI: 10.3390/genes15050625] [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: 03/27/2024] [Revised: 05/07/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Pathogenic variants in the Crumbs homolog 1 (CRB1) gene lead to severe, childhood-onset retinal degeneration leading to blindness in early adulthood. There are no approved therapies, and traditional adeno-associated viral vector-based gene therapy approaches are challenged by the existence of multiple CRB1 isoforms. Here, we describe three CRB1 variants, including a novel, previously unreported variant that led to retinal degeneration. We offer a CRISPR-Cas-mediated DNA base editing strategy as a potential future therapeutic approach. This study is a retrospective case series. Clinical and genetic assessments were performed, including deep phenotyping by retinal imaging. In silico analyses were used to predict the pathogenicity of the novel variant and to determine whether the variants are amenable to DNA base editing strategies. Case 1 was a 24-year-old male with cone-rod dystrophy and retinal thickening typical of CRB1 retinopathy. He had a relatively preserved central outer retinal structure and a best corrected visual acuity (BCVA) of 60 ETDRS letters in both eyes. Genetic testing revealed compound heterozygous variants in exon 9: c.2843G>A, p.(Cys948Tyr) and a novel variant, c.2833G>A, p.(Gly945Arg), which was predicted to likely be pathogenic by an in silico analysis. Cases 2 and 3 were two brothers, aged 20 and 24, who presented with severe cone-rod dystrophy and a significant disruption of the outer nuclear layers. The BCVA was reduced to hand movements in both eyes in Case 2 and to 42 ETDRS letters in both eyes in Case 3. Case 2 was also affected with marked cystoid macular lesions, which are common in CRB1 retinopathy, but responded well to treatment with oral acetazolamide. Genetic testing revealed two c.2234C>T, p.(Thr745Met) variants in both brothers. As G-to-A and C-to-T variants, all three variants are amenable to adenine base editors (ABEs) targeting the forward strand in the Case 1 variants and the reverse strand in Cases 2 and 3. Available PAM sites were detected for KKH-nSaCas9-ABE8e for the c.2843G>A variant, nSaCas9-ABE8e and KKH-nSaCas9-ABE8e for the c.2833G>A variant, and nSpCas9-ABE8e for the c.2234C>T variant. In this case series, we report three pathogenic CRB1 variants, including a novel c.2833G>A variant associated with early-onset cone-rod dystrophy. We highlight the severity and rapid progression of the disease and offer ABEs as a potential future therapeutic approach for this devastating blinding condition.
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Affiliation(s)
- Hoda Shamsnajafabadi
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK; (H.S.)
| | - Maria Kaukonen
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK; (H.S.)
| | - Julia-Sophia Bellingrath
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK; (H.S.)
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK; (H.S.)
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
| | - Jasmina Cehajic-Kapetanovic
- Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK; (H.S.)
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, UK
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6
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Heath Jeffery RC, Thompson JA, Lo J, Chelva ES, Armstrong S, Pulido JS, Procopio R, Vincent AL, Bianco L, Battaglia Parodi M, Ziccardi L, Antonelli G, Barbano L, Marques JP, Geada S, Carvalho AL, Tang WC, Chan CM, Boon CJF, Hensman J, Chen TC, Lin CY, Chen PL, Vincent A, Tumber A, Heon E, Grigg JR, Jamieson RV, Cornish EE, Nash BM, Borooah S, Ayton LN, Britten-Jones AC, Edwards TL, Ruddle JB, Sharma A, Porter RG, Lamey TM, McLaren TL, McLenachan S, Roshandel D, Chen FK. Retinal Dystrophies Associated With Peripherin-2: Genetic Spectrum and Novel Clinical Observations in 241 Patients. Invest Ophthalmol Vis Sci 2024; 65:22. [PMID: 38743414 PMCID: PMC11098050 DOI: 10.1167/iovs.65.5.22] [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: 02/10/2024] [Accepted: 04/12/2024] [Indexed: 05/16/2024] Open
Abstract
Purpose To describe the clinical, electrophysiological and genetic spectrum of inherited retinal diseases associated with variants in the PRPH2 gene. Methods A total of 241 patients from 168 families across 15 sites in 9 countries with pathogenic or likely pathogenic variants in PRPH2 were included. Records were reviewed for age at symptom onset, visual acuity, full-field ERG, fundus colour photography, fundus autofluorescence (FAF), and SD-OCT. Images were graded into six phenotypes. Statistical analyses were performed to determine genotype-phenotype correlations. Results The median age at symptom onset was 40 years (range, 4-78 years). FAF phenotypes included normal (5%), butterfly pattern dystrophy, or vitelliform macular dystrophy (11%), central areolar choroidal dystrophy (28%), pseudo-Stargardt pattern dystrophy (41%), and retinitis pigmentosa (25%). Symptom onset was earlier in retinitis pigmentosa as compared with pseudo-Stargardt pattern dystrophy (34 vs 44 years; P = 0.004). The median visual acuity was 0.18 logMAR (interquartile range, 0-0.54 logMAR) and 0.18 logMAR (interquartile range 0-0.42 logMAR) in the right and left eyes, respectively. ERG showed a significantly reduced amplitude across all components (P < 0.001) and a peak time delay in the light-adapted 30-Hz flicker and single-flash b-wave (P < 0.001). Twenty-two variants were novel. The central areolar choroidal dystrophy phenotype was associated with 13 missense variants. The remaining variants showed marked phenotypic variability. Conclusions We described six distinct FAF phenotypes associated with variants in the PRPH2 gene. One FAF phenotype may have multiple ERG phenotypes, demonstrating a discordance between structure and function. Given the vast spectrum of PRPH2 disease our findings are useful for future clinical trials.
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Affiliation(s)
- Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
- Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, 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
| | - Johnny Lo
- School of Science, Edith Cowan University, Perth, Western Australia, Australia
| | - Enid S. Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Sean Armstrong
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Jose S. Pulido
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson University, Philadelphia, PA, United States
| | - Rebecca Procopio
- Wills Eye Hospital, Mid Atlantic Retina, Thomas Jefferson University, Philadelphia, PA, United States
| | - Andrea L. Vincent
- Department of Ophthalmology, FMHS, New Zealand National Eye Centre, University of Auckland, Auckland, New Zealand
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland, New Zealand
| | - Lorenzo Bianco
- Department of Ophthalmology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | | | | | | | - João P. Marques
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Clinical and Academic Centre of Coimbra (CACC), Coimbra, Portugal
| | - Sara Geada
- Ophthalmology Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Clinical and Academic Centre of Coimbra (CACC), Coimbra, Portugal
| | - Ana L. Carvalho
- Medical Genetics Unit, Centro Hospitalar e Universitário de Coimbra (CHUC), Coimbra, Portugal
| | - Wei C. Tang
- Singapore National Eye Centre, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Choi M. Chan
- Singapore National Eye Centre, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Camiel J. F. Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Ophthalmology, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Jonathan Hensman
- Department of Ophthalmology, Amsterdam University Medical Center, University of Amsterdam, the Netherlands
| | - Ta-Ching Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
- Center of Frontier Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Yu Lin
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Lung Chen
- Department of Ophthalmology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ajoy Vincent
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anupreet Tumber
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Elise Heon
- Department of Ophthalmology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - John R. Grigg
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Robyn V. Jamieson
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Elisa E. Cornish
- Save Sight Institute, Faculty of Medicine and Health, The University of Sydney, Sydney, Australia
| | - Benjamin M. Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Shyamanga Borooah
- University of California San Diego, La Jolla, California
- The Viterbi Family Department of Ophthalmology and Shiley Eye Institute, University of California San Diego, La Jolla, CA, United States
| | - Lauren N. Ayton
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Alexis Ceecee Britten-Jones
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas L. Edwards
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan B. Ruddle
- Department of Optometry and Vision Sciences, University of Melbourne, Melbourne, Victoria, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
| | - Abhishek Sharma
- Ophthalmology Department, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | | | - 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
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, Western Australia, Australia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
- Royal Victorian Eye and Ear Hospital, East Melbourne, Victoria, Australia
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
- Centre for Eye Research Australia, Royal Victorian Eye and Ear Hospital, Melbourne, Victoria, Australia
- Ophthalmology, Department of Surgery, University of Melbourne, Melbourne, Victoria, Australia
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7
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Zeng B, Liu DC, Huang JG, Xia XB, Qin B. PdmIRD: missense variants pathogenicity prediction for inherited retinal diseases in a disease-specific manner. Hum Genet 2024; 143:331-342. [PMID: 38478153 DOI: 10.1007/s00439-024-02645-6] [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: 11/07/2023] [Accepted: 01/17/2024] [Indexed: 04/25/2024]
Abstract
Accurate discrimination of pathogenic and nonpathogenic variation remains an enormous challenge in clinical genetic testing of inherited retinal diseases (IRDs) patients. Computational methods for predicting variant pathogenicity are the main solutions for this dilemma. The majority of the state-of-the-art variant pathogenicity prediction tools disregard the differences in characteristics among different genes and treat all types of mutations equally. Since missense variants are the most common type of variation in the coding region of the human genome, we developed a novel missense mutation pathogenicity prediction tool, named Prediction of Deleterious Missense Mutation for IRDs (PdmIRD) in this study. PdmIRD was tailored for IRDs-related genes and constructed with the conditional random forest model. Population frequencies and a newly available prediction tool were incorporated into PdmIRD to improve the performance of the model. The evaluation of PdmIRD demonstrated its superior performance over nonspecific tools (areas under the curves, 0.984 and 0.910) and an existing eye abnormalities-specific tool (areas under the curves, 0.975 and 0.891). We also demonstrated the submodel that used a smaller gene panel further slightly improved performance. Our study provides evidence that a disease-specific model can enhance the prediction of missense mutation pathogenicity, especially when new and important features are considered. Additionally, this study provides guidance for exploring the characteristics and functions of the mutated proteins in a greater number of Mendelian disorders.
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Affiliation(s)
- Bing Zeng
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
- Department of Ophthalmology, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Dong Cheng Liu
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Jian Guo Huang
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China
| | - Xiao Bo Xia
- Eye Center of Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
| | - Bo Qin
- Shenzhen Aier Eye Hospital, Aier Eye Hospital, Jinan University, Shenzhen, 518031, Guangdong, China.
- Shenzhen Aier Ophthalmic Technology Institute, Shenzhen, 518031, Guangdong, China.
- Aier School of Ophthalmology, Central South University, Changsha, Hunan, China.
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8
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Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [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: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
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Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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9
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Zheng Y, Chen S. Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research. Front Cell Neurosci 2024; 18:1347436. [PMID: 38414750 PMCID: PMC10896975 DOI: 10.3389/fncel.2024.1347436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/19/2024] [Indexed: 02/29/2024] Open
Abstract
The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.
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Affiliation(s)
- Yiqiao Zheng
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
| | - Shiming Chen
- Molecular Genetics and Genomics Graduate Program, Division of Biological and Biomedical Sciences, Saint Louis, MO, United States
- Department of Ophthalmology and Visual Sciences, Saint Louis, MO, United States
- Department of Developmental Biology, Washington University in St. Louis, Saint Louis, MO, United States
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10
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Munir A, Afsar S, Rehman AU. A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023. BMC Ophthalmol 2024; 24:55. [PMID: 38317096 PMCID: PMC10840256 DOI: 10.1186/s12886-024-03319-7] [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: 06/01/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023. METHODS Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines. RESULTS A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. CONCLUSION In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.
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Affiliation(s)
- Asad Munir
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Salma Afsar
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan.
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11
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Liu X, Dai H, Li G, Jia R, Meng X, Yu S, Yang L, Hong J. Screening copy number variations in 35 unsolved inherited retinal disease families. Hum Genet 2024; 143:197-210. [PMID: 38282009 PMCID: PMC10881639 DOI: 10.1007/s00439-023-02631-4] [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: 09/11/2023] [Accepted: 12/15/2023] [Indexed: 01/30/2024]
Abstract
The purpose of this study was to screen Copy Number Variations (CNVs) in 35 unsolved Inherited Retinal Dystrophy (IRD) families. Initially, next generation sequencing, including a specific Hereditary Eye Disease Enrichment Panel or Whole exome sequencing, was employed to screen (likely) pathogenic Single-nucleotide Variants (SNVs) and small Insertions and Deletions (indels) for these cases. All available SNVs and indels were further validated and co-segregation analyses were performed in available family members by Sanger sequencing. If not, after excluding deep intronic variants, Multiplex ligation-dependent probe amplification (MLPA), quantitative fluorescence PCR (QF-PCR) and Sanger sequencing were employed to screen CNVs. We determined that 18 probands who had heterozygous SNVs/indels or whose parents were not consanguineous but had homozygous SNVs/indels in autosomal recessive IRDs genes had CNVs in another allele of these genes, 11 families had disease-causing hemizygous CNVs in X-linked IRD genes, 6 families had (likely) pathogenic heterozygous CNVs in PRPF31 gene. Of 35 families, 33 different CNVs in 16 IRD-associated genes were detected, with PRPF31, EYS and USH2A the most common disease-causing gene in CNVs. Twenty-six and 7 of them were deletion and duplication CNVs, respectively. Among them, 14 CNVs were first reported in this study. Our research indicates that CNVs contribute a lot to IRDs, and screening of CNVs substantially increases the diagnostic rate of IRD. Our results emphasize that MLPA and QF-PCR are ideal methods to validate CNVs, and the novel CNVs reported herein expand the mutational spectrums of IRDs.
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Affiliation(s)
- Xiaozhen Liu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Hehua Dai
- Department of Ophthalmology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan, 250014, China
| | - Genlin Li
- Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing Ophthalmology & Visual Sciences Key Lab, Beijing, 100730, China
| | - Ruixuan Jia
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Xiang Meng
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Shicheng Yu
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China
| | - Liping Yang
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China.
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
| | - Jing Hong
- Department of Ophthalmology, Peking University Third Hospital, Beijing, 100191, China.
- Beijing Key Laboratory of Restoration of Damaged Ocular Nerve, Peking University Third Hospital, Beijing, 100191, China.
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12
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Birtel J, Caswell R, De Silva SR, Herrmann P, Rehman S, Lotery AJ, Mahroo OA, Michaelides M, Webster AR, MacLaren RE, Charbel Issa P. IMPG2-Related Maculopathy. Am J Ophthalmol 2024; 258:32-42. [PMID: 37806544 DOI: 10.1016/j.ajo.2023.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 10/01/2023] [Accepted: 10/01/2023] [Indexed: 10/10/2023]
Abstract
PURPOSE To investigate the phenotype, variability, and penetrance of IMPG2-related maculopathy. DESIGN Retrospective observational case series. METHODS Clinical evaluation, multimodal retinal imaging, genetic testing, and molecular modeling. RESULTS A total of 25 individuals with a mono-allelic IMPG2 variant were included, 5 of whom were relatives of patients with IMPG2-associated retinitis pigmentosa. A distinct maculopathy was present in 17 individuals (median age, 52 years; range, 20-72 years), and included foveal elevation with or without subretinal vitelliform material or focal atrophy of the retinal pigment epithelium. Best-corrected visual acuity (BCVA) was ≥20/50 in the better eye (n = 15), and 5 patients were asymptomatic. Longitudinal observation (n = 8, up to 19 years) demonstrated stable maculopathy (n = 3), partial/complete resorption (n = 4) or increase (n = 1) of the subretinal material, with overall stable vision (n = 6). No manifest maculopathy was observed in 8 individuals (median age, 58 years; range, 43-83 years; BCVA ≥20/25), all were identified through segregation analysis. All 8 individuals were asymptomatic, with minimal foveal changes observed on optical coherence tomography in 3 cases. A total of 18 different variants were detected, 11 of them truncating. Molecular modeling of 5 missense variants [c.727G>C, c.1124C>A, c.2816T>A, c.3047T>C, and c.3193G>A] supported the hypothesis that these have a loss-of-function effect. CONCLUSIONS Mono-allelic IMPG2 variants may result in haploinsufficiency manifesting as a maculopathy with variable penetrance and expressivity. Family members of patients with IMPG2-related retinitis pigmentosa may present with vitelliform lesions. The maculopathy often remains limited to the fovea and is usually associated with moderate visual impairment.
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Affiliation(s)
- Johannes Birtel
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Department of Ophthalmology (J.B.), University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Ophthalmology (J.B., P.H.), University of Bonn, Bonn, Germany
| | - Richard Caswell
- Exeter Genomics Laboratory (R.C.), Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom
| | - Samantha R De Silva
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Philipp Herrmann
- Department of Ophthalmology (J.B., P.H.), University of Bonn, Bonn, Germany
| | - Salwah Rehman
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Andrew J Lotery
- Clinical Neurosciences (A.J.L.), Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom; Southampton Eye Unit (A.J.L.), University Hospital Southampton NHS Foundation Trust, Southampton, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust (S.R.D.S., O.A.M., M.M., A.R.W.), London, United Kingdom; UCL Institute of Ophthalmology (S.R.D.S., O.A.M., M.M., A.R.W.), University College London, London, United Kingdom
| | - Robert E MacLaren
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Peter Charbel Issa
- From the Oxford Eye Hospital (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom; Nuffield Laboratory of Ophthalmology (J.B., S.R.D.S., S.R., R.E.M., P.C.I.), Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
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13
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Kao HJ, Lin TY, Hsieh FJ, Chien JY, Yeh EC, Lin WJ, Chen YH, Ding KH, Yang Y, Chi SC, Tsai PH, Hsu CC, Hwang DK, Tsai HY, Peng ML, Lee SH, Chau SF, Chen CY, Cheang WM, Chen SJ, Kwok PY, Chiou SH, Lu MYJ, Huang SP. Highly efficient capture approach for the identification of diverse inherited retinal disorders. NPJ Genom Med 2024; 9:4. [PMID: 38195571 PMCID: PMC10776681 DOI: 10.1038/s41525-023-00388-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/01/2023] [Indexed: 01/11/2024] Open
Abstract
Our study presents a 319-gene panel targeting inherited retinal dystrophy (IRD) genes. Through a multi-center retrospective cohort study, we validated the assay's effectiveness and clinical utility and characterized the mutation spectrum of Taiwanese IRD patients. Between January 2018 and May 2022, 493 patients in 425 unrelated families, all initially suspected of having IRD without prior genetic diagnoses, underwent detailed ophthalmic and physical examinations (with extra-ocular features recorded) and genetic testing with our customized panel. Disease-causing variants were identified by segregation analysis and clinical interpretation, with validation via Sanger sequencing. We achieved a read depth of >200× for 94.2% of the targeted 1.2 Mb region. 68.5% (291/425) of the probands received molecular diagnoses, with 53.9% (229/425) resolved cases. Retinitis pigmentosa (RP) is the most prevalent initial clinical impression (64.2%), and 90.8% of the cohort have the five most prevalent phenotypes (RP, cone-rod syndrome, Usher's syndrome, Leber's congenital amaurosis, Bietti crystalline dystrophy). The most commonly mutated genes of probands that received molecular diagnosis are USH2A (13.7% of the cohort), EYS (11.3%), CYP4V2 (4.8%), ABCA4 (4.5%), RPGR (3.4%), and RP1 (3.1%), collectively accounted for 40.8% of diagnoses. We identify 87 unique unreported variants previously not associated with IRD and refine clinical diagnoses for 21 patients (7.22% of positive cases). We developed a customized gene panel and tested it on the largest Taiwanese cohort, showing that it provides excellent coverage for diverse IRD phenotypes.
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Affiliation(s)
- Hsiao-Jung Kao
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Ting-Yi Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
- Doctoral Degree Program of Translational Medicine, National Yang Ming Chiao Tung University and Academia Sinica, Taipei, 115201, Taiwan
| | - Feng-Jen Hsieh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Jia-Ying Chien
- Institute of Medical Sciences, Tzu Chi University, Hualien, 970374, Taiwan
| | - Erh-Chan Yeh
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Wan-Jia Lin
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan
| | - Yi-Hua Chen
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Kai-Hsuan Ding
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan
| | - Yu Yang
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
| | - Sheng-Chu Chi
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
| | - Ping-Hsing Tsai
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Chih-Chien Hsu
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - De-Kuang Hwang
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Hsien-Yang Tsai
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Mei-Ling Peng
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Shi-Huang Lee
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Siu-Fung Chau
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Chen Yu Chen
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Wai-Man Cheang
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan
| | - Shih-Jen Chen
- Department of Ophthalmology, Taipei Veterans General Hospital, Taipei, 112201, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan
| | - Pui-Yan Kwok
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 115201, Taiwan.
- Institute for Human Genetics, Cardiovascular Research Institute, and Department of Dermatology, University of California, San Francisco, CA, USA.
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital, Taipei, 112201, Taiwan.
- Institute of Pharmacology, National Yang Ming Chiao Tung University, Taipei, 112304, Taiwan.
- Genomic Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| | - Mei-Yeh Jade Lu
- Biodiversity Research Center, Academia Sinica, Taipei, 115201, Taiwan.
| | - Shun-Ping Huang
- Institute of Medical Sciences, Tzu Chi University, Hualien, 970374, Taiwan.
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, 427003, Taiwan.
- Department of Molecular Biology and Human Genetics, Tzu Chi University, Hualien, 970374, Taiwan.
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Fan X, Yang Y, Wu G, Kong Y, Zhang Y, Zha X. Circ-CARD6 inhibits oxidative stress-induced apoptosis and autophagy in ARPE-19 cells via the miR-29b-3p/PRDX6/PI3K/Akt axis. Exp Eye Res 2024; 238:109690. [PMID: 37939831 DOI: 10.1016/j.exer.2023.109690] [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: 02/23/2023] [Revised: 09/28/2023] [Accepted: 10/22/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Oxidative stress-induced damage and dysfunction of retinal pigment epithelium (RPE) cells are important pathogenetic factors of age-related macular degeneration (AMD) and hereditary retinopathy diseases (HRDs). This study aimed to elucidate the roles and mechanisms of circ-CARD6 and miR-29b-3p in oxidative stress-induced RPE and provide new ideas for the diagnosis and treatment of retinopathy disease (RD). METHODS A model of oxidative stress-induced RPE (ARPE-19) was established, and the level of malondialdehyde (MDA) and concentration of reactive oxygen species (ROS) were detected by a DCFH-DA fluorescent probe and MDA kit. The cell viability was measured by a CCK-8 assay. The expression of PRDX6/PI3K/Akt axis genes and proteins related to apoptosis and autophagy were determined by RT‒qPCR and Western blot analyses. The dual-luciferase reporter system confirmed the targeting relationship between miR-29b-3p and circ-CARD6 and between miR-29b-3p and PRDX6. RESULTS In H2O2-treated ARPE-19 cells, the expression of circ-CARD6 and PRDX6 was decreased, while the expression of miR-29b-3p was increased. The overexpression of circ-CARD6 inhibits oxidative stress-induced increases in ROS, apoptosis and autophagy in ARPE-19 cells. circ-CARD6 targets miR-29b-3p, miR-29b-3p targets PRDX6, and circ-CARD6 regulates PRDX6 via miR-29b-3p. Further studies showed that circ-CARD6 acts as a competitive endogenous RNA of miR-29b-3p to affect the expression of PRDX6, thereby inhibiting autophagy and apoptosis in ARPE-19 cells. CONCLUSION circ-CARD6 can inhibit oxidative stress and apoptosis by regulating the miR-29b-3p/PRDX6/PI3K/Akt axis.
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Affiliation(s)
- Xinyu Fan
- Department of Ophthalmology, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Yanni Yang
- Ophthalmology Department, The Second Hospital of Ningbo, Ningbo, 315010, Zhejiang, China
| | - Guojiu Wu
- Department of Ophthalmology, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Yanbo Kong
- Department of Ophthalmology, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Yuanping Zhang
- Department of Ophthalmology, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China
| | - Xu Zha
- Department of Ophthalmology, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, 650101, Yunnan, China.
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15
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Moekotte L, Kuiper JJW, Hiddingh S, Nguyen XTA, Boon CJF, van den Born LI, de Boer JH, van Genderen MM. CRB1-Associated Retinal Dystrophy Patients Have Expanded Lewis Glycoantigen-Positive T Cells. Invest Ophthalmol Vis Sci 2023; 64:6. [PMID: 37792335 PMCID: PMC10565706 DOI: 10.1167/iovs.64.13.6] [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: 03/24/2023] [Accepted: 08/31/2023] [Indexed: 10/05/2023] Open
Abstract
Purpose Eye inflammation may occur in patients with inherited retinal dystrophies (IRDs) and is seen frequently in IRDs associated with mutations in the CRB1 gene. The purpose of this study was to determine the types of inflammatory cells involved in IRDs, by deep profiling the composition of peripheral blood mononuclear cells of patients with a CRB1-associated IRD. Methods This study included 33 patients with an IRD with confirmed CRB1 mutations and 32 healthy controls. A 43-parameter flow cytometry analysis was performed on peripheral blood mononuclear cells isolated from venous blood. FlowSOM and manual Boolean combination gating were used to identify and quantify immune cell subsets. Results Comparing patients with controls revealed a significant increase in patients in the abundance of circulating CD4+ T cells and CD8+ T cells that express sialyl Lewis X antigen. Furthermore, we detected a decrease in plasmacytoid dendritic cells and an IgA+CD24+CD38+ transitional B-cell subset in patients with an IRD. Conclusions Patients with a CRB1-associated IRD show marked changes in blood leukocyte composition, affecting lymphocyte and dendritic cell populations. These results implicate inflammatory pathways in the disease manifestations of IRDs.
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Affiliation(s)
- Lude Moekotte
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Jonas J. W. Kuiper
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Sanne Hiddingh
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Xuan-Thanh-An Nguyen
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
| | - Camiel J. F. Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, the Netherlands
- Department of Ophthalmology, Amsterdam University Medical Centers, Amsterdam, the Netherlands
| | | | - Joke H. de Boer
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Maria M. van Genderen
- Department of Ophthalmology, University Medical Center Utrecht, Utrecht, the Netherlands
- Bartiméus, Diagnostic Center for complex visual disorders, Zeist, the Netherlands
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16
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Lenassi E, Carvalho A, Thormann A, Abrahams L, Arno G, Fletcher T, Hardcastle C, Lopez J, Hunt SE, Short P, Sergouniotis PI, Michaelides M, Webster A, Cunningham F, Ramsden SC, Kasperaviciute D, Fitzpatrick DR, Black GC, Ellingford JM. EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders. J Med Genet 2023; 60:810-818. [PMID: 36669873 PMCID: PMC10423522 DOI: 10.1136/jmg-2022-108618] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 12/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genomic variant prioritisation is one of the most significant bottlenecks to mainstream genomic testing in healthcare. Tools to improve precision while ensuring high recall are critical to successful mainstream clinical genomic testing, in particular for whole genome sequencing where millions of variants must be considered for each patient. METHODS We developed EyeG2P, a publicly available database and web application using the Ensembl Variant Effect Predictor. EyeG2P is tailored for efficient variant prioritisation for individuals with inherited ophthalmic conditions. We assessed the sensitivity of EyeG2P in 1234 individuals with a broad range of eye conditions who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we assessed the precision of EyeG2P in comparison with routine diagnostic approaches. For 10 additional individuals, we assessed the utility of EyeG2P for whole genome analysis. RESULTS EyeG2P had 99.5% sensitivity for genomic variants previously identified as clinically relevant through routine diagnostic analysis (n=1234 individuals). Prospectively, EyeG2P enabled a significant increase in precision (35% on average) in comparison with routine testing strategies (p<0.001). We demonstrate that incorporation of EyeG2P into whole genome sequencing analysis strategies can reduce the number of variants for analysis to six variants, on average, while maintaining high diagnostic yield. CONCLUSION Automated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.
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Affiliation(s)
- Eva Lenassi
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Ana Carvalho
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Genetic Unit, Pediatric Hospital, Coimbra Hospital and Universitary Centre (CHUC), Coimbra, Portugal
| | - Anja Thormann
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Gavin Arno
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Tracy Fletcher
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Claire Hardcastle
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - Sarah E Hunt
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | | | - Panagiotis I Sergouniotis
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
- Manchester Royal Eye Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Michel Michaelides
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew Webster
- UCL Institute of Ophthalmology, University College London, London, UK
- Department of Ophthalmology, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Fiona Cunningham
- European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | | | - David R Fitzpatrick
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Graeme C Black
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Jamie M Ellingford
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Genomics England Ltd, London, UK
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17
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Schlottmann PG, Luna JD, Labat N, Yadarola MB, Bainttein S, Esposito E, Ibañez A, Barbaro EI, Álvarez Mendiara A, Picotti CP, Chirino Misisian A, Andreussi L, Gras J, Capalbo L, Visotto M, Dipierri JE, Alcoba E, Fernández Gabrielli L, Ávila S, Aucar ME, Martin DM, Ormaechea GJ, Inga ME, Francone AA, Charles M, Zompa T, Pérez PJ, Lotersztein V, Nuova PJ, Canonero IB, Mahroo OA, Michaelides M, Arno G, Daich Varela M. Nationwide genetic analysis of more than 600 families with inherited eye diseases in Argentina. NPJ Genom Med 2023; 8:8. [PMID: 37217489 DOI: 10.1038/s41525-023-00352-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 04/05/2023] [Indexed: 05/24/2023] Open
Abstract
This study corresponds to the first large-scale genetic analysis of inherited eye diseases (IED) in Argentina and describes the comprehensive genetic profile of a large cohort of patients. Medical records of 22 ophthalmology and genetics services throughout 13 Argentinian provinces were analyzed retrospectively. Patients with a clinical diagnosis of an ophthalmic genetic disease and a history of genetic testing were included. Medical, ophthalmological and family history was collected. A total of 773 patients from 637 families were included, with 98% having inherited retinal disease. The most common phenotype was retinitis pigmentosa (RP, 62%). Causative variants were detected in 379 (59%) patients. USH2A, RPGR, and ABCA4 were the most common disease-associated genes. USH2A was the most frequent gene associated with RP, RDH12 early-onset severe retinal dystrophy, ABCA4 Stargardt disease, PROM1 cone-rod dystrophy, and BEST1 macular dystrophy. The most frequent variants were RPGR c.1345 C > T, p.(Arg449*) and USH2A c.15089 C > A, p.(Ser5030*). The study revealed 156/448 (35%) previously unreported pathogenic/likely pathogenic variants and 8 possible founder mutations. We present the genetic landscape of IED in Argentina and the largest cohort in South America. This data will serve as a reference for future genetic studies, aid diagnosis, inform counseling, and assist in addressing the largely unmet need for clinical trials to be conducted in the region.
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Affiliation(s)
| | - José D Luna
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | - Natalia Labat
- Centro Privado de Ojos Romagosa SA, Córdoba, Argentina
| | | | | | - Evangelina Esposito
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | - Agustina Ibañez
- University Clinic Reina Fabiola, Córdoba, Córdoba, Argentina
- Catholic University of Cordoba, Cordoba, Argentina
| | | | | | | | | | | | | | | | - Mauro Visotto
- Instituto Oftalmológico Trelew, Trelew, Chubut, Argentina
| | | | - Emilio Alcoba
- Hospital Materno Infantil Dr Héctor Quintana, Jujuy, Argentina
| | | | - Silvia Ávila
- Facultad de Ciencias Médicas, Universidad Nacional del Comahue, Río Negro, Argentina
| | | | | | | | - M Eugenia Inga
- Organización Medica de Investigación, Buenos Aires, Argentina
| | | | | | - Tamara Zompa
- Charles Centro Oftalmológico, Buenos Aires, Argentina
| | | | | | - Pedro J Nuova
- Ocularyb Oftalmoclinica, Yerba Buena, Tucumán, Argentina
| | | | - Omar A Mahroo
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Michel Michaelides
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital, London, UK
- UCL Institute of Ophthalmology, University College London, London, UK
| | - Malena Daich Varela
- Moorfields Eye Hospital, London, UK.
- UCL Institute of Ophthalmology, University College London, London, UK.
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18
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Shah AH, Park E, Luke T, Xu Q, Jewell A, Couser NL. The Role of Genetic Testing in Avoiding Diagnostic Delays in Inherited Retinal Disease. Retin Cases Brief Rep 2023; Publish Ahead of Print:01271216-990000000-00171. [PMID: 37116464 PMCID: PMC10603209 DOI: 10.1097/icb.0000000000001436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
PURPOSE To identify and highlight potential delays in diagnosis and improve the characterization of the providers referring individuals affected with suspected IRDs for specialty care, we performed an analysis of the patients with IRDs seen by an ophthalmic genetics specialty service. In addition, we analyzed the diagnostic yield of genetic testing in patients with IRD in our series and compared this information with other previous studies. METHODS We analyzed 131 consecutive patients with suspected IRDs referred to an ophthalmic genetics specialty service at a tertiary hospital. Provider referral patterns, delays in diagnosis and the diagnostic yield of genetic testing were evaluated. RESULTS Mean age in the cohort was 24 years. From the 51 patients that underwent genetic testing, the diagnostic yield was 69%. Of these, genetic testing revealed 51% of patients had an incorrect initial referral clinical diagnosis. The average delay to reach a correct diagnosis was 15 years. Ophthalmologists represented the largest referral base at 80%, followed by neurologists representing 5% of referrals. Pediatric and retinal specialists were the largest referral of ophthalmic subspecialties at 44% and 35%, respectively. CONCLUSION A significant number of patients experienced a prolonged delay in reaching a correct diagnosis largely due to a delay in initiating the genetic evaluation and testing process. The initial suspected clinical diagnosis was incorrect in a significant number of cases, revealing that affected patients were potentially denied from appropriate recurrence risk counseling, relevant educational resources, specialty referrals in syndromic cases, and clinical trial eligibility in a timely manner.
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Affiliation(s)
- Arth H. Shah
- Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Elisse Park
- Department of Ophthalmology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Tamara Luke
- Division of Genomic Diagnostics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Qingguo Xu
- Department of Ophthalmology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
- Department of Pharmaceutics, School of Pharmacy, Virginia Commonwealth University, Richmond, VA, USA
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children’s Hospital of Richmond at VCU, Richmond, VA, USA
| | - Ann Jewell
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Natario L. Couser
- Department of Ophthalmology, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children’s Hospital of Richmond at VCU, Richmond, VA, USA
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19
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McClinton B, Crinnion LA, McKibbin M, Mukherjee R, Poulter JA, Smith CEL, Ali M, Watson CM, Inglehearn CF, Toomes C. Targeted nanopore sequencing enables complete characterisation of structural deletions initially identified using exon-based short-read sequencing strategies. Mol Genet Genomic Med 2023:e2164. [PMID: 36934458 DOI: 10.1002/mgg3.2164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 02/23/2023] [Indexed: 03/20/2023] Open
Abstract
BACKGROUND The widespread adoption of exome sequencing has greatly increased the rate of genetic diagnosis for inherited conditions. However, the detection and validation of large deletions remains challenging. While numerous bioinformatics approaches have been developed to detect deletions from whole - exome sequencing and targeted panels, further work is typically required to define the physical breakpoints or integration sites. Accurate characterisation requires either expensive follow - up whole - genome sequencing or the time - consuming, laborious process of PCR walking, both of which are challenging when dealing with the repeat sequences which frequently intersect deletion breakpoints. The aim of this study was to develop a cost-effective, long-range sequencing method to characterise deletions. METHODS Genomic DNA was amplified with primers spanning the deletion using long-range PCR and the products purified. Sequencing was performed on MinION flongle flowcells. The resulting fast5 files were basecalled using Guppy, trimmed using Porechop and aligned using Minimap2. Filtering was performed using NanoFilt. Nanopore sequencing results were verified by Sanger sequencing. RESULTS Four cases with deletions detected following comparative read-depth analysis of targeted short-read sequencing were analysed. Nanopore sequencing defined breakpoints at the molecular level in all cases including homozygous breakpoints in EYS, CNGA1 and CNGB1 and a heterozygous deletion in PRPF31. All breakpoints were verified by Sanger sequencing. CONCLUSIONS In this study, a quick, accurate and cost - effective method is described to characterise deletions identified from exome, and similar data, using nanopore sequencing.
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Affiliation(s)
- Benjamin McClinton
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Laura A Crinnion
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, UK
| | | | - James A Poulter
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Claire E L Smith
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Manir Ali
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Christopher M Watson
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK.,North East and Yorkshire Genomic Laboratory Hub, Central Lab, St James's University Hospital, Leeds, UK
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
| | - Carmel Toomes
- Leeds Institute of Medical Research, School of Medicine, University of Leeds, Leeds, UK
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20
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Wu KY, Kulbay M, Toameh D, Xu AQ, Kalevar A, Tran SD. Retinitis Pigmentosa: Novel Therapeutic Targets and Drug Development. Pharmaceutics 2023; 15:685. [PMID: 36840007 PMCID: PMC9963330 DOI: 10.3390/pharmaceutics15020685] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/12/2023] [Accepted: 02/16/2023] [Indexed: 02/19/2023] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of hereditary diseases characterized by progressive degeneration of retinal photoreceptors leading to progressive visual decline. It is the most common type of inherited retinal dystrophy and has a high burden on both patients and society. This condition causes gradual loss of vision, with its typical manifestations including nyctalopia, concentric visual field loss, and ultimately bilateral central vision loss. It is one of the leading causes of visual disability and blindness in people under 60 years old and affects over 1.5 million people worldwide. There is currently no curative treatment for people with RP, and only a small group of patients with confirmed RPE65 mutations are eligible to receive the only gene therapy on the market: voretigene neparvovec. The current therapeutic armamentarium is limited to retinoids, vitamin A supplements, protection from sunlight, visual aids, and medical and surgical interventions to treat ophthalmic comorbidities, which only aim to slow down the progression of the disease. Considering such a limited therapeutic landscape, there is an urgent need for developing new and individualized therapeutic modalities targeting retinal degeneration. Although the heterogeneity of gene mutations involved in RP makes its target treatment development difficult, recent fundamental studies showed promising progress in elucidation of the photoreceptor degeneration mechanism. The discovery of novel molecule therapeutics that can selectively target specific receptors or specific pathways will serve as a solid foundation for advanced drug development. This article is a review of recent progress in novel treatment of RP focusing on preclinical stage fundamental research on molecular targets, which will serve as a starting point for advanced drug development. We will review the alterations in the molecular pathways involved in the development of RP, mainly those regarding endoplasmic reticulum (ER) stress and apoptotic pathways, maintenance of the redox balance, and genomic stability. We will then discuss the therapeutic approaches under development, such as gene and cell therapy, as well as the recent literature identifying novel potential drug targets for RP.
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Affiliation(s)
- Kevin Y. Wu
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Merve Kulbay
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Dana Toameh
- Faculty of Medicine, McGill University, Montreal, QC H3G 2M1, Canada
| | - An Qi Xu
- Faculty of Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Ananda Kalevar
- Division of Ophthalmology, Department of Surgery, University of Sherbrooke, Sherbrooke, QC J1G 2E8, Canada
| | - Simon D. Tran
- Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal, QC H3A 1G1, Canada
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21
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Poli FE, Yusuf IH, Clouston P, Shanks M, Whitfield J, Charbel Issa P, MacLaren RE. MERTK missense variants in three patients with retinitis pigmentosa. Ophthalmic Genet 2023; 44:74-82. [PMID: 36036427 PMCID: PMC9615558 DOI: 10.1080/13816810.2022.2113541] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND MERTK (MER proto-oncogene, tyrosine kinase) is a transmembrane protein essential in regulating photoreceptor outer segment phagocytosis. Biallelic mutations in MERTK cause retinal degeneration. Here we present the retinal phenotype of three patients with missense variants in MERTK. MATERIALS AND METHODS All patients underwent a full clinical examination, fundus photography, short-wavelength fundus autofluorescence and optical coherence tomography imaging. Two patients also underwent Goldmann visual field testing and electroretinography was undertaken for the third patient. Molecular genetic testing was undertaken using next generation or whole-exome sequencing with all variants confirmed by Sanger sequencing. RESULTS The first patient was a 29-year-old female heterozygous for a missense variant (c.1133C>T, p.Thr378 Met) and a nonsense variant (c.1744_1751delinsT, p.Ile582Ter) in MERTK. The second patient was a 26-year-old male homozygous for a c.2163T>A, p.His721Gln variant in MERTK. The third patient was an 11-year-old female heterozygous for a deletion of exons 5-19 and a missense variant (c.1866 G>C, p.Lys622Asn) in MERTK. Reduced night vision was the initial symptom in all patients. Fundoscopy revealed typical signs of retinitis pigmentosa (RP) with early-onset macular atrophy. All three MERTK missense variants affect highly conserved residues within functional domains, have low population frequencies and are predicted to be pathogenic in silico. CONCLUSIONS We report three missense variants in MERTK and present the associated phenotypic data, which are supportive of non-syndromic RP. MERTK is a promising candidate for viral-mediated gene replacement therapy. Moreover, one variant represents a single nucleotide transition, which is theoretically targetable with CRISPR-Cas9 base-editing.
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Affiliation(s)
- Federica E. Poli
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Imran H. Yusuf
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Penny Clouston
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Morag Shanks
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Jennifer Whitfield
- Oxford Regional Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Peter Charbel Issa
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Oxford Eye Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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22
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Mc Clinton B, Corradi Z, McKibbin M, Panneman DM, Roosing S, Boonen EGM, Ali M, Watson CM, Steel DH, Cremers FPM, Inglehearn CF, Hitti-Malin RJ, Toomes C. Effective smMIPs-Based Sequencing of Maculopathy-Associated Genes in Stargardt Disease Cases and Allied Maculopathies from the UK. Genes (Basel) 2023; 14:191. [PMID: 36672932 PMCID: PMC9859292 DOI: 10.3390/genes14010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/06/2023] [Accepted: 01/07/2023] [Indexed: 01/13/2023] Open
Abstract
Macular dystrophies are a group of individually rare but collectively common inherited retinal dystrophies characterised by central vision loss and loss of visual acuity. Single molecule Molecular Inversion Probes (smMIPs) have proved effective in identifying genetic variants causing macular dystrophy. Here, a previously established smMIPs panel tailored for genes associated with macular diseases has been used to examine 57 UK macular dystrophy cases, achieving a high solve rate of 63.2% (36/57). Among 27 bi-allelic STGD1 cases, only three novel ABCA4 variants were identified, illustrating that the majority of ABCA4 variants in Caucasian STGD1 cases are currently known. We examined cases with ABCA4-associated disease in detail, comparing our results with a previously reported variant grading system, and found this model to be accurate and clinically useful. In this study, we showed that ABCA4-associated disease could be distinguished from other forms of macular dystrophy based on clinical evaluation in the majority of cases (34/36).
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Affiliation(s)
- Benjamin Mc Clinton
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- Department of Ophthalmology, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Christopher M. Watson
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
- North East and Yorkshire Genomic Laboratory Hub, Central Lab, St. James’s University Hospital, Leeds LS9 7TF, UK
| | - David H. Steel
- Sunderland Eye Infirmary, Sunderland SR2 9HP, UK
- The Bioscience Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
| | - Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James’s University Hospital, Leeds LS9 7TF, UK
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23
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Yahya S, Smith CEL, Poulter JA, McKibbin M, Arno G, Ellingford J, Kämpjärvi K, Khan MI, Cremers FPM, Hardcastle AJ, Castle B, Steel DHW, Webster AR, Black GC, El-Asrag ME, Ali M, Toomes C, Inglehearn CF. Late-Onset Autosomal Dominant Macular Degeneration Caused by Deletion of the CRX Gene. Ophthalmology 2023; 130:68-76. [PMID: 35934205 DOI: 10.1016/j.ophtha.2022.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 01/06/2023] Open
Abstract
PURPOSE To characterize the phenotype observed in a case series with macular disease and determine the cause. DESIGN Multicenter case series. PARTICIPANTS Six families (7 patients) with sporadic or multiplex macular disease with onset at 20 to 78 years, and 1 patient with age-related macular degeneration. METHODS Patients underwent ophthalmic examination; exome, genome, or targeted sequencing; and/or polymerase chain reaction (PCR) amplification of the breakpoint, followed by cloning and Sanger sequencing or direct Sanger sequencing. MAIN OUTCOME MEASURES Clinical phenotypes, genomic findings, and a hypothesis explaining the mechanism underlying disease in these patients. RESULTS All 8 cases carried the same deletion encompassing the genes TPRX1, CRX, and SULT2A1, which was absent from 382 control individuals screened by breakpoint PCR and 13 096 Clinical Genetics patients with a range of other inherited conditions screened by array comparative genomic hybridization. Microsatellite genotypes showed that these 7 families are not closely related, but genotypes immediately adjacent to the deletion breakpoints suggest they may share a distant common ancestor. CONCLUSIONS Previous studies had found that carriers for a single defective CRX allele that was predicted to produce no functional CRX protein had a normal ocular phenotype. Here, we show that CRX whole-gene deletion in fact does cause a dominant late-onset macular disease.
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Affiliation(s)
- Samar Yahya
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Medical Genetics, School of Medicine, King Abdulaziz University, Rabigh, Saudi Arabia
| | - Claire E L Smith
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - James A Poulter
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Martin McKibbin
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Ophthalmology, St. James's University Hospital, Leeds, United Kingdom
| | - Gavin Arno
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Jamie Ellingford
- Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom
| | | | - Muhammad I Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Alison J Hardcastle
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Bruce Castle
- Peninsula Genetics Service, Royal Devon and Exeter Hospitals NHS Trust, Exeter, United Kingdom
| | - David H W Steel
- Sunderland Eye Infirmary, Sunderland, United Kingdom; The Bioscience Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Andrew R Webster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust & UCL Institute of Ophthalmology, London, United Kingdom
| | - Graeme C Black
- Manchester Academic Health Science Centre, School of Biological Sciences, University of Manchester, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, United Kingdom
| | - Mohammed E El-Asrag
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom; Department of Zoology, Faculty of Science, Benha University, Benha, Egypt; Institute of Cancer and Genomic Science, University of Birmingham, Birmingham, United Kingdom
| | - Manir Ali
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Carmel Toomes
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom
| | - Chris F Inglehearn
- Leeds Institute of Medical Research, University of Leeds, St James's University Hospital, Leeds, United Kingdom.
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24
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The Diagnostic Yield of Next Generation Sequencing in Inherited Retinal Diseases: A Systematic Review and Meta-analysis. Am J Ophthalmol 2022; 249:57-73. [PMID: 36592879 DOI: 10.1016/j.ajo.2022.12.027] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/16/2022] [Accepted: 12/23/2022] [Indexed: 01/01/2023]
Abstract
PURPOSE Accurate genotyping of individuals with inherited retinal diseases (IRD) is essential for patient management and identifying suitable candidates for gene therapies. This study evaluated the diagnostic yield of next generation sequencing (NGS) in IRDs. DESIGN Systematic review and meta-analysis. METHODS This systematic review was prospectively registered (CRD42021293619). Ovid MEDLINE and Ovid Embase were searched on 6 June 2022. Clinical studies evaluating the diagnostic yield of NGS in individuals with IRDs were eligible for inclusion. Risk of bias assessment was performed. Studies were pooled using a random...effects inverse variance model. Sources of heterogeneity were explored using stratified analysis, meta-regression, and sensitivity analysis. RESULTS This study included 105 publications from 28 countries. Most studies (90 studies) used targeted gene panels. The diagnostic yield of NGS was 61.3% (95% confidence interval: 57.8-64.7%; 51 studies) in mixed IRD phenotypes, 58.2% (51.6-64.6%; 41 studies) in rod-cone dystrophies, 57.7% (46.8-68.3%; eight studies) in macular and cone/cone-rod dystrophies, and 47.6% (95% CI: 41.0-54.3%; four studies) in familial exudative vitreoretinopathy. For mixed IRD phenotypes, a higher diagnostic yield was achieved pooling studies published between 2018-2022 (64.2% [59.5-68.7%]), studies using exome sequencing (73.5% [58.9-86.1%]), and studies using the American College of Medical Genetics variant interpretation standards (65.6% [60.8-70.4%]). CONCLUSION The current diagnostic yield of NGS in IRDs is between 52-74%. The certainty of the evidence was judged as low or very low. A key limitation of the current evidence is the significant heterogeneity between studies. Adoption of standardized reporting guidelines could improve confidence in future meta-analyses.
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25
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Gene Therapy with Voretigene Neparvovec Improves Vision and Partially Restores Electrophysiological Function in Pre-School Children with Leber Congenital Amaurosis. Biomedicines 2022; 11:biomedicines11010103. [PMID: 36672611 PMCID: PMC9855623 DOI: 10.3390/biomedicines11010103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 01/03/2023] Open
Abstract
Leber congenital amaurosis caused by mutations in the RPE65 gene belongs to the most severe early-onset hereditary childhood retinopathies naturally progressing to legal blindness. The novel gene therapy voretigene neparvovec is the first approved causative treatment option for this devastating eye disease and is specifically designed to treat RPE65-mediated retinal dystrophies. Herein, we present a follow-up of the youngest treated patients in Germany so far, including four pre-school children who received treatment with voretigene neparvovec at a single treatment center between January 2020 and May 2022. All patients underwent pars plana vitrectomy with circumferential peeling of the internal limiting membrane at the injection site and subretinal injection of voretigene neparvovec. Pre- and postoperative diagnostics included imaging (spectral domain optical coherence tomography, fundus autofluorescence, fundus wide-angle imaging), electrophysiologic examination (ERG), retinal light sensitivity measurements (FST) and visual acuity testing. Behavioral changes were assessed using a questionnaire and by observing the children's vision-guided behavior in different levels of illumination. All children showed marked increase in vision-guided behavior shortly after therapy, as well as marked increase in visual acuity in the postoperative course up to full visual acuity in one child. Two eyes showed partial electrophysiological recovery of an ERG that was undetectable before treatment-a finding that has not been described in humans before.
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26
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Chen Z, Chen J, Gao M, Liu Y, Wu Y, Wang Y, Gong Y, Yu S, Liu W, Wan X, Sun X. Comprehensive analysis of the PRPF31 gene in retinitis pigmentosa patients: Four novel Alu-mediated copy number variations at the PRPF31 locus. Hum Mutat 2022; 43:2279-2294. [PMID: 36317469 DOI: 10.1002/humu.24494] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 10/10/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022]
Abstract
Retinitis pigmentosa (RP) is a monogenic disease characterized by irreversible degeneration of the retina. PRPF31, the second most common causative gene of autosomal dominant RP, frequently harbors copy number variations (CNVs), but the underlying mechanism is unclear. In this study, we summarized the phenotypic and genotypic characteristics of 18 RP families (F01-F18) with variants in PRPF31. The prevalence of PRPF31 variants in our cohort of Chinese RP families was 1.7% (18/1024). Seventeen different variants in PRPF31 were detected, including eight novel variants. Notably, four novel CNVs encompassing PRPF31, with a proportion of 22.2% (4/18), were validated to harbor gross deletions involving Alu/Alu-mediated rearrangements (AAMRs) in the same orientation. Among a total of 12 CNVs of PRPF31 with breakpoints mapped on nucleotide-resolution, 10 variants (83.3%) were presumably mediated by Alu elements. Furthermore, we described the correlation between the genotypes and phenotypes in PRPF31-related RP. Our findings expand the mutational spectrum of the PRPF31 gene and provide strong evidence that Alu elements of PRPF31 probably contribute to the susceptibility to genomic rearrangement in this locus.
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Affiliation(s)
- Zhixuan Chen
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Jieqiong Chen
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Min Gao
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yang Liu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yidong Wu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yafang Wang
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Yuanyuan Gong
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Suqin Yu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Wenjia Liu
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaoling Wan
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
| | - Xiaodong Sun
- Department of Ophthalmology, School of Medicine, Shanghai General Hospital (Shanghai First People's Hospital), Shanghai Jiao Tong University, Shanghai, China.,Department of Ophthalmology, National Clinical Research Center for Eye Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.,Department of Ophthalmology, Shanghai Engineering Center for Visual Science and Photomedicine, Shanghai, China
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27
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Optogenetic Therapy for Visual Restoration. Int J Mol Sci 2022; 23:ijms232315041. [PMID: 36499371 PMCID: PMC9735806 DOI: 10.3390/ijms232315041] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Optogenetics is a recent breakthrough in neuroscience, and one of the most promising applications is the treatment of retinal degenerative diseases. Multiple clinical trials are currently ongoing, less than a decade after the first attempt at visual restoration using optogenetics. Optogenetic therapy has great value in providing hope for visual restoration in late-stage retinal degeneration, regardless of the genotype. This alternative gene therapy consists of multiple elements including the choice of target retinal cells, optogenetic tools, and gene delivery systems. Currently, there are various options for each element, all of which have been developed as a product of technological success. In particular, the performance of optogenetic tools in terms of light and wavelength sensitivity have been improved by engineering microbial opsins and applying human opsins. To provide better post-treatment vision, the optimal choice of optogenetic tools and effective gene delivery to retinal cells is necessary. In this review, we provide an overview of the advancements in optogenetic therapy for visual restoration, focusing on available options for optogenetic tools and gene delivery methods.
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28
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Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, Arno G. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype. NPJ Genom Med 2022; 7:60. [PMID: 36266294 PMCID: PMC9581764 DOI: 10.1038/s41525-022-00330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK.
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Catherina H Z Li
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert A Heaton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - Janine Reurink
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James Bellingham
- Institute of Ophthalmology, University College London, London, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Georgia Yioti
- University of Ioannina Medical School, Ioannina, Greece
| | | | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK. .,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK.
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29
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Liu Y, Chen J, Sager R, Sasaki E, Hu H. Interactions between C8orf37 and FAM161A, Two Ciliary Proteins Essential for Photoreceptor Survival. Int J Mol Sci 2022; 23:12033. [PMID: 36233334 PMCID: PMC9570145 DOI: 10.3390/ijms231912033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations in C8orf37 cause Bardet-Biedl syndrome (BBS), retinitis pigmentosa (RP), and cone-rod dystrophy (CRD), all manifest in photoreceptor degeneration. Little is known about which proteins C8orf37 interacts with to contribute to photoreceptor survival. To determine the proteins that potentially interact with C8orf37, we carried out a yeast two-hybrid (Y2H) screen using C8orf37 as a bait. FAM161A, a microtubule-binding protein localized at the photoreceptor cilium required for photoreceptor survival, was identified as one of the preys. Double immunofluorescence staining and proximity ligation assay (PLA) of marmoset retinal sections showed that C8orf37 was enriched and was co-localized with FAM161A at the ciliary base of photoreceptors. Epitope-tagged C8orf37 and FAM161A, expressed in HEK293 cells, were also found to be co-localized by double immunofluorescence staining and PLA. Furthermore, interaction domain mapping assays identified that the N-terminal region of C8orf37 and amino acid residues 341-517 within the PFAM UPF0564 domain of FAM161A were critical for C8orf37-FAM161A interaction. These data suggest that the two photoreceptor survival proteins, C8orf37 and FAM161A, interact with each other which may contribute to photoreceptor health.
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Affiliation(s)
- Yu Liu
- Center for Vision Research, Departments of Neuroscience and Physiology and of Ophthalmology and Visual Sciences, Upstate Medical University, Syracuse, NY 13210, USA
| | - Jinjun Chen
- Center for Vision Research, Departments of Neuroscience and Physiology and of Ophthalmology and Visual Sciences, Upstate Medical University, Syracuse, NY 13210, USA
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Rachel Sager
- Center for Vision Research, Departments of Neuroscience and Physiology and of Ophthalmology and Visual Sciences, Upstate Medical University, Syracuse, NY 13210, USA
| | - Erika Sasaki
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Tonomachi, Kawasaki 210-0821, Kanagawa, Japan
| | - Huaiyu Hu
- Center for Vision Research, Departments of Neuroscience and Physiology and of Ophthalmology and Visual Sciences, Upstate Medical University, Syracuse, NY 13210, USA
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30
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A Novel Autosomal Recessive Variant of the NRL Gene Causing Enhanced S-Cone Syndrome: A Morpho-Functional Analysis of Two Unrelated Pediatric Patients. Diagnostics (Basel) 2022; 12:diagnostics12092183. [PMID: 36140584 PMCID: PMC9497687 DOI: 10.3390/diagnostics12092183] [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: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Enhanced S-cone syndrome (ESCS) is a rare autosomal recessive retinal degeneration mainly associated with pathogenic variations in the NR2E3 gene. Only a few pathogenic variations in the NRL gene associated with ESCS have been reported to date. Here, we describe the clinical and genetic findings of two unrelated pediatric patients with a novel frameshift homozygous variant in the NRL gene. Fundus examinations showed signs of peripheral degeneration in both patients, more severe in Proband 2, with relative sparing of the macular area. Spectral domain optical coherence tomography (SD-OCT) revealed a significant macular involvement with cysts in Proband 1, and minimal foveal alteration with peripheral retina involvement in Proband 2. Visual acuity was abnormal in both patients, but more severely affected in Proband 1 than Proband 2. The electroretinogram recordings showed reduced scotopic, mixed and single flash cone responses, with a typical supernormal S-cone response, meeting the criteria for a clinical diagnosis of ESCS in both patients. The present report expands the clinical and genetic spectrum of NRL-associated ESCS, and confirms the age-independent variability of phenotypic presentation already described in the NR2E3-associated ESCS.
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Hahn LC, Georgiou M, Almushattat H, van Schooneveld MJ, de Carvalho ER, Wesseling NL, Ten Brink JB, Florijn RJ, Lissenberg-Witte BI, Strubbe I, van Cauwenbergh C, de Zaeytijd J, Walraedt S, de Baere E, Mukherjee R, McKibbin M, Meester-Smoor MA, Thiadens AAHJ, Al-Khuzaei S, Akyol E, Lotery AJ, van Genderen MM, Ossewaarde-van Norel J, van den Born LI, Hoyng CB, Klaver CCW, Downes SM, Bergen AA, Leroy BP, Michaelides M, Boon CJF. The Natural History of Leber Congenital Amaurosis and Cone-Rod Dystrophy Associated with Variants in the GUCY2D Gene. Ophthalmol Retina 2022; 6:711-722. [PMID: 35314386 DOI: 10.1016/j.oret.2022.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 02/20/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
OBJECTIVE To describe the spectrum of Leber congenital amaurosis (LCA) and cone-rod dystrophy (CORD) associated with the GUCY2D gene and to identify potential end points and optimal patient selection for future therapeutic trials. DESIGN International, multicenter, retrospective cohort study. SUBJECTS Eighty-two patients with GUCY2D-associated LCA or CORD from 54 families. METHODS Medical records were reviewed for medical history, best-corrected visual acuity (BCVA), ophthalmoscopy, visual fields, full-field electroretinography, and retinal imaging (fundus photography, spectral-domain OCT [SD-OCT], fundus autofluorescence). MAIN OUTCOMES MEASURES Age of onset, evolution of BCVA, genotype-phenotype correlations, anatomic characteristics on funduscopy, and multimodal imaging. RESULTS Fourteen patients with autosomal recessive LCA and 68 with autosomal dominant CORD were included. The median follow-up times were 5.2 years (interquartile range [IQR] 2.6-8.8 years) for LCA and 7.2 years (IQR 2.2-14.2 years) for CORD. Generally, LCA presented in the first year of life. The BCVA in patients with LCA ranged from no light perception to 1.00 logarithm of the minimum angle of resolution (logMAR) and remained relatively stable during follow-up. Imaging for LCA was limited but showed little to no structural degeneration. In patients with CORD, progressive vision loss started around the second decade of life. The BCVA declined annually by 0.022 logMAR (P < 0.001) with no difference between patients with the c.2513G>A and the c.2512C>T GUCY2D variants (P = 0.798). At the age of 40 years, the probability of being blind or severely visually impaired was 32%. The integrity of the ellipsoid zone (EZ) and that of the external limiting membrane (ELM) on SD-OCT correlated significantly with BCVA (Spearman ρ = 0.744, P = 0.001, and ρ = 0.712, P < 0.001, respectively) in those with CORD. CONCLUSIONS Leber congenital amaurosis associated with GUCY2D caused severe congenital visual impairment with relatively intact macular anatomy on funduscopy and available imaging, suggesting long preservation of photoreceptors. Despite large variability, GUCY2D-associated CORD generally presented during adolescence, with a progressive loss of vision, and culminated in severe visual impairment during mid-to-late adulthood. The integrity of the ELM and EZ may be suitable structural end points for therapeutic studies of GUCY2D-associated CORD.
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Affiliation(s)
- Leo C Hahn
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Michalis Georgiou
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Hind Almushattat
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Mary J van Schooneveld
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands
| | - Emanuel R de Carvalho
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom
| | - Nieneke L Wesseling
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ralph J Florijn
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Birgit I Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Ine Strubbe
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Caroline van Cauwenbergh
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Julie de Zaeytijd
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Sophie Walraedt
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium
| | - Elfride de Baere
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium
| | - Rajarshi Mukherjee
- Department of Ophthalmology, St James's University Hospital, Leeds, United Kingdom
| | - Martin McKibbin
- Department of Ophthalmology, St James's University Hospital, Leeds, United Kingdom
| | | | | | - Saoud Al-Khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals National Health Service Foundation Trust, & Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
| | - Engin Akyol
- Eye Unit, University Hospital Southampton, Southampton, United Kingdom
| | - Andrew J Lotery
- Eye Unit, University Hospital Southampton, Southampton, United Kingdom
| | - Maria M van Genderen
- Bartiméus Diagnostic Center for Complex Visual Disorders, Zeist, The Netherlands; Department of Ophthalmology, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | | | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Susan M Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals National Health Service Foundation Trust, & Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, United Kingdom
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; The Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University Hospital, Ghent University, Ghent, Belgium; Center for Medical Genetics Ghent, Ghent University Hospital & Ghent University, Ghent, Belgium; Division of Ophthalmology and Center for Cellular and Molecular Therapeutics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Michel Michaelides
- Moorfields Eye Hospital National Health Service Foundation Trust, London, United Kingdom; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Camiel J F Boon
- Department of Ophthalmology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands; Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.
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Tanner A, Chan HW, Schiff E, Mahroo OM, Pulido JS. Exploring the mutational landscape of genes associated with inherited retinal disease using large genomic datasets: identifying loss of function intolerance and outlying propensities for missense changes. BMJ Open Ophthalmol 2022; 7:bmjophth-2022-001079. [PMID: 36161854 PMCID: PMC9422814 DOI: 10.1136/bmjophth-2022-001079] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/18/2022] [Indexed: 11/11/2022] Open
Abstract
Background Large databases permit quantitative description of genes in terms of intolerance to loss of function (‘haploinsufficiency’) and prevalence of missense variants. We explored these parameters in inherited retinal disease (IRD) genes. Methods IRD genes (from the ‘RetNet’ resource) were classified by probability of loss of function intolerance (pLI) using online Genome Aggregation Database (gnomAD) and DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources (DECIPHER) databases. Genes were identified having pLI ≥0.9 together with one or both of the following: upper bound of CI <0.35 for observed to expected (o/e) ratio of loss of function variants in the gnomAD resource; haploinsufficiency score <10 in the DECIPHER resource. IRD genes in which missense variants appeared under-represented or over-represented (Z score for o/e ratio of <−2.99 or >2.99, respectively) were also identified. The genes were evaluated in the gene ontology Protein Analysis THrough Evolutionary Relationships (PANTHER) resource. Results Of 280 analysed genes, 39 (13.9%) were predicted loss of function intolerant. A greater proportion of X-linked than autosomal IRD genes fulfilled these criteria, as expected. Most autosomal genes were associated with dominant disease. PANTHER analysis showed >100 fold enrichment of spliceosome tri-snRNP complex assembly. Most encoded proteins were longer than the median length in the UniProt database. Fourteen genes (11 of which were in the ‘haploinsufficient’ group) showed under-representation of missense variants. Six genes (SAMD11, ALMS1, WFS1, RP1L1, KCNV2, ADAMTS18) showed over-representation of missense variants. Conclusion A minority of IRD-associated genes appear to be ‘haploinsufficient’. Over-representation of spliceosome pathways was observed. When interpreting genetic tests, variants found in genes with over-representation of missense variants should be interpreted with caution.
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Solaki M, Baumann B, Reuter P, Andreasson S, Audo I, Ayuso C, Balousha G, Benedicenti F, Birch D, Bitoun P, Blain D, Bocquet B, Branham K, Català-Mora J, De Baere E, Dollfus H, Falana M, Giorda R, Golovleva I, Gottlob I, Heckenlively JR, Jacobson SG, Jones K, Jägle H, Janecke AR, Kellner U, Liskova P, Lorenz B, Martorell-Sampol L, Messias A, Meunier I, Belga Ottoni Porto F, Papageorgiou E, Plomp AS, de Ravel TJL, Reiff CM, Renner AB, Rosenberg T, Rudolph G, Salati R, Sener EC, Sieving PA, Stanzial F, Traboulsi EI, Tsang SH, Varsanyi B, Weleber RG, Zobor D, Stingl K, Wissinger B, Kohl S. Comprehensive variant spectrum of the CNGA3 gene in patients affected by achromatopsia. Hum Mutat 2022; 43:832-858. [PMID: 35332618 DOI: 10.1002/humu.24371] [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: 08/13/2021] [Revised: 02/23/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022]
Abstract
Achromatopsia (ACHM) is a congenital cone photoreceptor disorder characterized by impaired color discrimination, low visual acuity, photosensitivity, and nystagmus. To date, six genes have been associated with ACHM (CNGA3, CNGB3, GNAT2, PDE6C, PDE6H, and ATF6), the majority of these being implicated in the cone phototransduction cascade. CNGA3 encodes the CNGA3 subunit of the cyclic nucleotide-gated ion channel in cone photoreceptors and is one of the major disease-associated genes for ACHM. Herein, we provide a comprehensive overview of the CNGA3 variant spectrum in a cohort of 1060 genetically confirmed ACHM patients, 385 (36.3%) of these carrying "likely disease-causing" variants in CNGA3. Compiling our own genetic data with those reported in the literature and in public databases, we further extend the CNGA3 variant spectrum to a total of 316 variants, 244 of which we interpreted as "likely disease-causing" according to ACMG/AMP criteria. We report 48 novel "likely disease-causing" variants, 24 of which are missense substitutions underlining the predominant role of this mutation class in the CNGA3 variant spectrum. In addition, we provide extensive in silico analyses and summarize reported functional data of previously analyzed missense, nonsense and splicing variants to further advance the pathogenicity assessment of the identified variants.
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Affiliation(s)
- Maria Solaki
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Britta Baumann
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Peggy Reuter
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Sten Andreasson
- Department of Ophthalmology, University Hospital Lund, Lund, Sweden
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- CHNO des Quinze-Vingts, Centre de Référence Maladies Rares REFERET, and INSERM-DGOS CIC1423, Paris, France
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz University Hospital - Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Ghassan Balousha
- Department of Pathology and Histology, Faculty of Medicine, Al-Quds University, Eastern Jerusalem, Palestine
| | - Francesco Benedicenti
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - David Birch
- Retina Foundation of the Southwest, Dallas, Texas, USA
| | - Pierre Bitoun
- Genetique Medicale, CHU Paris Nord, Hopital Jean Verdier, Bondy Cedex, France
| | | | - Beatrice Bocquet
- National Reference Centre for Inherited Sensory Diseases, Institute for Neurosciences of Montpellier (INM), University of Montpellier, INSERM, Montpellier, France
| | - Kari Branham
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Jaume Català-Mora
- Unitat de Distròfies Hereditàries de Retina Hospital Sant Joan de Déu, Barcelona, Esplugues de Llobregat, Spain
| | - Elfride De Baere
- Department of Biomolecular Medicine, Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Helene Dollfus
- CARGO, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- U-1112, Inserm, Faculté de Médecine, Université de Strasbourg, Strasbourg, France
| | - Mohammed Falana
- Department of Pathology and Histology, Faculty of Medicine, Al-Quds University, Eastern Jerusalem, Palestine
| | - Roberto Giorda
- Molecular Biology Laboratory, Scientific Institute IRCCS E. Medea, Bosisio Parini, Lecco, Italy
| | - Irina Golovleva
- Department of Medical Biosciences/Medical and Clinical Genetics, University of Umea, Umea, Sweden
| | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Leicester Royal Infirmary, Leicester, UK
| | - John R Heckenlively
- Department of Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, USA
| | - Samuel G Jacobson
- Department of Ophthalmology, Perelman School of Medicine, Scheie Eye Institute, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kaylie Jones
- Retina Foundation of the Southwest, Dallas, Texas, USA
| | - Herbert Jägle
- Department of Ophthalmology, University of Regensburg, Regensburg, Germany
| | - Andreas R Janecke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ulrich Kellner
- Zentrum für Seltene Netzhauterkrankungen, AugenZentrum Siegburg, MVZ Augenärztliches Diagnostik- und Therapiecentrum Siegburg GmbH, Siegburg, Germany
- RetinaScience, Bonn, 53192, Germany
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Prague, Czech Republic
| | - Birgit Lorenz
- Department of Ophthalmology, Justus-Liebig University Giessen, Giessen, Germany
- Department of Ophthalmology, Universitaetsklinikum Bonn, Bonn, Germany
| | | | - André Messias
- Department of Ophthalmology, Otorhinolaryngology, and Head and Neck Surgery, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Isabelle Meunier
- National Reference Centre for Inherited Sensory Diseases, Montpellier University Hospital, University of Montpellier, Montpellier, France
- Sensgene Care Network, France
| | | | - Eleni Papageorgiou
- Department of Ophthalmology, University Hospital of Larissa, Mezourlo, Larissa, Greece
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Thomy J L de Ravel
- Centre for Medical Genetics, University Hospital Brussels, Brussels, Belgium
| | | | | | - Thomas Rosenberg
- Department of Ophthalmology, National Eye Clinic, Glostrup Hospital, Glostrup, Denmark
| | - Günther Rudolph
- University Eye Hospital, Ludwig Maximilians University, Munich, Germany
| | - Roberto Salati
- Scientific Institute, IRCCS Eugenio Medea, Pediatric Ophthalmology Unit, Bosisio Parini, Lecco, Italy
| | - E Cumhur Sener
- Strabismus and Pediatric Ophthalmology, Private Practice, Ankara, Turkey
| | - Paul A Sieving
- Center for Ocular Regenerative Therapy, School of Medicine, University of California Davis, Sacramento, USA
| | - Franco Stanzial
- Clinical Genetics Service and South Tyrol Coordination Center for Rare Diseases, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Elias I Traboulsi
- Center for Genetic Eye Diseases, Cole Eye Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Stephen H Tsang
- Department of Ophthalmology, Pathology and Cell Biology, College of Physicians and Surgeons, Columbia Stem Cell Initiative, Columbia University, New York City, New York, USA
| | - Balázs Varsanyi
- Department of Ophthalmology, Medical School, University of Pécs and Ganglion Medical Center, Pécs, Pécs, Hungary
| | - Richard G Weleber
- Oregon Health & Science University, Ophthalmic Genetics Service of the Casey Eye Institute, 515 SW Campus Drive, 97239, Portland, Oregon, USA
| | - Ditta Zobor
- Centre for Ophthalmology, Institute for Ophthalmic Research, University Hospital Tübingen, Tübingen, Germany
- Department of Ophthalmology, Semmelweis University Budapest, Budapest, Hungary
| | - Katarina Stingl
- Center for Ophthalmology, University Eye Hospital, University of Tübingen, Tübingen, Germany
- Center for Rare Eye Diseases, University of Tübingen, Tübingen, Germany
| | - Bernd Wissinger
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
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Ganapathi M, Thomas-Wilson A, Buchovecky C, Dharmadhikari A, Barua S, Lee W, Ruan MZC, Soucy M, Ragi S, Tanaka J, Clark LN, Naini AB, Liao J, Mansukhani M, Tsang S, Jobanputra V. Clinical exome sequencing for inherited retinal degenerations at a tertiary care center. Sci Rep 2022; 12:9358. [PMID: 35672425 PMCID: PMC9174483 DOI: 10.1038/s41598-022-13026-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022] Open
Abstract
Inherited retinal degenerations are clinically and genetically heterogeneous diseases characterized by progressive deterioration of vision. This study aimed at assessing the diagnostic yield of exome sequencing (ES) for an unselected cohort of individuals with hereditary retinal disorders. It is a retrospective study of 357 unrelated affected individuals, diagnosed with retinal disorders who underwent clinical ES. Variants from ES were filtered, prioritized, and classified using the ACMG recommendations. Clinical diagnosis of the individuals included rod-cone dystrophy (60%), macular dystrophy (20%), cone-rod dystrophy (9%), cone dystrophy (4%) and other phenotypes (7%). Majority of the cases (74%) were singletons and 6% were trios. A confirmed molecular diagnosis was obtained in 24% of cases. In 6% of cases, two pathogenic variants were identified with phase unknown, bringing the potential molecular diagnostic rate to ~ 30%. Including the variants of uncertain significance (VUS), potentially significant findings were reported in 57% of cases. Among cases with a confirmed molecular diagnosis, variants in EYS, ABCA4, USH2A, KIZ, CERKL, DHDDS, PROM1, NR2E3, CNGB1, ABCC6, PRPH2, RHO, PRPF31, PRPF8, SNRNP200, RP1, CHM, RPGR were identified in more than one affected individual. Our results support the utility of clinical ES in the diagnosis of genetically heterogeneous retinal disorders.
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Affiliation(s)
- Mythily Ganapathi
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Amanda Thomas-Wilson
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Christie Buchovecky
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Avinash Dharmadhikari
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Subit Barua
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Merry Z C Ruan
- College of Physicians and Surgeons, Columbia University Irving Medical Center, New York, NY, USA
| | - Megan Soucy
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Sara Ragi
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
| | - Joy Tanaka
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Lorraine N Clark
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Ali B Naini
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Jun Liao
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Mahesh Mansukhani
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA
| | - Stephen Tsang
- Department of Ophthalmology, Columbia University, Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, NY, USA
- Jonas Children's Vision Care, Bernard & Shirlee Brown Glaucoma Laboratory, Columbia Stem Cell Initiative-Departments of Ophthalmology, Biomedical Engineering, Pathology & Cell Biology, Institute of Human Nutrition, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Vaidehi Jobanputra
- Laboratory of Personalized Genomic Medicine, Department of Pathology & Cell Biology, Columbia University Medical Center, New York, NY, USA.
- Precision Genomics Laboratory, Columbia University Irving Medical Center, 701 West 168th St., HHSC 1412, New York, NY, 10032, USA.
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Iosifidis C, Liu J, Gale T, Ellingford JM, Campbell C, Ingram S, Chandler K, Parry NRA, Black GC, Sergouniotis PI. Clinical and genetic findings in TRPM1-related congenital stationary night blindness. Acta Ophthalmol 2022; 100:e1332-e1339. [PMID: 35633130 DOI: 10.1111/aos.15186] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
PURPOSE Congenital stationary night blindness (CSNB) is a heterogeneous group of Mendelian retinal disorders that present in childhood. Biallelic variants altering the protein-coding region of the TRPM1 gene are one of the commonest causes of CSNB. Here, we report the clinical and genetic findings in 10 unrelated individuals with TRPM1-retinopathy. METHODS Study subjects were recruited through a tertiary clinical ophthalmic genetic service at Manchester, UK. All participants underwent visual electrodiagnostic testing and panel-based genetic analysis. RESULTS Study subjects had a median age of 8 years (range: 3-20 years). All probands were myopic and had electroretinographic findings in keeping with complete CSNB. Notably, three probands reported no night vision problems. Fourteen different disease-associated TRPM1 variants were detected. One individual was homozygous for the NM_001252024.2 (TRPM1):c.965 + 29G>A variant and a mini-gene assay highlighted that this change results in mis-splicing and premature protein termination. Additionally, two unrelated probands who had CSNB and mild neurodevelopmental abnormalities were found to carry a 15q13.3 microdeletion. This copy number variant encompasses seven genes, including TRPM1, and was encountered in the heterozygous state and in trans with a missense TRPM1 variant in each case. CONCLUSION Our findings highlight the importance of comprehensive genomic analysis, beyond the exons and protein-coding regions of genes, for individuals with CSNB. When this characteristic retinal phenotype is accompanied by extraocular findings (including learning and/or behavioural difficulties), a 15q13.3 microdeletion should be suspected. Focused analysis (e.g. microarray testing) is recommended to look for large-scale deletions encompassing TRPM1 in patients with CSNB and neurodevelopmental abnormalities.
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Affiliation(s)
- Christos Iosifidis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jingshu Liu
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Jamie M. Ellingford
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Christopher Campbell
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Stuart Ingram
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Kate Chandler
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Neil R. A. Parry
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
| | - Graeme C. Black
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
| | - Panagiotis I. Sergouniotis
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicines and Health University of Manchester Manchester UK
- Manchester Centre for Genomic Medicine, Saint Mary's Hospital Manchester University NHS Foundation Trust Manchester UK
- Manchester Royal Eye Hospital Manchester University NHS Foundation Trust Manchester UK
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine University of Ljubljana Ljubljana Slovenia
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Wang J, Wang Y, Jiang Y, Li X, Xiao X, Li S, Jia X, Sun W, Wang P, Zhang Q. Autosomal Dominant Retinitis Pigmentosa-Associated TOPORS Protein Truncating Variants Are Exclusively Located in the Region of Amino Acid Residues 807 to 867. Invest Ophthalmol Vis Sci 2022; 63:19. [PMID: 35579903 PMCID: PMC9123486 DOI: 10.1167/iovs.63.5.19] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose Heterozygous truncating variants of TOPORS have been reported to cause autosomal dominant retinitis pigmentosa (adRP). The purpose of this study was to investigate whether all heterozygous truncating variants, including copy number variants (CNVs), are pathogenic. Methods TOPORS truncating variants were collected and reviewed through an in-house dataset and existing databases. Individuals with truncating variants underwent ophthalmological evaluation. Results Six truncating variants were detected in seven families. Three N-terminus truncating variants were detected in three families without RP, and the other three were identified in four unrelated families with typical RP. Based on the in-house dataset and published literature, 17 truncating variants were identified in 47 families with RP. All RP-associated truncating alleles, except one, were distributed in the last exon of TOPORS and clustered in amino acid residues 807 to 867 (46/47, 97.9%). Conversely, in the gnomAD database, only one truncating allele (1/27, 3.7%) was in this region, and the others were outside (26/27, 96.3%), suggesting that the pathogenic truncating variants were significantly clustered in residues 807 to 867 (χ2 = 65.6, P = 1.1 × 10–17). Additionally, three CNVs involving the N-terminus of TOPORS were recorded in control populations but were absent in affected patients. Conclusions This study suggests that all pathogenic truncating variants of TOPORS were clustered in residues 807 to 867, whereas the truncating variants outside this region and the CNVs involving the N-terminus were not associated with RP. A dominant-negative effect, rather than haploinsufficiency, is speculated to be the underlying pathogenesis. These findings provide valuable information for interpreting variation in TOPORS and other genes in similar situations, especially for CNVs.
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Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
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Demain LA, Metcalfe K, Boetje E, Clayton P, Martindale EA, Busby G, O'Keefe RT, Newman WG. Homozygous missense variants in BMPR15 can result in primary ovarian insufficiency. Reprod Biomed Online 2022; 45:727-729. [DOI: 10.1016/j.rbmo.2022.05.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/15/2022]
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Bedoukian EC, O'Neil EC, Aleman TS. RP1-associated recessive retinitis pigmentosa caused by paternal uniparental disomy. Ophthalmic Genet 2022; 43:555-560. [PMID: 35484846 DOI: 10.1080/13816810.2022.2062389] [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: 10/18/2022]
Abstract
BACKGROUND We report on a patient with a juvenile-onset inherited retinal degeneration (IRD) associated with homozygous RP1 mutations inherited by uniparental disomy (UPD). MATERIAL AND METHODS A 6-year-old healthy girl failed school vision screening and was diagnosed with a bull's eye maculopathy. She underwent complete ophthalmic examination, full-field electroretinograms (ERG), kinetic fields, full-field sensitivity testing (FST), and retinal imaging with spectral domain optical coherence tomography (SD-OCT) and near-infrared (NIR) and short wavelength (SW) fundus autofluorescence (FAF). RESULTS Visual acuities were relatively preserved (20/30+). There was subtle foveal depigmentation but an otherwise normal fundus examination. SD-OCT revealed a relatively preserved fovea with thinning of the photoreceptor outer nuclear layer with increasing distance from the foveal center coinciding with marked attenuation of the NIR and less marked loss of the SW-FAF signal. ERGs were non-detectable. Kinetic visual fields were generally full to large (V-4e) target but constricted to ~10°of eccentricity to I-4e stimuli. Dark-adapted thresholds by FST were rod-mediated and elevated by ~2 log units. Homozygous pathogenic mutations in RP1 (c.1720_1721del; p.Ser574Asnfs*8) were identified. Family member testing revealed father and siblings to be unaffected carriers; the mother carried wild-type alleles. Further testing suggested UPD of chromosome 8. CONCLUSION This report adds support to UPD as a mechanism of inheritance in IRDs and stresses the importance of familial testing for genetic diagnosis and counseling. Consistent with earlier descriptions of autosomal recessive RP1-IRDs our patient showed an early rod and cone photoreceptor degeneration.
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Affiliation(s)
- Emma C Bedoukian
- Division of Ophthalmology, Children's Hospital of Philadelphia.,Roberts Individualized Medical Genetics Center, Children's Hospital of Philadelphia, Pennsylvania, USA
| | - Erin C O'Neil
- Division of Ophthalmology, Children's Hospital of Philadelphia.,Center for Advanced Retinal and Ocular Therapeutics
| | - Tomas S Aleman
- Division of Ophthalmology, Children's Hospital of Philadelphia.,Center for Advanced Retinal and Ocular Therapeutics.,Scheie Eye Institute at the Perelman Center for Advanced Medicine, Department of Ophthalmology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies. Int J Mol Sci 2022; 23:ijms23073905. [PMID: 35409265 PMCID: PMC8999823 DOI: 10.3390/ijms23073905] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 12/15/2022] Open
Abstract
The inherited retinal dystrophies (IRDs) are a clinically and genetically complex group of disorders primarily affecting the rod and cone photoreceptors or other retinal neuronal layers, with emerging therapies heralding the need for accurate molecular diagnosis. Targeted capture and panel-based strategies examining the partial or full exome deliver molecular diagnoses in many IRD families tested. However, approximately one in three families remain unsolved and unable to obtain personalised recurrence risk or access to new clinical trials or therapy. In this study, we investigated whole genome sequencing (WGS), focused assays and functional studies to assist with unsolved IRD cases and facilitate integration of these approaches to a broad molecular diagnostic clinical service. The WGS approach identified variants not covered or underinvestigated by targeted capture panel-based clinical testing strategies in six families. This included structural variants, with notable benefit of the WGS approach in repetitive regions demonstrated by a family with a hybrid gene and hemizygous missense variant involving the opsin genes, OPN1LW and OPN1MW. There was also benefit in investigation of the repetitive GC-rich ORF15 region of RPGR. Further molecular investigations were facilitated by focused assays in these regions. Deep intronic variants were identified in IQCB1 and ABCA4, with functional RNA based studies of the IQCB1 variant revealing activation of a cryptic splice acceptor site. While targeted capture panel-based methods are successful in achieving an efficient molecular diagnosis in a proportion of cases, this study highlights the additional benefit and clinical value that may be derived from WGS, focused assays and functional genomics in the highly heterogeneous IRDs.
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40
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Schneider N, Sundaresan Y, Gopalakrishnan P, Beryozkin A, Hanany M, Levanon EY, Banin E, Ben-Aroya S, Sharon D. Inherited retinal diseases: Linking genes, disease-causing variants, and relevant therapeutic modalities. Prog Retin Eye Res 2021; 89:101029. [PMID: 34839010 DOI: 10.1016/j.preteyeres.2021.101029] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Inherited retinal diseases (IRDs) are a clinically complex and heterogenous group of visual impairment phenotypes caused by pathogenic variants in at least 277 nuclear and mitochondrial genes, affecting different retinal regions, and depleting the vision of affected individuals. Genes that cause IRDs when mutated are unique by possessing differing genotype-phenotype correlations, varying inheritance patterns, hypomorphic alleles, and modifier genes thus complicating genetic interpretation. Next-generation sequencing has greatly advanced the identification of novel IRD-related genes and pathogenic variants in the last decade. For this review, we performed an in-depth literature search which allowed for compilation of the Global Retinal Inherited Disease (GRID) dataset containing 4,798 discrete variants and 17,299 alleles published in 31 papers, showing a wide range of frequencies and complexities among the 194 genes reported in GRID, with 65% of pathogenic variants being unique to a single individual. A better understanding of IRD-related gene distribution, gene complexity, and variant types allow for improved genetic testing and therapies. Current genetic therapeutic methods are also quite diverse and rely on variant identification, and range from whole gene replacement to single nucleotide editing at the DNA or RNA levels. IRDs and their suitable therapies thus require a range of effective disease modelling in human cells, granting insight into disease mechanisms and testing of possible treatments. This review summarizes genetic and therapeutic modalities of IRDs, provides new analyses of IRD-related genes (GRID and complexity scores), and provides information to match genetic-based therapies such as gene-specific and variant-specific therapies to the appropriate individuals.
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Affiliation(s)
- Nina Schneider
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Yogapriya Sundaresan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Prakadeeswari Gopalakrishnan
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Mor Hanany
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel
| | - Shay Ben-Aroya
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 5290002, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, 91120, Israel.
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41
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Rowlands C, Thomas HB, Lord J, Wai HA, Arno G, Beaman G, Sergouniotis P, Gomes-Silva B, Campbell C, Gossan N, Hardcastle C, Webb K, O'Callaghan C, Hirst RA, Ramsden S, Jones E, Clayton-Smith J, Webster AR, Douglas AGL, O'Keefe RT, Newman WG, Baralle D, Black GCM, Ellingford JM. Comparison of in silico strategies to prioritize rare genomic variants impacting RNA splicing for the diagnosis of genomic disorders. Sci Rep 2021; 11:20607. [PMID: 34663891 PMCID: PMC8523691 DOI: 10.1038/s41598-021-99747-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/13/2021] [Indexed: 12/22/2022] Open
Abstract
The development of computational methods to assess pathogenicity of pre-messenger RNA splicing variants is critical for diagnosis of human disease. We assessed the capability of eight algorithms, and a consensus approach, to prioritize 249 variants of uncertain significance (VUSs) that underwent splicing functional analyses. The capability of algorithms to differentiate VUSs away from the immediate splice site as being 'pathogenic' or 'benign' is likely to have substantial impact on diagnostic testing. We show that SpliceAI is the best single strategy in this regard, but that combined usage of tools using a weighted approach can increase accuracy further. We incorporated prioritization strategies alongside diagnostic testing for rare disorders. We show that 15% of 2783 referred individuals carry rare variants expected to impact splicing that were not initially identified as 'pathogenic' or 'likely pathogenic'; one in five of these cases could lead to new or refined diagnoses.
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Affiliation(s)
- Charlie Rowlands
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Huw B Thomas
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Jenny Lord
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Htoo A Wai
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Gavin Arno
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Glenda Beaman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Panagiotis Sergouniotis
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Beatriz Gomes-Silva
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Christopher Campbell
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Nicole Gossan
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Claire Hardcastle
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Kevin Webb
- Manchester Adult Cystic Fibrosis Centre, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Christopher O'Callaghan
- Respiratory, Critical Care and Anaesthesia, UCL Great Ormond Street Institute of Child Health & Great Ormond Street Children's Hospital & NIHR Great Ormond Street Hospital Biomedical Research Centre, London, UK
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Robert A Hirst
- Centre for PCD Diagnosis and Research, Department of Infection, Immunity and Inflammation, RKCSB, University of Leicester, Leicester, UK
| | - Simon Ramsden
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Elizabeth Jones
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
| | - Jill Clayton-Smith
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Andrew R Webster
- Institute of Ophthalmology, UCL, London, UK
- Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew G L Douglas
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Raymond T O'Keefe
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - William G Newman
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Diana Baralle
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Graeme C M Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK.
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary's Hospital, Manchester, UK.
- Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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43
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Demain LAM, Boetje E, Edgerley JJ, Miles E, Fitzgerald CT, Busby G, Beaman GM, O'Sullivan J, O'Keefe RT, Newman WG. Biallelic loss of function variants in STAG3 result in primary ovarian insufficiency. Reprod Biomed Online 2021; 43:899-902. [PMID: 34497033 DOI: 10.1016/j.rbmo.2021.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/24/2021] [Accepted: 07/06/2021] [Indexed: 11/27/2022]
Abstract
RESEARCH QUESTION Does a genetic condition underlie the diagnosis of primary ovarian insufficiency (POI) in a 21-year-old woman with primary amenorrhoea? DESIGN A karyotype and genetic testing for Fragile X syndrome was undertaken. A next-generation sequencing panel of 24 genes associated with syndromal and non-syndromal POI was conducted. RESULTS A nonsense variant c.1336G>T, p.(Glu446Ter) and whole gene deletion in STAG3 were identified. CONCLUSIONS Biallelic loss of function variants in STAG3 are associated with primary ovarian failure type 8 and are a rare cause of POI.
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Affiliation(s)
- Leigh A M Demain
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Eline Boetje
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Hanze University of Applied Sciences, Groningen, the Netherlands
| | - Jonathan J Edgerley
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Emma Miles
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Cheryl T Fitzgerald
- Reproductive Medicine, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Gail Busby
- Gynaecology Department, St Mary's Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Glenda M Beaman
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - James O'Sullivan
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK
| | - Raymond T O'Keefe
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - William G Newman
- Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, UK.
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44
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Mutated CCDC51 Coding for a Mitochondrial Protein, MITOK Is a Candidate Gene Defect for Autosomal Recessive Rod-Cone Dystrophy. Int J Mol Sci 2021; 22:ijms22157875. [PMID: 34360642 PMCID: PMC8346125 DOI: 10.3390/ijms22157875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 11/17/2022] Open
Abstract
The purpose of this work was to identify the gene defect underlying a relatively mild rod-cone dystrophy (RCD), lacking disease-causing variants in known genes implicated in inherited retinal disorders (IRD), and provide transcriptomic and immunolocalization data to highlight the best candidate. The DNA of the female patient originating from a consanguineous family revealed no large duplication or deletion, but several large homozygous regions. In one of these, a homozygous frameshift variant, c.244_246delins17 p.(Trp82Valfs*4); predicted to lead to a nonfunctional protein, was identified in CCDC51. CCDC51 encodes the mitochondrial coiled-coil domain containing 51 protein, also called MITOK. MITOK ablation causes mitochondrial dysfunction. Here we show for the first time that CCDC51/MITOK localizes in the retina and more specifically in the inner segments of the photoreceptors, well known to contain mitochondria. Mitochondrial proteins have previously been implicated in IRD, although usually in association with syndromic disease, unlike our present case. Together, our findings add another ultra-rare mutation implicated in non-syndromic IRD, whose pathogenic mechanism in the retina needs to be further elucidated.
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45
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García Bohórquez B, Aller E, Rodríguez Muñoz A, Jaijo T, García García G, Millán JM. Updating the Genetic Landscape of Inherited Retinal Dystrophies. Front Cell Dev Biol 2021; 9:645600. [PMID: 34327195 PMCID: PMC8315279 DOI: 10.3389/fcell.2021.645600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Inherited retinal dystrophies (IRD) are a group of diseases characterized by the loss or dysfunction of photoreceptors and a high genetic and clinical heterogeneity. Currently, over 270 genes have been associated with IRD which makes genetic diagnosis very difficult. The recent advent of next generation sequencing has greatly facilitated the diagnostic process, enabling to provide the patients with accurate genetic counseling in some cases. We studied 92 patients who were clinically diagnosed with IRD with two different custom panels. In total, we resolved 53 patients (57.6%); in 12 patients (13%), we found only one mutation in a gene with a known autosomal recessive pattern of inheritance; and 27 patients (29.3%) remained unsolved. We identified 120 pathogenic or likely pathogenic variants; 30 of them were novel. Among the cone-rod dystrophy patients, ABCA4 was the most common mutated gene, meanwhile, USH2A was the most prevalent among the retinitis pigmentosa patients. Interestingly, 10 families carried pathogenic variants in more than one IRD gene, and we identified two deep-intronic variants previously described as pathogenic in ABCA4 and CEP290. In conclusion, the IRD study through custom panel sequencing demonstrates its efficacy for genetic diagnosis, as well as the importance of including deep-intronic regions in their design. This genetic diagnosis will allow patients to make accurate reproductive decisions, enroll in gene-based clinical trials, and benefit from future gene-based treatments.
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Affiliation(s)
- Belén García Bohórquez
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Elena Aller
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Ana Rodríguez Muñoz
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - Teresa Jaijo
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
- Unit of Genetics, University Hospital La Fe, Valencia, Spain
| | - Gema García García
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
| | - José M. Millán
- Molecular, Cellular and Genomics Biomedicine, Health Research Institute La Fe, Valencia, Spain
- CIBER of Rare Diseases, Madrid, Spain
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Mullin NK, Voigt AP, Cooke JA, Bohrer LR, Burnight ER, Stone EM, Mullins RF, Tucker BA. Patient derived stem cells for discovery and validation of novel pathogenic variants in inherited retinal disease. Prog Retin Eye Res 2021; 83:100918. [PMID: 33130253 PMCID: PMC8559964 DOI: 10.1016/j.preteyeres.2020.100918] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/22/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Our understanding of inherited retinal disease has benefited immensely from molecular genetic analysis over the past several decades. New technologies that allow for increasingly detailed examination of a patient's DNA have expanded the catalog of genes and specific variants that cause retinal disease. In turn, the identification of pathogenic variants has allowed the development of gene therapies and low-cost, clinically focused genetic testing. Despite this progress, a relatively large fraction (at least 20%) of patients with clinical features suggestive of an inherited retinal disease still do not have a molecular diagnosis today. Variants that are not obviously disruptive to the codon sequence of exons can be difficult to distinguish from the background of benign human genetic variations. Some of these variants exert their pathogenic effect not by altering the primary amino acid sequence, but by modulating gene expression, isoform splicing, or other transcript-level mechanisms. While not discoverable by DNA sequencing methods alone, these variants are excellent targets for studies of the retinal transcriptome. In this review, we present an overview of the current state of pathogenic variant discovery in retinal disease and identify some of the remaining barriers. We also explore the utility of new technologies, specifically patient-derived induced pluripotent stem cell (iPSC)-based modeling, in further expanding the catalog of disease-causing variants using transcriptome-focused methods. Finally, we outline bioinformatic analysis techniques that will allow this new method of variant discovery in retinal disease. As the knowledge gleaned from previous technologies is informing targets for therapies today, we believe that integrating new technologies, such as iPSC-based modeling, into the molecular diagnosis pipeline will enable a new wave of variant discovery and expanded treatment of inherited retinal disease.
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Affiliation(s)
- Nathaniel K Mullin
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Andrew P Voigt
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Jessica A Cooke
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Laura R Bohrer
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Erin R Burnight
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Edwin M Stone
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Robert F Mullins
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Budd A Tucker
- The Institute for Vision Research, University of Iowa, Iowa City, IA, USA; Department of Ophthalmology and Visual Sciences, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
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Nassisi M, Smirnov VM, Solis Hernandez C, Mohand‐Saïd S, Condroyer C, Antonio A, Kühlewein L, Kempf M, Kohl S, Wissinger B, Nasser F, Ragi SD, Wang N, Sparrow JR, Greenstein VC, Michalakis S, Mahroo OA, Ba‐Abbad R, Michaelides M, Webster AR, Degli Esposti S, Saffren B, Capasso J, Levin A, Hauswirth WW, Dhaenens C, Defoort‐Dhellemmes S, Tsang SH, Zrenner E, Sahel J, Petersen‐Jones SM, Zeitz C, Audo I. CNGB1-related rod-cone dystrophy: A mutation review and update. Hum Mutat 2021; 42:641-666. [PMID: 33847019 PMCID: PMC8218941 DOI: 10.1002/humu.24205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/26/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Cyclic nucleotide-gated channel β1 (CNGB1) encodes the 240-kDa β subunit of the rod photoreceptor cyclic nucleotide-gated ion channel. Disease-causing sequence variants in CNGB1 lead to autosomal recessive rod-cone dystrophy/retinitis pigmentosa (RP). We herein present a comprehensive review and analysis of all previously reported CNGB1 sequence variants, and add 22 novel variants, thereby enlarging the spectrum to 84 variants in total, including 24 missense variants (two of which may also affect splicing), 21 nonsense, 19 splicing defects (7 at noncanonical positions), 10 small deletions, 1 small insertion, 1 small insertion-deletion, 7 small duplications, and 1 gross deletion. According to the American College of Medical Genetics and Genomics classification criteria, 59 variants were considered pathogenic or likely pathogenic and 25 were variants of uncertain significance. In addition, we provide further phenotypic data from 34 CNGB1-related RP cases, which, overall, are in line with previous findings suggesting that this form of RP has long-term retention of useful central vision despite the early onset of night blindness, which is valuable for patient counseling, but also has implications for it being considered a priority target for gene therapy trials.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- Department of Clinical Sciences and Community HealthUniversity of MilanMilanItaly
- Ophthalmological Unit, Fondazione IRCCS Ca' GrandaOspedale Maggiore PoliclinicoMilanItaly
| | - Vasily M. Smirnov
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Exploration de la vision et Neuro‐Ophthalmologie, CHU de LilleLilleFrance
- Faculté de MédecineUniversité de LilleLilleFrance
| | - Cyntia Solis Hernandez
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Saddek Mohand‐Saïd
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
| | - Christel Condroyer
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Aline Antonio
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Laura Kühlewein
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Melanie Kempf
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Fadi Nasser
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Sara D. Ragi
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | - Nan‐Kai Wang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- College of MedicineChang Gung UniversityTaoyuanTaiwan
- Department of Ophthalmology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuanTaiwan
| | - Janet R. Sparrow
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | | | | | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Rola Ba‐Abbad
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Michel Michaelides
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Simona Degli Esposti
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Brooke Saffren
- Philadelphia College of Osteopathic MedicinePhiladelphiaPennsylvaniaUSA
| | | | - Alex Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's HospitalUniversity of RochesterRochesterNew YorkUSA
| | | | - Claire‐Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172‐LilNCog‐Lille Neuroscience & CognitionLilleFrance
| | | | - Stephen H. Tsang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma LaboratoryNew YorkNew YorkUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Stem Cell Initiative (CSCI), Institute of Human Nutrition, Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Eberhart Zrenner
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Jose‐Alain Sahel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Department of OphthalmologyThe University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Fondation Ophtalmologique Adolphe de RothschildParisFrance
| | - Simon M. Petersen‐Jones
- Department of Small Animal Clinical SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Christina Zeitz
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Isabelle Audo
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- University College London Institute of OphthalmologyLondonUK
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Next-Generation Sequencing Applications for Inherited Retinal Diseases. Int J Mol Sci 2021; 22:ijms22115684. [PMID: 34073611 PMCID: PMC8198572 DOI: 10.3390/ijms22115684] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/12/2022] Open
Abstract
Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.
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Mizobuchi K, Hayashi T, Oishi N, Kubota D, Kameya S, Higasa K, Futami T, Kondo H, Hosono K, Kurata K, Hotta Y, Yoshitake K, Iwata T, Matsuura T, Nakano T. Genotype-Phenotype Correlations in RP1-Associated Retinal Dystrophies: A Multi-Center Cohort Study in JAPAN. J Clin Med 2021; 10:jcm10112265. [PMID: 34073704 PMCID: PMC8197273 DOI: 10.3390/jcm10112265] [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: 04/17/2021] [Revised: 05/14/2021] [Accepted: 05/21/2021] [Indexed: 12/13/2022] Open
Abstract
Background: Little is known about genotype–phenotype correlations of RP1-associated retinal dystrophies in the Japanese population. We aimed to investigate the genetic spectrum of RP1 variants and provide a detailed description of the clinical findings in Japanese patients. Methods: In total, 607 patients with inherited retinal diseases were examined using whole-exome/whole-genome sequencing (WES/WGS). PCR-based screening for an Alu element insertion (c.4052_4053ins328/p.Tyr1352AlafsTer9) was performed in 18 patients with autosomal-recessive (AR)-retinitis pigmentosa (RP) or AR-cone dystrophy (COD)/cone-rod dystrophy (CORD), including seven patients with heterozygous RP1 variants identified by WES/WGS analysis, and 11 early onset AR-RP patients, in whom no pathogenic variant was identified. We clinically examined 25 patients (23 families) with pathogenic RP1 variants, including five patients (five families) with autosomal-dominant (AD)-RP, 13 patients (11 families) with AR-RP, and seven patients (seven families) with AR-COD/CORD. Results: We identified 18 pathogenic RP1 variants, including seven novel variants. Interestingly, the Alu element insertion was the most frequent variant (32.0%, 16/50 alleles). The clinical findings revealed that the age at onset and disease progression occurred significantly earlier and faster in AR-RP patients compared to AD-RP or AR-COD/CORD patients. Conclusions: Our results suggest a genotype–phenotype correlation between variant types/locations and phenotypes (AD-RP, AR-RP, and AR-COD/CORD), and the Alu element insertion was the most major variant in Japanese patients with RP1-associated retinal dystrophies.
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Affiliation(s)
- Kei Mizobuchi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-19-18, Nishi-shimbashi, Minato-ku, Tokyo 105-8471, Japan; (T.H.); (T.N.)
- Correspondence: ; Tel.: +81-3-3433-1111
| | - Takaaki Hayashi
- Department of Ophthalmology, The Jikei University School of Medicine, 3-19-18, Nishi-shimbashi, Minato-ku, Tokyo 105-8471, Japan; (T.H.); (T.N.)
- Department of Ophthalmology, Katsushika Medical Center, The Jikei University School of Medicine, 6-41-2 Aoto, Katsushika-ku, Tokyo 125-8506, Japan
| | - Noriko Oishi
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, 1715 Kamagari, Inzai, Chiba 270-1694, Japan; (N.O.); (D.K.); (S.K.)
| | - Daiki Kubota
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, 1715 Kamagari, Inzai, Chiba 270-1694, Japan; (N.O.); (D.K.); (S.K.)
| | - Shuhei Kameya
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, 1715 Kamagari, Inzai, Chiba 270-1694, Japan; (N.O.); (D.K.); (S.K.)
| | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shinmachi, Hirakata, Osaka 573-1010, Japan;
| | - Takuma Futami
- Department of Ophthalmology, University of Occupational and Environmental Health, 1-1, Iseigaoka, Yahatanishi-ku Kitakyushu-shi, Fu-kuoka 807-8555, Japan; (T.F.); (H.K.)
| | - Hiroyuki Kondo
- Department of Ophthalmology, University of Occupational and Environmental Health, 1-1, Iseigaoka, Yahatanishi-ku Kitakyushu-shi, Fu-kuoka 807-8555, Japan; (T.F.); (H.K.)
| | - Katsuhiro Hosono
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1, Handayama, Higashi-ku, Shizuoka, Hamamatsu 431-3192, Japan; (K.H.); (K.K.); (Y.H.)
| | - Kentaro Kurata
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1, Handayama, Higashi-ku, Shizuoka, Hamamatsu 431-3192, Japan; (K.H.); (K.K.); (Y.H.)
| | - Yoshihiro Hotta
- Department of Ophthalmology, Hamamatsu University School of Medicine, 1-20-1, Handayama, Higashi-ku, Shizuoka, Hamamatsu 431-3192, Japan; (K.H.); (K.K.); (Y.H.)
| | - Kazutoshi Yoshitake
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo 152-8902, Japan; (K.Y.); (T.I.)
| | - Takeshi Iwata
- National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, 2-5-1 Higashigaoka, Meguro-ku, Tokyo 152-8902, Japan; (K.Y.); (T.I.)
| | - Tomokazu Matsuura
- Department of Laboratory Medicine, The Jikei University School of Medicine, 3-19-18, Nishi-shimbashi, Minato-ku, Tokyo 105-8471, Japan;
| | - Tadashi Nakano
- Department of Ophthalmology, The Jikei University School of Medicine, 3-19-18, Nishi-shimbashi, Minato-ku, Tokyo 105-8471, Japan; (T.H.); (T.N.)
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Daich Varela M, Ullah E, Yousaf S, Brooks BP, Hufnagel RB, Huryn LA. PDE6C: Novel Mutations, Atypical Phenotype, and Differences Among Children and Adults. Invest Ophthalmol Vis Sci 2021; 61:1. [PMID: 33001157 PMCID: PMC7545085 DOI: 10.1167/iovs.61.12.1] [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: 01/20/2023] Open
Abstract
Purpose Genetic variation in PDE6C is associated with achromatopsia and cone dystrophy, with only a few reports of cone-rod dystrophy in the literature. We describe two pediatric and two adult patients with PDE6C related cone and cone-rod dystrophy and the first longitudinal data of a pediatric patient with PDE6C-related cone dystrophy. Methods This cohort of four patients underwent comprehensive ophthalmologic evaluation at the National Eye Institute's Ophthalmic Genetics clinic, including visual field testing, retinal imaging and electroretinogram (ERG). Next-generation sequencing-based genetic testing was performed and subsequent analysis of the variants was done through three-dimensional protein models generated by Phyre2 and Chimera. Results All cases shared decreased best-corrected visual acuity and poor color discrimination. Three of the four patients had a cone-rod dystrophy, presenting with an ERG showing decreased amplitude on both photopic and scotopic waveforms and a mild to moderately constricted visual field. One of the children was diagnosed with cone dystrophy, having a preserved peripheral field. The children had none to minor structural retinal changes, whereas the adults had clear macular dystrophy. Conclusions PDE6C-related cone-rod dystrophy consists of a severe phenotype characterized by early-onset nystagmus, decreased best-corrected visual acuity, poor color discrimination, progressive constriction of the visual field, and night blindness. Our work contributes with valuable information toward understanding the visual prognosis and allelic heterogeneity of PDE6C-related cone and cone-rod dystrophy.
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Affiliation(s)
- Malena Daich Varela
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Sairah Yousaf
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Brian P Brooks
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States
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