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Hui Min Lau S, Jiin Ying L, Jasmine Goh CY, Chood J, Chow C, Ling S, Hong Ng Y, Hua TY, Teo JX, Chua KP, Chin M, Lim WK, Jamuar SS, Meeng Lai AH, Goh JLK. Dilated aorta in CNOT3-related neurodevelopmental disorder: 'expanding' the phenotype. Clin Dysmorphol 2024:00019605-990000000-00077. [PMID: 39140378 DOI: 10.1097/mcd.0000000000000495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2024]
Abstract
INTRODUCTION Neurodevelopmental disorders (NDDs) comprise conditions that emerge during the child's development and contribute significantly to global health and economic burdens. De-novo variants in CNOT3 have been linked to NDDs and understanding the genotype-phenotype relationship between CNOT3 and NDDs will aid in improving diagnosis and management. METHODS In this study, we report a case of a patient with CNOT3-related NDD who presented with progressive aortic dilatation, a feature not reported previously. RESULTS Our patient presented with intellectual disorder, dysmorphic facial features, and cardiac anomalies, notably progressive aortic dilatation - a novel finding in CNOT3-related NDD. Genetic testing identified a de-novo 6.3 kbp intragenic deletion in CNOT3, providing a possible genetic basis for her condition. CONCLUSION This study presents the first case of CNOT3-related NDD in Southeast Asia, expanding the phenotype to include progressive aortic dilatation and suggesting merit in cardiac surveillance of patients with CNOT3-related NDD. It also emphasizes the importance of genetic testing in diagnosing complex NDD cases as well as reanalysis of 'negative' cases using advanced sequencing technologies to uncover potential hidden genetic etiologies in undiagnosed NDDs.
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Affiliation(s)
| | - Lim Jiin Ying
- Genetics Service, Department of Paediatrics , KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
| | - Chew Yin Jasmine Goh
- Genetics Service, Department of Paediatrics , KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
| | - Jonathan Chood
- Cardiology Service, Department of Paediatric Subspecialties
| | - Cristelle Chow
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
- Complex Care Service, Department of Paediatrics
| | - Simon Ling
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
- Neurology Service, Department of Paediatrics
| | - Yong Hong Ng
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
- Nephrology Service, Department of Paediatrics
| | - Tan Yi Hua
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
- Respiratory Medicine Service, Department of Paediatrics , KK Women's and Children's Hospital
| | - Jing Xian Teo
- SingHealth Duke-NUS Genomic Medicine Centre
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Khi Pin Chua
- Pacific BioSciences, Menlo Park, California, USA
| | - Minning Chin
- Pacific BioSciences, Menlo Park, California, USA
| | - Weng Khong Lim
- SingHealth Duke-NUS Genomic Medicine Centre
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
- Singapore Cancer and Stem Cell Biology Program, Duke-NUS Medical School and
- Singapore Laboratory of Genome Variation Analytics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
| | - Saumya Shekhar Jamuar
- Genetics Service, Department of Paediatrics , KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore, Singapore
| | - Angeline Hwei Meeng Lai
- Lee Kong Chian School of Medicine , Nanyang Technological University
- Genetics Service, Department of Paediatrics , KK Women's and Children's Hospital
- SingHealth Duke-NUS Genomic Medicine Centre
- Paediatric Academic Clinical Programme, Duke-NUS Medical School
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Bodenbender JP, Bethge L, Stingl K, Mazzola P, Haack T, Biskup S, Wissinger B, Weisschuh N, Kohl S, Kühlewein L. Clinical and Genetic Findings in a Cohort of Patients with PRPF31-Associated Retinal Dystrophy. Am J Ophthalmol 2024; 267:213-229. [PMID: 38909744 DOI: 10.1016/j.ajo.2024.06.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2023] [Revised: 06/12/2024] [Accepted: 06/13/2024] [Indexed: 06/25/2024]
Abstract
PURPOSE The purpose of our study was to assess the phenotypic and genotypic spectrum in a large cohort of patients with PRPF31-associated retinal dystrophy. DESIGN Retrospective cohort study. METHODS In this retrospective chart review study, we collected cross-sectional data on the phenotype and genotype of patients with PRPF31-associated retinal dystrophy from the clinics for inherited retinal dystrophies at the University of Tuebingen and the local RetDis database and biobank. Patients underwent thorough ophthalmological examinations and genetic testing. RESULTS Eighty-six patients from 61 families were available for clinical assessment, while genomic DNA was available for 111 individuals (index patients and family members). Fifty-three different disease-associated variants were observed in our cohort. Point mutations were the most common class. All but two patients exhibited features of a typical Retinitis pigmentosa (RP). One patient showed a cone-rod dystrophy pattern. One mutation carrier revealed no signs of a retinal dystrophy. There was a statistically significant better visual acuity for patients with large deletions in the 20-39 age group. Cystoid macular edema was common in those with preserved central retina and showed an association with female sex. CONCLUSION Our study confirms high phenotypic variability in disease onset and age at which legal blindness is reached in PRPF31-associated RP. Non-penetrance is commonly documented in family history, although poorly represented in our study, possibly indicating that true asymptomatic mutation carriers are rare if followed-up over lifetime with thorough ophthalmologic workup.
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Affiliation(s)
- Jan-Philipp Bodenbender
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Leon Bethge
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany
| | - Pascale Mazzola
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University (P.M., T.H.), Tübingen, Germany
| | - Tobias Haack
- Institute of Medical Genetics and Applied Genomics, Eberhard Karls University (P.M., T.H.), Tübingen, Germany; Center for Rare Diseases, Eberhard Karls University (T.H.), Tübingen, Germany
| | | | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (B.W., N.W., S.K.), Tübingen, Germany
| | - Laura Kühlewein
- University Eye Hospital, Center for Ophthalmology, Eberhard Karls University (J.P.B., L.B., K.S., L.K.), Tübingen, Germany; Institute for Ophthalmic Research, Center for Ophthalmology, Eberhard Karls University (L.K.), Tübingen, Germany.
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Ciampi L, Serrano L, Irimia M. Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States. Mol Syst Biol 2024; 20:296-310. [PMID: 38438733 PMCID: PMC10987577 DOI: 10.1038/s44320-024-00020-1] [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: 10/31/2023] [Revised: 01/04/2024] [Accepted: 01/12/2024] [Indexed: 03/06/2024] Open
Abstract
Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
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Affiliation(s)
- Ludovica Ciampi
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Luis Serrano
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
| | - Manuel Irimia
- Center for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
- Universitat Pompeu Fabra, Barcelona, Spain.
- ICREA, Barcelona, Spain.
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Lisbjerg K, Bertelsen M, Grønskov K, Kessel L. Clinical characterization of patients with PRPF31-related retinitis pigmentosa and asymptomatic carriers: a cross-sectional study. Ophthalmic Genet 2023; 44:456-464. [PMID: 37293790 DOI: 10.1080/13816810.2023.2219732] [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: 12/29/2022] [Revised: 04/27/2023] [Accepted: 05/25/2023] [Indexed: 06/10/2023]
Abstract
BACKGROUND/AIM To describe the clinical phenotype of retinitis pigmentosa (RP) caused by PRPF31-variants and clinical characterization of asymptomatic PRPF31 carriers. MATERIALS AND METHODS We conducted a descriptive cross-sectional deep phenotyping study. We included subjects with PRPF31 variants predicted to be disease-causing, both individuals with RP and asymptomatic carriers. Participants underwent a comprehensive clinical examination of standard visual function parameters (visual acuity, contrast sensitivity, Goldmann visual field), full-field stimulus threshold (FST), full-field electroretinogram (ff-ERG), and a structural investigation with slit lamp and multimodal imaging. We used Spearman correlation analyses to evaluate associations between quantitative outcomes. RESULTS We included 21 individuals with disease-causing PRPF31-variants: 16 symptomatic and 5 asymptomatic subjects. The symptomatic subjects demonstrated a typical RP phenotype with constricted visual fields, extinguished ff-ERG, and disrupted outer retinal anatomy. FST was impaired and correlated significantly with other outcome measures in RP subjects. Structure-function correlations with Spearman correlation analysis showed moderate correlation coefficients due to a few outliers in each analysis. The asymptomatic individuals had normal best-corrected visual acuity and visual fields, but showed reduced ff-ERG amplitudes, borderline FST sensitivity, and structural abnormalities on OCT and fundoscopy. CONCLUSIONS RP11 has a typical RP phenotype but varies in terms of severity. FST measurements correlated well with other functional and structural metrics and may be a reliable outcome measure in future trials as it is sensitive to a broad range of disease severities. Asymptomatic carriers showed sub-clinical disease manifestations, and our findings underline that reported non-penetrance in PRPF31-related RP is not an all-or-none phenomenon.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Daich Varela M, Georgiadis A, Michaelides M. Genetic treatment for autosomal dominant inherited retinal dystrophies: approaches, challenges and targeted genotypes. Br J Ophthalmol 2023; 107:1223-1230. [PMID: 36038193 DOI: 10.1136/bjo-2022-321903] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/01/2022] [Indexed: 11/04/2022]
Abstract
Inherited retinal diseases (IRDs) have been in the front line of gene therapy development for the last decade, providing a useful platform to test novel therapeutic approaches. More than 40 clinical trials have been completed or are ongoing, tackling autosomal recessive and X-linked conditions, mostly through adeno-associated viral vector delivery of a normal copy of the disease-causing gene. However, only recently has autosomal dominant (ad) disease been targeted, with the commencement of a trial for rhodopsin (RHO)-associated retinitis pigmentosa (RP), implementing antisense oligonucleotide (AON) therapy, with promising preliminary results (NCT04123626).Autosomal dominant RP represents 15%-25% of all RP, with RHO accounting for 20%-30% of these cases. Autosomal dominant macular and cone-rod dystrophies (MD/CORD) correspond to approximately 7.5% of all IRDs, and approximately 35% of all MD/CORD cases, with the main causative gene being BEST1 Autosomal dominant IRDs are not only less frequent than recessive, but also tend to be less severe and have later onset; for example, an individual with RHO-adRP would typically become severely visually impaired at an age 2-3 times older than in X-linked RPGR-RP.Gain-of-function and dominant negative aetiologies are frequently seen in the prevalent adRP genes RHO, RP1 and PRPF31 among others, which would not be effectively addressed by gene supplementation alone and need creative, novel approaches. Zinc fingers, RNA interference, AON, translational read-through therapy, and gene editing by clustered regularly interspaced short palindromic repeats/Cas are some of the strategies that are currently under investigation and will be discussed here.
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Affiliation(s)
- Malena Daich Varela
- 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
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Lisbjerg K, Grønskov K, Bertelsen M, Møller LB, Kessel L. Genetic Modifiers of Non-Penetrance and RNA Expression Levels in PRPF31-Associated Retinitis Pigmentosa in a Danish Cohort. Genes (Basel) 2023; 14:435. [PMID: 36833363 PMCID: PMC9956082 DOI: 10.3390/genes14020435] [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: 12/29/2022] [Revised: 02/03/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
(1) Background/aims: To examine potential genetic modifiers of disease penetrance in PRPF31-associated retinitis pigmentosa 11 (RP11). (2) Methods: Blood samples from individuals (n = 37) with PRPF31 variants believed to be disease-causing were used for molecular genetic testing and, in some cases (n = 23), also for mRNA expression analyses. Medical charts were used to establish if individuals were symptomatic (RP) or asymptomatic non-penetrant carriers (NPC). RNA expression levels of PRPF31 and CNOT3 were measured on peripheral whole blood using quantitative real-time PCR normalized to GAPDH. Copy number variation of minisatellite repeat element 1 (MSR1) was performed with DNA fragment analysis. (3) Results: mRNA expression analyses on 22 individuals (17 with RP and 5 non-penetrant carriers) revealed no statistically significant differences in PRPF31 or CNOT3 mRNA expression levels between individuals with RP and non-penetrant carriers. Among 37 individuals, we found that all three carriers of a 4-copy MSR1 sequence on their wild-type (WT) allele were non-penetrant carriers. However, copy number variation of MSR1 is not the sole determinant factor of non-penetrance, as not all non-penetrant carriers carried a 4-copy WT allele. A 4-copy MSR1 mutant allele was not associated with non-penetrance. (4) Conclusions: In this Danish cohort, a 4-copy MSR1 WT allele was associated with non-penetrance of retinitis pigmentosa caused by PRPF31 variants. The level of PRPF31 mRNA expression in peripheral whole blood was not a useful indicator of disease status.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital-Rigshospitalet, 2600 Glostrup, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Lisbeth Birk Møller
- Department of Clinical Genetics, Copenhagen University Hospital-Rigshospitalet, 2100 Copenhagen, Denmark
| | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital-Rigshospitalet, 2600 Glostrup, Denmark
- Department of Clinical Medicine, University of Copenhagen, 2200 Copenhagen, Denmark
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Huang D, Thompson JA, Chen SC, Adams A, Pitout I, Lima A, Zhang D, Jeffery RCH, Attia MS, McLaren TL, Lamey TM, De Roach JN, McLenachan S, Aung-Htut MT, Fletcher S, Wilton SD, Chen FK. Characterising splicing defects of ABCA4 variants within exons 13-50 in patient-derived fibroblasts. Exp Eye Res 2022; 225:109276. [PMID: 36209838 DOI: 10.1016/j.exer.2022.109276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/12/2022] [Accepted: 09/28/2022] [Indexed: 12/29/2022]
Abstract
The ATP-binding cassette subfamily A member 4 gene (ABCA4)-associated retinopathy, Stargardt disease, is the most common monogenic inherited retinal disease. Given the pathogenicity of numerous ABCA4 variants is yet to be examined and a significant proportion (more than 15%) of ABCA4 variants are categorized as splice variants in silico, we therefore established a fibroblast-based splice assay to analyze ABCA4 variants in an Australian Stargardt disease cohort and characterize the pathogenic mechanisms of ABCA4 variants. A cohort of 67 patients clinically diagnosed with Stargardt disease was recruited. Genomic DNA was analysed using a commercial panel for ABCA4 variant detection and the consequences of ABCA4 variants were predicted in silico. Dermal fibroblasts were propagated from skin biopsies, total RNA was extracted and the ABCA4 transcript was amplified by RT-PCR. Our analysis identified a total of 67 unique alleles carrying 74 unique variants. The most prevalent splice-affecting complex allele c.[5461-10T>C; 5603A>T] was carried by 10% of patients in a compound heterozygous state. ABCA4 transcripts from exon 13 to exon 50 were readily detected in fibroblasts. In this region, aberrant splicing was evident in 10 out of 57 variant transcripts (18%), carried by 19 patients (28%). Patient-derived fibroblasts provide a feasible platform for identification of ABCA4 splice variants located within exons 13-50. Experimental evidence of aberrant splicing contributes to the pathogenic classification for ABCA4 variants. Moreover, identification of variants that affect splicing processes provides opportunities for intervention, in particular antisense oligonucleotide-mediated splice correction.
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Affiliation(s)
- Di Huang
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
| | - Shang-Chih Chen
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Abbie Adams
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Ianthe Pitout
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Alanis Lima
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia
| | - Dan Zhang
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Rachael C Heath Jeffery
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Royal Victorian Eye and Ear Hospital, Centre for Eye Research Australia, East Melbourne, Victoria, Australia
| | - Mary S Attia
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Terri L McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, 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; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - John N De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Samuel McLenachan
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, Western Australia, Australia; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - May Thandar Aung-Htut
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia; PYC Therapeutics, Harry Perkins Institute of Medical Research, Verdun St, Nedlands, Western Australia, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Western Australia, Australia; Perron Institute for Neurological and Translational Science, Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Australia
| | - Fred K Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, 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; Centre for Ophthalmology and Visual Sciences, The University of Western Australia, Nedlands, Western Australia, Australia; Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia; Ophthalmology, Department of Surgery, University of Melbourne, East Melbourne, Victoria, Australia; Royal Victorian Eye and Ear Hospital, Centre for Eye Research Australia, East Melbourne, Victoria, Australia.
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A 69 kb Deletion in chr19q13.42 including PRPF31 Gene in a Chinese Family Affected with Autosomal Dominant Retinitis Pigmentosa. J Clin Med 2022; 11:jcm11226682. [PMID: 36431159 PMCID: PMC9695658 DOI: 10.3390/jcm11226682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 10/20/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify the genetic cause of autosomal dominant retinitis pigmentosa (adRP) and characterize the underlying molecular mechanisms of incomplete penetrance in a Chinese family affected with adRP. All enrolled family members underwent ophthalmic examinations. Whole-genome sequencing (WGS), multiplex ligation-dependent probe amplification (MLPA), linkage analysis and haplotype construction were performed in all participants. RNA-seq was performed to analyze the regulating mechanism of incomplete penetrance among affected patients, mutation carriers and healthy controls. In the studied family, 14 individuals carried a novel heterozygous large deletion of 69 kilobase (kb) in 19q13.42 encompassing exon 1 of the PRPF31 gene and five upstream genes: TFPT, OSCAR, NDUFA3, TARM1, and VSTM1. Three family members were sequenced and diagnosed as non-penetrant carriers (NPCs). RNA-seq showed significant differential expression of genes in deletion between mutation carriers and healthy control. The RP11 pedigree in this study was the largest pedigree compared to other reported RP11 pedigrees with large deletions. Early onset in all affected members in this pedigree was considered to be a special phenotype and was firstly reported in a RP11 family for the first time. Differential expression of PRPF31 between affected and unaffected subjects indicates a haploinsufficiency to cause the disease in the family. The other genes with significant differential expression might play a cooperative effect on the penetrance of RP11.
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Ali-Nasser T, Zayit-Soudry S, Banin E, Sharon D, Ben-Yosef T. Autosomal dominant retinitis pigmentosa with incomplete penetrance due to an intronic mutation of the PRPF31 gene. Mol Vis 2022; 28:359-368. [PMID: 36338669 PMCID: PMC9603903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 10/04/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose To identify the molecular mechanisms of the development of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance in an Israeli Muslim Arab family. Methods Two patients with adRP underwent a detailed ophthalmic evaluation, including funduscopic examination, visual field testing, optical coherence tomography, and electroretinography. Genetic analysis was performed using a combination of whole exome sequencing (WES) and Sanger sequencing. The pathogenicity of the identified intronic variant was evaluated in silico using several web-based tools, in vitro using a minigene-based assay, and in vivo using reverse transcription PCR analysis of lymphocyte-derived RNA. The relative abundance of alternatively spliced transcripts was evaluated using amplicon-based next-generation sequencing. The relative expression levels of PRPF31 and CNOT3 were measured using quantitative PCR (qPCR) analysis. Results The two patients recruited in this study had childhood-onset RP, with night blindness as the initial symptom, followed by concentric restriction of the visual field. The funduscopic findings included narrowed retinal blood vessels and peripheral bone spicule pigmentation. By the third decade of life, the full-field electroretinography findings had been remarkably attenuated. In these patients, we identified a novel heterozygous intronic variant at position +5 of PRPF31 intron 11 (c.1146+5G>T). The same variant was also detected in one asymptomatic family member. Through in silico analysis, the variant was predicted to alter the splicing of intron 11. An in vitro splicing assay and a reverse transcription PCR analysis of lymphocyte-derived RNA revealed that the mutant allele yielded mainly a shorter transcript in which exon 11 was skipped. The skipping of exon 11 was expected to cause a frameshift and an aberrant truncated protein (p.Tyr359Serfs*29). The qPCR analysis revealed reduced PRPF31 expression levels in the mutation carriers, without a significant difference between the affected patient and his asymptomatic brother. We evaluated several factors that have been suggested to correlate with non-penetrance of PRPF31 mutations, including the number of cis-acting MSR1 elements adjacent to the PRPF31 core promoter, CNOT3 expression level, and CNOT3 rs4806718 single-nucleotide polymorphism. None of these factors correlated with non-penetrance in the family in this study. Conclusions We report a novel intronic mutation in PRPF31 underlying adRP. This report expands the spectrum of pathogenic mutations in PRPF31 and further demonstrates the importance of intronic mutations. Moreover, it demonstrates the phenomenon of incomplete penetrance previously associated with PRPF31 mutations. The fact that the non-penetrance in the family in this study could not be explained by any of the known mechanisms suggests the possible contribution of a novel modifier of PRPF31 penetrance.
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Affiliation(s)
- Tahleel Ali-Nasser
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Shiri Zayit-Soudry
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel,Department of Ophthalmology, Rambam Health Care Campus, Haifa, Israel,Clinical Research Institute at Rambam, Rambam Health Care Campus, Haifa, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
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