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Aweidah H, Xi Z, Sahel JA, Byrne LC. PRPF31-retinitis pigmentosa: Challenges and opportunities for clinical translation. Vision Res 2023; 213:108315. [PMID: 37714045 PMCID: PMC10872823 DOI: 10.1016/j.visres.2023.108315] [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: 04/30/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/17/2023]
Abstract
Mutations in pre-mRNA processing factor 31 cause autosomal dominant retinitis pigmentosa (PRPF31-RP), for which there is currently no efficient treatment, making this disease a prime target for the development of novel therapeutic strategies. PRPF31-RP exhibits incomplete penetrance due to haploinsufficiency, in which reduced levels of gene expression from the mutated allele result in disease. A variety of model systems have been used in the investigation of disease etiology and therapy development. In this review, we discuss recent advances in both in vivo and in vitro model systems, evaluating their advantages and limitations in the context of therapy development for PRPF31-RP. Additionally, we describe the latest approaches for treatment, including AAV-mediated gene augmentation, genome editing, and late-stage therapies such as optogenetics, cell transplantation, and retinal prostheses.
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Affiliation(s)
- Hamzah Aweidah
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zhouhuan Xi
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Ophthalmology, Eye Center, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - José-Alain Sahel
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Leah C Byrne
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Neurobiology, University of Pittsburgh, Pittsburgh, PA, USA; Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA.
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2
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Sen P, Srikrupa N, Maitra P, Srilekha S, Porkodi P, Gnanasekaran H, Bhende M, Khetan V, Mathavan S, Bhende P, Ratra D, Raman R, Rao C, Sripriya S. Next-generation sequencing--based genetic testing and phenotype correlation in retinitis pigmentosa patients from India. Indian J Ophthalmol 2023; 71:2512-2520. [PMID: 37322672 PMCID: PMC10417947 DOI: 10.4103/ijo.ijo_2579_22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 06/17/2023] Open
Abstract
Purpose Inherited retinal dystrophies (IRD) are a heterogeneous group of retinal diseases leading to progressive loss of photoreceptors through apoptosis. Retinitis pigmentosa (RP) is considered the most common form of IRD. Panel-based testing in RP has proven effective in identifying the causative genetic mutations in 70% and 80% of the patients. This is a retrospective, observational, single-center study of 107 RP patients who had undergone next-generation sequencing-based targeted gene panel testing for IRD genes. These patients were inspected for common phenotypic features to arrive at meaningful genotype-phenotype correlation. Methods Patients underwent complete ophthalmic examination, and blood was collected from the proband for DNA extraction after documenting the pedigree. Targeted Next Generation Sequencing (NGS) was done by panel-based testing for IRD genes followed by co-segregation analysis wherever applicable. Results Of the 107 patients, 72 patients had pathogenic mutations. The mean age of onset of symptoms was 14 ± 12 years (range: 5-55). Mean (Best Corrected Visual Acuity) BCVA was 6/48 (0.9 logMAR) (range 0.0-3.0). At presentation, over one-third of eyes had BCVA worse than 6/60 (<1 logMAR). Phenotype analysis with the gene defects showed overlapping features, such as peripheral well-defined chorioretinal atrophic patches in patients with CERKL, PROM1, and RPE65 gene mutations and large macular lesions in patients with RDH12 and CRX gene mutations, respectively. Nummular or clump-like pigmentation was noted in CRB1, TTC8, PDE6A, and PDE6B. Conclusion NGS-based genetic testing can help clinicians to diagnose RP more accurately, and phenotypic correlations can also help in better patient counselling with respect to prognosis and guidance regarding ongoing newer gene-based therapies.
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Affiliation(s)
- Parveen Sen
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Natarajan Srikrupa
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Puja Maitra
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Sundaramurthy Srilekha
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Periyasamy Porkodi
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Harshavardhini Gnanasekaran
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Muna Bhende
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Vikas Khetan
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Sinnakaruppan Mathavan
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Pramod Bhende
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Dhanashree Ratra
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Rajiv Raman
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Chetan Rao
- Shri Bhagwan Mahavir Vitreoretinal Services, Medical Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
| | - Sarangapani Sripriya
- SNONGC Department of Genetics and Molecular Biology, Vision Research Foundation, Sankara Nethralaya, Chennai, Tamil Nadu, India
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Lisbjerg K, Bertelsen M, Lyng Forman J, Grønskov K, Prener Holtan J, Kessel L. Disease progression of retinitis pigmentosa caused by PRPF31 variants in a Nordic population: a retrospective study with up to 36 years follow-up. Ophthalmic Genet 2023; 44:139-146. [PMID: 36164253 DOI: 10.1080/13816810.2022.2123006] [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: 10/14/2022]
Abstract
BACKGROUND/AIMS To investigate the natural history of PRPF31-related retinitis pigmentosa (RP11). MATERIALS AND METHODS We identified individuals with RP11 and collected retrospective data from disease onset to present date including genetics, demographic data, Goldmann visual field areas, and visual acuity measurements. Visual fields were evaluated as summed squared degrees and best-corrected visual acuity was converted to logMAR. We performed linear mixed model regression analysis to evaluate annual disease progression, and survival analysis to evaluate the age of legal blindness. RESULTS We included 46 subjects with RP11. Median age of disease onset was 10 years (range 5-65). Follow-up spanned from 0 to 36 years with a median of 8 years. Median Goldmann visual field areas decreased by 10.0% per year (95% CI 7.5%-12.4%) with target IV4e, 7.9% (95% CI 4.5% - 11.2%) with target III4e, and 9.3% (95% CI: 7.0% -11.5%) when combining target sizes. Individuals with RP11 maintained good visual acuity until late stage of disease. Legal blindness was reached at a median age of 57 years (95% CI 50-75 years). CONCLUSIONS PRPF31 variants cause autosomal dominant retinitis pigmentosa that most commonly manifests in childhood with a variable disease progression. Visual field area deteriorates faster than visual acuity and was the major cause of legal blindness in our study population. This study characterizes disease progression in retinitis pigmentosa caused by PRPF31-variants and demonstrates the importance of differentiation between specific genotypes when counselling patients and conducting natural history studies of RP.
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Affiliation(s)
- Kristian Lisbjerg
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet-Glostrup, Copenhagen, Denmark
| | - Mette Bertelsen
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Julie Lyng Forman
- Section of Biostatistics, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Karen Grønskov
- Department of Clinical Genetics, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | | | - Line Kessel
- Department of Ophthalmology, Copenhagen University Hospital - Rigshospitalet-Glostrup, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Gene augmentation prevents retinal degeneration in a CRISPR/Cas9-based mouse model of PRPF31 retinitis pigmentosa. Nat Commun 2022; 13:7695. [PMID: 36509783 PMCID: PMC9744804 DOI: 10.1038/s41467-022-35361-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
Mutations in PRPF31 cause autosomal dominant retinitis pigmentosa, an untreatable form of blindness. Gene therapy is a promising treatment for PRPF31-retinitis pigmentosa, however, there are currently no suitable animal models in which to develop AAV-mediated gene augmentation. Here we establish Prpf31 mutant mouse models using AAV-mediated CRISPR/Cas9 knockout, and characterize the resulting retinal degeneration phenotype. Mouse models with early-onset morphological and functional impairments like those in patients were established, providing new platforms in which to investigate pathogenetic mechanisms and develop therapeutic methods. AAV-mediated PRPF31 gene augmentation restored the retinal structure and function in a rapidly degenerating mouse model, demonstrating the first in vivo proof-of-concept for AAV-mediated gene therapy to treat PRPF31-retinitis pigmentosa. AAV-CRISPR/Cas9-PRPF31 knockout constructs also mediated efficient PRPF31 knockout in human and non-human primate retinal explants, laying a foundation for establishing non-human primate models using the method developed here.
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Modeling PRPF31 retinitis pigmentosa using retinal pigment epithelium and organoids combined with gene augmentation rescue. NPJ Regen Med 2022; 7:39. [PMID: 35974011 PMCID: PMC9381579 DOI: 10.1038/s41536-022-00235-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Mutations in the ubiquitously expressed pre-mRNA processing factor (PRPF) 31 gene, one of the most common causes of dominant form of Retinitis Pigmentosa (RP), lead to a retina-specific phenotype. It is uncertain which retinal cell types are affected and animal models do not clearly present the RP phenotype observed in PRPF31 patients. Retinal organoids and retinal pigment epithelial (RPE) cells derived from human-induced pluripotent stem cells (iPSCs) provide potential opportunities for studying human PRPF31-related RP. We demonstrate here that RPE cells carrying PRPF31 mutations present important morphological and functional changes and that PRPF31-mutated retinal organoids recapitulate the human RP phenotype, with a rod photoreceptor cell death followed by a loss of cones. The low level of PRPF31 expression may explain the defective phenotypes of PRPF31-mutated RPE and photoreceptor cells, which were not observed in cells derived from asymptomatic patients or after correction of the pathogenic mutation by CRISPR/Cas9. Transcriptome profiles revealed differentially expressed and mis-spliced genes belonging to pathways in line with the observed defective phenotypes. The rescue of RPE and photoreceptor defective phenotypes by PRPF31 gene augmentation provide the proof of concept for future therapeutic strategies.
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Georgiou M, Yang C, Atkinson R, Pan K, Buskin A, Molina MM, Collin J, Al‐Aama J, Goertler F, Ludwig SEJ, Davey T, Lührmann R, Nagaraja‐Grellscheid S, Johnson CA, Ali R, Armstrong L, Korolchuk V, Urlaub H, Mozaffari‐Jovin S, Lako M. Activation of autophagy reverses progressive and deleterious protein aggregation in PRPF31 patient-induced pluripotent stem cell-derived retinal pigment epithelium cells. Clin Transl Med 2022; 12:e759. [PMID: 35297555 PMCID: PMC8926896 DOI: 10.1002/ctm2.759] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 02/21/2022] [Accepted: 02/23/2022] [Indexed: 01/18/2023] Open
Abstract
INTRODUCTION Mutations in pre-mRNA processing factor 31 (PRPF31), a core protein of the spliceosomal tri-snRNP complex, cause autosomal-dominant retinitis pigmentosa (adRP). It has remained an enigma why mutations in ubiquitously expressed tri-snRNP proteins result in retina-specific disorders, and so far, the underlying mechanism of splicing factors-related RP is poorly understood. METHODS We used the induced pluripotent stem cell (iPSC) technology to generate retinal organoids and RPE models from four patients with severe and very severe PRPF31-adRP, unaffected individuals and a CRISPR/Cas9 isogenic control. RESULTS To fully assess the impacts of PRPF31 mutations, quantitative proteomics analyses of retinal organoids and RPE cells were carried out showing RNA splicing, autophagy and lysosome, unfolded protein response (UPR) and visual cycle-related pathways to be significantly affected. Strikingly, the patient-derived RPE and retinal cells were characterised by the presence of large amounts of cytoplasmic aggregates containing the mutant PRPF31 and misfolded, ubiquitin-conjugated proteins including key visual cycle and other RP-linked tri-snRNP proteins, which accumulated progressively with time. The mutant PRPF31 variant was not incorporated into splicing complexes, but reduction of PRPF31 wild-type levels led to tri-snRNP assembly defects in Cajal bodies of PRPF31 patient retinal cells, altered morphology of nuclear speckles and reduced formation of active spliceosomes giving rise to global splicing dysregulation. Moreover, the impaired waste disposal mechanisms further exacerbated aggregate formation, and targeting these by activating the autophagy pathway using Rapamycin reduced cytoplasmic aggregates, leading to improved cell survival. CONCLUSIONS Our data demonstrate that it is the progressive aggregate accumulation that overburdens the waste disposal machinery rather than direct PRPF31-initiated mis-splicing, and thus relieving the RPE cells from insoluble cytoplasmic aggregates presents a novel therapeutic strategy that can be combined with gene therapy studies to fully restore RPE and retinal cell function in PRPF31-adRP patients.
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Affiliation(s)
- Maria Georgiou
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Chunbo Yang
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Robert Atkinson
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Kuan‐Ting Pan
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
| | - Adriana Buskin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Joseph Collin
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | - Jumana Al‐Aama
- Faculty of MedicineKing Abdulaziz UniversitySaudi Arabia
| | | | | | - Tracey Davey
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | | | | | | | - Lyle Armstrong
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
| | | | - Henning Urlaub
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Bioanalytics, Department of Clinical ChemistryUniversity Medical CenterGoettingenGermany
| | - Sina Mozaffari‐Jovin
- Max Planck Institute for Multidisciplinary SciencesGöttingenGermany
- Medical Genetics Research CenterMashhad University of Medical SciencesMashhadIran
- Department of Medical Genetics, Faculty of MedicineMashhad University of Medical SciencesMashhadIran
| | - Majlinda Lako
- Newcastle University Biosciences InstituteNewcastle upon TyneUK
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How Far Are Non-Viral Vectors to Come of Age and Reach Clinical Translation in Gene Therapy? Int J Mol Sci 2021; 22:ijms22147545. [PMID: 34299164 PMCID: PMC8304344 DOI: 10.3390/ijms22147545] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/10/2021] [Indexed: 01/14/2023] Open
Abstract
Efficient delivery of genetic material into cells is a critical process to translate gene therapy into clinical practice. In this sense, the increased knowledge acquired during past years in the molecular biology and nanotechnology fields has contributed to the development of different kinds of non-viral vector systems as a promising alternative to virus-based gene delivery counterparts. Consequently, the development of non-viral vectors has gained attention, and nowadays, gene delivery mediated by these systems is considered as the cornerstone of modern gene therapy due to relevant advantages such as low toxicity, poor immunogenicity and high packing capacity. However, despite these relevant advantages, non-viral vectors have been poorly translated into clinical success. This review addresses some critical issues that need to be considered for clinical practice application of non-viral vectors in mainstream medicine, such as efficiency, biocompatibility, long-lasting effect, route of administration, design of experimental condition or commercialization process. In addition, potential strategies for overcoming main hurdles are also addressed. Overall, this review aims to raise awareness among the scientific community and help researchers gain knowledge in the design of safe and efficient non-viral gene delivery systems for clinical applications to progress in the gene therapy field.
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8
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Roshandel D, Thompson JA, Charng J, Zhang D, Chelva E, Arunachalam S, Attia MS, Lamey TM, McLaren TL, De Roach JN, Mackey DA, Wilton SD, Fletcher S, McLenachan S, Chen FK. Exploring microperimetry and autofluorescence endpoints for monitoring disease progression in PRPF31-associated retinopathy. Ophthalmic Genet 2020; 42:1-14. [PMID: 32985313 DOI: 10.1080/13816810.2020.1827442] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
BACKGROUND Mutations in the splicing factor pre-messenger RNA processing factor 31 (PRPF31) gene cause autosomal dominant retinitis pigmentosa 11 (RP11) through a haplo-insufficiency mechanism. We describe the phenotype and progression of microperimetry and autofluorescence endpoints in an Indigenous Australian RP11 family. PATIENTS AND METHODS Ophthalmic examination, optical coherence tomography, fundus autofluorescence and microperimetry were performed at baseline and every 6-12 months. Baseline and annual change in best-corrected visual acuity (BCVA), microperimetry mean sensitivity (MS) and number of scotoma loci, residual ellipsoid zone (EZ) span and hyperautofluorescent ring (HAR) area were reported. Next-generation and Sanger sequencing were performed in available members. RESULTS 12 affected members from three generations were examined. Mean (SD, range) age at onset of symptoms was 11 (4.5, 4-19) years. MS declined steadily from the third decade and EZ span and HAR area declined rapidly during the second decade. Serial microperimetry showed negligible change in MS over 2-3 years. However, mean EZ span, near-infrared and short-wavelength HAR area reduction was 203 (6.4%) µm/year, 1.8 (8.7%) mm2/year and 1.1 (8.6%) mm2/year, respectively. Genetic testing was performed on 11 affected and 10 asymptomatic members and PRPF31 c.1205 C > A (p.Ser402Ter) mutation was detected in all affected and two asymptomatic members (non-penetrant carriers). CONCLUSIONS Our findings suggest that in the studied cohort, the optimal window for therapeutic intervention is the second decade of life and residual EZ span and HAR area can be considered as efficacy outcome measures. Further studies on larger samples with different PRPF31 mutations and longer follow-up duration are recommended.
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Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Jason Charng
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Dan Zhang
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Enid Chelva
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Sukanya Arunachalam
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Mary S Attia
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Tina M Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Terri L McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - John N De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - David A Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia
| | - Steve D Wilton
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Sue Fletcher
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University , Murdoch, Australia.,The Perron Institute, The University of Western Australia , Nedlands, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia
| | - Fred K Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia , Perth, Australia.,Ocular Tissue Engineering Laboratory, Lions Eye Institute , Nedlands, Australia.,Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital , Nedlands, Australia.,Department of Ophthalmology, Royal Perth Hospital , Perth, Australia.,Department of Ophthalmology, Perth Children's Hospital , Nedlands, Australia
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Yang D, Yao Q, Li Y, Xu Y, Wang J, Zhao H, Liu F, Zhang Z, Liu Y, Bie X, Wang Y, Xu L, Luan Y, Yang S, Yang G, He Y. A c.544_618del75bp mutation in the splicing factor gene PRPF31 is involved in non-syndromic retinitis pigmentosa by reducing the level of mRNA expression. Ophthalmic Physiol Opt 2020; 40:289-299. [PMID: 32031697 DOI: 10.1111/opo.12672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 01/02/2020] [Indexed: 01/08/2023]
Abstract
PURPOSE A previous study reported a novel c.544_618del75bp mutation in exon 7 of the PRPF31 gene in a Chinese family with autosomal dominant retinal pigmentosa (ADRP). However, the selected pedigree was a small part of the whole family and the function of the c.544_618del75bp mutation was not explored deeply. The aim of the present study was to validate the previous results and explore the functional significance of the c.544_618del75bp mutation. METHODS We extended the size of the ADRP pedigree and sequenced DNA and cDNA of the PRPF31 gene for all members of the family and 100 healthy controls. Real-time quantitative polymerase chain reaction (PCR) analysis was performed on the cDNA of patients in the family and cell culture, plasmids transfection and western blot analysis were done to evaluate the functional effect of the mutation in vitro. RESULTS Sanger sequencing showed that the mutation was present in all patients and absent in all normal individuals, except for participant III-9. Bioinformatics analysis revealed that the c.544_618del75bp mutation caused a 25 amino acid deletion in the PRPF31 protein. In addition, the mRNA expression assay revealed that the mRNA expression level of the PRPF31 and RP9 genes were significantly lower in RP patients than controls (p < 0.05). Finally, the in vitro transfection assay demonstrated that the mRNA expression level of the mutant transfection group was significantly lower than the wild-type transfection group (p < 0.05). CONCLUSIONS Our study suggested that the c.544_618del75bp mutation in the PRPF31 gene was a causative mutation in this ADRP family and affected the expression of RP9 gene by influencing the formation of U4/U6-U5 tri-snRNP, eventually leading to the occurrence of RP.
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Affiliation(s)
- Dongzhi Yang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Qihui Yao
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ya Li
- Henan Eye Institute, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yan Xu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jun Wang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Huiling Zhao
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Fuyong Liu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhaojing Zhang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yang Liu
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Xiaoshuai Bie
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Yuanli Wang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liyan Xu
- Henan Eye Institute, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yingying Luan
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shangdong Yang
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ge Yang
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying He
- Department of Medical Genetics & Cell Biology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
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10
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Mutation spectrum of PRPF31, genotype-phenotype correlation in retinitis pigmentosa, and opportunities for therapy. Exp Eye Res 2020; 192:107950. [PMID: 32014492 PMCID: PMC7065041 DOI: 10.1016/j.exer.2020.107950] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 01/13/2020] [Accepted: 01/27/2020] [Indexed: 12/11/2022]
Abstract
Pathogenic variants in pre-messenger RNA (pre-mRNA) splicing factor 31, PRPF31, are the second most common genetic cause of autosomal dominant retinitis pigmentosa (adRP) in most populations. This remains a completely untreatable and incurable form of blindness, and it can be difficult to predict the clinical course of disease. In order to design appropriate targeted therapies, a thorough understanding of the genetics and molecular mechanism of this disease is required. Here, we present the structure of the PRPF31 gene and PRPF31 protein, current understanding of PRPF31 protein function and the full spectrum of all reported clinically relevant variants in PRPF31. We delineate the correlation between specific PRPF31 genotype and RP phenotype, suggesting that, except in cases of complete gene deletion or large-scale deletions, dominant negative effects contribute to phenotype as well as haploinsufficiency. This has important impacts on design of targeted therapies, particularly the feasibility of gene augmentation as a broad approach for treatment of PRPF31-associated RP. We discuss other opportunities for therapy, including antisense oligonucleotide therapy and gene-independent approaches and offer future perspectives on treatment of this form of RP. PRPF31 is the second most common cause of autosomal dominant retinitis pigmentosa and a potential target for gene therapy. We present all reported pathogenic variants in PRPF31 as a resource for clinicians, diagnostic genetics labs, and researchers. Genotype-phenotype correlations suggest that, dominant negative effects contribute to disease in addition to haploinsufficiency. This finding has important impacts on the suitability of gene augmentation approaches across all mutation types. This finding may aid prognosis of disease in PRPF31-associated RP patients.
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11
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Booth KT, Azaiez H, Kahrizi K, Wang D, Zhang Y, Frees K, Nishimura C, Najmabadi H, Smith RJ. Exonic mutations and exon skipping: Lessons learned from DFNA5. Hum Mutat 2018; 39:433-440. [PMID: 29266521 PMCID: PMC5805621 DOI: 10.1002/humu.23384] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 11/27/2017] [Accepted: 12/12/2017] [Indexed: 02/06/2023]
Abstract
Dysregulation of splicing is a common factor underlying many inherited diseases including deafness. For one deafness-associated gene, DFNA5, perturbation of exon 8 splicing results in a constitutively active truncated protein. To date, only intronic mutations have been reported to cause exon 8 skipping in patients with DFNA5-related deafness. In five families with postlingual progressive autosomal dominant non-syndromic hearing loss, we employed two next-generation sequencing platforms-OtoSCOPE and whole exome sequencing-followed by variant filtering and prioritization based on both minor allele frequency and functional consequence using a customized bioinformatics pipeline to identify three novel and two recurrent mutations in DFNA5 that segregated with hearing loss in these families. The three novel mutations are all missense variants within exon 8 that are predicted computationally to decrease splicing efficiency or abolish it completely. We confirmed their functional impact in vitro using mini-genes carrying each mutant DFNA5 exon 8. In so doing, we present the first exonic mutations in DFNA5 to cause deafness, expand the mutational spectrum of DFNA5-related hearing loss, and highlight the importance of assessing the effect of coding variants on splicing.
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Affiliation(s)
- Kevin T Booth
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
- The Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Hela Azaiez
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Donghong Wang
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Yuzhou Zhang
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Kathy Frees
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Carla Nishimura
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Richard J Smith
- Department of Otolaryngology-Head Neck Surgery, Molecular Otolaryngology Renal Research Laboratories, University of Iowa, Iowa City, Iowa
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12
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Zheng Y, Wang HL, Li JK, Xu L, Tellier L, Li XL, Huang XY, Li W, Niu TT, Yang HM, Zhang JG, Liu DN. A novel mutation in PRPF31, causative of autosomal dominant retinitis pigmentosa, using the BGISEQ-500 sequencer. Int J Ophthalmol 2018; 11:31-35. [PMID: 29375987 DOI: 10.18240/ijo.2018.01.06] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/13/2017] [Indexed: 11/23/2022] Open
Abstract
AIM To study the genes responsible for retinitis pigmentosa. METHODS A total of 15 Chinese families with retinitis pigmentosa, containing 94 sporadically afflicted cases, were recruited. The targeted sequences were captured using the Target_Eye_365_V3 chip and sequenced using the BGISEQ-500 sequencer, according to the manufacturer's instructions. Data were aligned to UCSC Genome Browser build hg19, using the Burroughs Wheeler Aligner MEM algorithm. Local realignment was performed with the Genome Analysis Toolkit (GATK v.3.3.0) IndelRealigner, and variants were called with the Genome Analysis Toolkit Haplotypecaller, without any use of imputation. Variants were filtered against a panel derived from 1000 Genomes Project, 1000G_ASN, ESP6500, ExAC and dbSNP138. In all members of Family ONE and Family TWO with available DNA samples, the genetic variant was validated using Sanger sequencing. RESULTS A novel, pathogenic variant of retinitis pigmentosa, c.357_358delAA (p.Ser119SerfsX5) was identified in PRPF31 in 2 of 15 autosomal-dominant retinitis pigmentosa (ADRP) families, as well as in one, sporadic case. Sanger sequencing was performed upon probands, as well as upon other family members. This novel, pathogenic genotype co-segregated with retinitis pigmentosa phenotype in these two families. CONCLUSION ADRP is a subtype of retinitis pigmentosa, defined by its genotype, which accounts for 20%-40% of the retinitis pigmentosa patients. Our study thus expands the spectrum of PRPF31 mutations known to occur in ADRP, and provides further demonstration of the applicability of the BGISEQ500 sequencer for genomics research.
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Affiliation(s)
- Yu Zheng
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Hai-Lin Wang
- The Fourth People's Hospital of Shenyang, Shenyang 110031, Liaoning Province, China
| | - Jian-Kang Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Li Xu
- The Fourth People's Hospital of Shenyang, Shenyang 110031, Liaoning Province, China
| | - Laurent Tellier
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Xiao-Lin Li
- The Fourth People's Hospital of Shenyang, Shenyang 110031, Liaoning Province, China
| | - Xiao-Yan Huang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.,BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Wei Li
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Tong-Tong Niu
- The Fourth People's Hospital of Shenyang, Shenyang 110031, Liaoning Province, China
| | - Huan-Ming Yang
- BGI-Shenzhen, Shenzhen 518083, China.,James D. Watson Institute of Genome Sciences, Hangzhou 310058, China
| | - Jian-Guo Zhang
- BGI-Shenzhen, Shenzhen 518083, China.,China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Dong-Ning Liu
- The Fourth People's Hospital of Shenyang, Shenyang 110031, Liaoning Province, China
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13
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Huang D, Fletcher S, Wilton SD, Palmer N, McLenachan S, Mackey DA, Chen FK. Inherited Retinal Disease Therapies Targeting Precursor Messenger Ribonucleic Acid. Vision (Basel) 2017; 1:vision1030022. [PMID: 31740647 PMCID: PMC6836112 DOI: 10.3390/vision1030022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Revised: 07/24/2017] [Accepted: 08/24/2017] [Indexed: 02/07/2023] Open
Abstract
Inherited retinal diseases are an extremely diverse group of genetically and phenotypically heterogeneous conditions characterized by variable maturation of retinal development, impairment of photoreceptor cell function and gradual loss of photoreceptor cells and vision. Significant progress has been made over the last two decades in identifying the many genes implicated in inherited retinal diseases and developing novel therapies to address the underlying genetic defects. Approximately one-quarter of exonic mutations related to human inherited diseases are likely to induce aberrant splicing products, providing opportunities for the development of novel therapeutics that target splicing processes. The feasibility of antisense oligomer mediated splice intervention to treat inherited diseases has been demonstrated in vitro, in vivo and in clinical trials. In this review, we will discuss therapeutic approaches to treat inherited retinal disease, including strategies to correct splicing and modify exon selection at the level of pre-mRNA. The challenges of clinical translation of this class of emerging therapeutics will also be discussed.
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Affiliation(s)
- Di Huang
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Sue Fletcher
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Steve D. Wilton
- Molecular Therapy Laboratory, Murdoch University, Murdoch 6150, Australia
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Norman Palmer
- Perron Institute, 4th Floor A Block, Queen Elizabeth II Medical Centre, Verdun Street, Nedlands 6009, Australia
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science (Incorporating Lions Eye Institute), The University of Western Australia, Nedlands 6009, Australia
- Department of Ophthalmology, Royal Perth Hospital, Perth 6000, Australia
- Correspondence: ; Tel.: +61-8-9381-0817
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14
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Murray RD, Merchant ML, Hardin E, Clark B, Khundmiri SJ, Lederer ED. Identification of an RNA-binding protein that is phosphorylated by PTH and potentially mediates PTH-induced destabilization of Npt2a mRNA. Am J Physiol Cell Physiol 2015; 310:C205-15. [PMID: 26834145 DOI: 10.1152/ajpcell.00192.2015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/19/2015] [Indexed: 12/19/2022]
Abstract
Parathyroid hormone (PTH) is a key regulator of the expression and function of the type IIa sodium-phosphate cotransporter (Npt2a), the protein responsible for regulated renal phosphate reabsorption. We previously showed that PTH induces rapid decay of Npt2a mRNA through posttranscriptional mechanisms. We hypothesized that PTH-induced changes in RNA-binding protein (RBP) activity mediate the degradation of Npt2a mRNA. To address this aim, we treated opossum kidney (OK) cells, a PTH-sensitive proximal tubule cell culture model, with 100 nM PTH for 30 min and 2 h, followed by mass spectrometry characterization of the PTH-stimulated phosphoproteome. We identified 1,182 proteins differentially phosphorylated in response to PTH, including 68 RBPs. Preliminary analysis identified a phospho-RBP, hnRNPK-homology-type-splicing regulatory protein (KSRP), with predicted binding sites for the 3'-untranslated region (UTR) of Npt2a mRNA. Western blot analysis confirmed expression of KSRP in OK cells and showed PTH-dependent translocation to the nucleus. Immunoprecipitation of KSRP from control and PTH-treated cells followed by RNA isolation and RT-quantitative PCR analysis identified Npt2a mRNA from both control and PTH-treated KSRP pulldowns. Knockdown of KSRP followed by PTH treatment showed that KSRP is required for mediating PTH-stimulated reduction in sodium/hydrogen exchanger 3 mRNA, but not Npt2a mRNA. We conclude that 1) PTH is a major regulator of both transcription and translation, and 2) KSRP binds Npt2a mRNA but its role in PTH regulation of Npt2a mRNA is not clear.
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Affiliation(s)
- Rebecca D Murray
- Department of Physiology and Biophysics, University of Louisville, Louisville, Kentucky; Department of Medicine/Kidney Disease Program, University of Louisville, Louisville, Kentucky
| | - Michael L Merchant
- Department of Medicine/Kidney Disease Program, University of Louisville, Louisville, Kentucky
| | - Ericka Hardin
- Western Kentucky University, Bowling Green, Kentucky; and
| | - Barbara Clark
- Department of Biochemistry, University of Louisville, Louisville, Kentucky
| | - Syed J Khundmiri
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky; Department of Physiology and Biophysics, University of Louisville, Louisville, Kentucky; Department of Medicine/Kidney Disease Program, University of Louisville, Louisville, Kentucky
| | - Eleanor D Lederer
- Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky; Department of Physiology and Biophysics, University of Louisville, Louisville, Kentucky; Department of Medicine/Kidney Disease Program, University of Louisville, Louisville, Kentucky;
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15
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Bizarro J, Dodré M, Huttin A, Charpentier B, Schlotter F, Branlant C, Verheggen C, Massenet S, Bertrand E. NUFIP and the HSP90/R2TP chaperone bind the SMN complex and facilitate assembly of U4-specific proteins. Nucleic Acids Res 2015; 43:8973-89. [PMID: 26275778 PMCID: PMC4605303 DOI: 10.1093/nar/gkv809] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 07/27/2015] [Indexed: 12/17/2022] Open
Abstract
The Sm proteins are loaded on snRNAs by the SMN complex, but how snRNP-specific proteins are assembled remains poorly characterized. U4 snRNP and box C/D snoRNPs have structural similarities. They both contain the 15.5K and proteins with NOP domains (PRP31 for U4, NOP56/58 for snoRNPs). Biogenesis of box C/D snoRNPs involves NUFIP and the HSP90/R2TP chaperone system and here, we explore the function of this machinery in U4 RNP assembly. We show that yeast Prp31 interacts with several components of the NUFIP/R2TP machinery, and that these interactions are separable from each other. In human cells, PRP31 mutants that fail to stably associate with U4 snRNA still interact with components of the NUFIP/R2TP system, indicating that these interactions precede binding of PRP31 to U4 snRNA. Knock-down of NUFIP leads to mislocalization of PRP31 and decreased association with U4. Moreover, NUFIP is associated with the SMN complex through direct interactions with Gemin3 and Gemin6. Altogether, our data suggest a model in which the NUFIP/R2TP system is connected with the SMN complex and facilitates assembly of U4 snRNP-specific proteins.
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Affiliation(s)
- Jonathan Bizarro
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Maxime Dodré
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Alexandra Huttin
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Florence Schlotter
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Céline Verheggen
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
| | - Séverine Massenet
- Ingénierie Moléculaire et Physiopathologie Articulaire, UMR 7365 CNRS-Université de Lorraine, Biopôle de l'Université de Lorraine, avenue de la forêt de Haye, BP 184, 54505 Vandoeuvre-les-Nancy Cedex, France
| | - Edouard Bertrand
- Equipe labélisée Ligue contre le Cancer, Institut de Génétique Moléculaire de Montpellier, IGMM-UMR 5535 du CNRS-Université de Montpellier, 1919, route de Mende, 34293 Montpellier Cedex 5, France
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16
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Abstract
One of the most amazing findings in molecular biology was the discovery that eukaryotic genes are discontinuous, with coding DNA being interrupted by stretches of non-coding sequence. The subsequent realization that the intervening regions are removed from pre-mRNA transcripts via the activity of a common set of small nuclear RNAs (snRNAs), which assemble together with associated proteins into a complex known as the spliceosome, was equally surprising. How do cells coordinate the assembly of this molecular machine? And how does the spliceosome accurately recognize exons and introns to carry out the splicing reaction? Insights into these questions have been gained by studying the life cycle of spliceosomal snRNAs from their transcription, nuclear export and re-import to their dynamic assembly into the spliceosome. This assembly process can also affect the regulation of alternative splicing and has implications for human disease.
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Affiliation(s)
- A Gregory Matera
- Department of Biology, Department of Genetics and Integrative Program for Biological and Genome Sciences, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Zefeng Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
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17
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Rose AM, Shah AZ, Venturini G, Rivolta C, Rose GE, Bhattacharya SS. Dominant PRPF31 mutations are hypostatic to a recessive CNOT3 polymorphism in retinitis pigmentosa: a novel phenomenon of "linked trans-acting epistasis". Ann Hum Genet 2013; 78:62-71. [PMID: 24116917 PMCID: PMC4240469 DOI: 10.1111/ahg.12042] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/01/2013] [Indexed: 12/31/2022]
Abstract
Mutations in PRPF31 are responsible for autosomal dominant retinitis pigmentosa (adRP, RP11 form) and affected families show nonpenetrance. Differential expression of the wildtype PRPF31 allele is responsible for this phenomenon: coinheritance of a mutation and a higher expressing wildtype allele provide protection against development of disease. It has been suggested that a major modulating factor lies in close proximity to the wildtype PRPF31 gene on Chromosome 19, implying that a cis-acting factor directly alters PRPF31 expression. Variable expression of CNOT3 is one determinant of PRPF31 expression. This study explored the relationship between CNOT3 (a trans-acting factor) and its paradoxical cis-acting nature in relation to RP11. Linkage analysis on Chromosome 19 was performed in mutation-carrying families, and the inheritance of the wildtype PRPF31 allele in symptomatic–asymptomatic sibships was assessed—confirming that differential inheritance of wildtype chromosome 19q13 determines the clinical phenotype (P < 2.6 × 10−7). A theoretical model was constructed that explains the apparent conflict between the linkage data and the recent demonstration that a trans-acting factor (CNOT3) is a major nonpenetrance factor: we propose that this apparently cis-acting effect arises due to the intimate linkage of CNOT3 and PRPF31 on Chromosome 19q13—a novel mechanism that we have termed “linked trans-acting epistasis.”
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Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
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18
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Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013; 132:1077-130. [PMID: 23820649 PMCID: PMC3778950 DOI: 10.1007/s00439-013-1331-2] [Citation(s) in RCA: 417] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 06/15/2013] [Indexed: 02/06/2023]
Abstract
Some individuals with a particular disease-causing mutation or genotype fail to express most if not all features of the disease in question, a phenomenon that is known as 'reduced (or incomplete) penetrance'. Reduced penetrance is not uncommon; indeed, there are many known examples of 'disease-causing mutations' that fail to cause disease in at least a proportion of the individuals who carry them. Reduced penetrance may therefore explain not only why genetic diseases are occasionally transmitted through unaffected parents, but also why healthy individuals can harbour quite large numbers of potentially disadvantageous variants in their genomes without suffering any obvious ill effects. Reduced penetrance can be a function of the specific mutation(s) involved or of allele dosage. It may also result from differential allelic expression, copy number variation or the modulating influence of additional genetic variants in cis or in trans. The penetrance of some pathogenic genotypes is known to be age- and/or sex-dependent. Variable penetrance may also reflect the action of unlinked modifier genes, epigenetic changes or environmental factors. At least in some cases, complete penetrance appears to require the presence of one or more genetic variants at other loci. In this review, we summarize the evidence for reduced penetrance being a widespread phenomenon in human genetics and explore some of the molecular mechanisms that may help to explain this enigmatic characteristic of human inherited disease.
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Affiliation(s)
- David N. Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN UK
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Christian-Albrechts University, 24105 Kiel, Germany
| | | | - Chris Tyler-Smith
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
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