1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Daich Varela M, Sen S, De Guimaraes TAC, Kabiri N, Pontikos N, Balaskas K, Michaelides M. Artificial intelligence in retinal disease: clinical application, challenges, and future directions. Graefes Arch Clin Exp Ophthalmol 2023; 261:3283-3297. [PMID: 37160501 PMCID: PMC10169139 DOI: 10.1007/s00417-023-06052-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/20/2023] [Accepted: 03/24/2023] [Indexed: 05/11/2023] Open
Abstract
Retinal diseases are a leading cause of blindness in developed countries, accounting for the largest share of visually impaired children, working-age adults (inherited retinal disease), and elderly individuals (age-related macular degeneration). These conditions need specialised clinicians to interpret multimodal retinal imaging, with diagnosis and intervention potentially delayed. With an increasing and ageing population, this is becoming a global health priority. One solution is the development of artificial intelligence (AI) software to facilitate rapid data processing. Herein, we review research offering decision support for the diagnosis, classification, monitoring, and treatment of retinal disease using AI. We have prioritised diabetic retinopathy, age-related macular degeneration, inherited retinal disease, and retinopathy of prematurity. There is cautious optimism that these algorithms will be integrated into routine clinical practice to facilitate access to vision-saving treatments, improve efficiency of healthcare systems, and assist clinicians in processing the ever-increasing volume of multimodal data, thereby also liberating time for doctor-patient interaction and co-development of personalised management plans.
Collapse
Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | | | | | - Nikolas Pontikos
- UCL Institute of Ophthalmology, London, UK
- Moorfields Eye Hospital, London, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London, UK.
- Moorfields Eye Hospital, London, UK.
| |
Collapse
|
3
|
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: 8] [Impact Index Per Article: 4.0] [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.
Collapse
|
4
|
Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
Collapse
Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, 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 M13 9WL, 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 M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, 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 M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, 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 M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
| |
Collapse
|
5
|
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.
Collapse
|
6
|
Xie D, Peng K, Yi Q, Liu W, Yang Y, Sun K, Zhu X, Lu F. Targeted Next Generation Sequencing Revealed Novel PRPF31 Mutations in Autosomal Dominant Retinitis Pigmentosa. Genet Test Mol Biomarkers 2018; 22:425-432. [PMID: 29957067 DOI: 10.1089/gtmb.2018.0036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Retinitis pigmentosa (RP) is a rare type of inherited retinal dystrophy that can result in progressive vision loss. Molecular diagnosis of RP is challenging due to phenotypic and genotypic heterogeneities. AIMS This study aimed to identify the pathogenic mutations in two Chinese families with autosomal dominant RP (adRP) and in a patient with sporadic RP. MATERIALS AND METHODS Peripheral blood DNA samples were obtained from the participants. Targeted next generation sequencing (NGS) was applied to identify mutations in these patients. For pathogenic mutation analyses, stringent NGS data analyses and segregation analyses were applied. Primers were designed to validate the identified mutations by Sanger sequencing analyses. RESULTS A novel heterozygous insertion frameshift mutation c.1226_1227insA, p.T410Dfs*65, and a novel heterozygous stopgain mutation c.1015C>T, p.Q339* were identified in PRPF31. A known c.527 + 3A>G splicing mutation was identified in one of the adRP-074 families. All mutations were found to co-segregate with the disease, and none of these mutations were detected in 500 control samples. CONCLUSIONS Our data identified two new autosomal dominant mutations in PRPF31, expanding the mutational spectrum of this gene.
Collapse
Affiliation(s)
- Dan Xie
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Kun Peng
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Qian Yi
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Wenjinag Liu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Yeming Yang
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Kuanxiang Sun
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China
| | - Xianjun Zhu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China .,3 Institute of Laboratory Animal Sciences, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| | - Fang Lu
- 1 Sichuan Provincial Key Laboratory for Human Disease Gene Study, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China , Chengdu, Sichuan, China .,2 Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, Sichuan Translational Medicine Research Hospital , Chengdu, Sichuan, China
| |
Collapse
|
7
|
Rose AM, Bhattacharya SS. Variant haploinsufficiency and phenotypic non-penetrance in PRPF31-associated retinitis pigmentosa. Clin Genet 2016; 90:118-26. [PMID: 26853529 DOI: 10.1111/cge.12758] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 11/30/2022]
Abstract
Retinitis pigmentosa (RP) is a genetically heterogenous group of inherited disorders, characterized by death of the retinal photoreceptor cells, leading to progressive visual impairment. One form of RP is caused by mutations in the ubiquitously expressed splicing factor, PRPF31, this form being known as RP11. An intriguing feature of RP11 is the presence of non-penetrance, which has been observed in the majority of PRPF31 mutation-carrying families. In contrast to variable expressivity, which is highly pervasive, true non-penetrance is a very rare phenomenon in Mendelian disorders. In this article, the molecular mechanisms underlying phenotypic non-penetrance in RP11 are explored. It is an elegant example of how our understanding of monogenic disorders has evolved from studying only the disease gene, to considering a mutation on the genetic background of the individual - the logical evolution in this genomic era.
Collapse
Affiliation(s)
- A M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| | - S S Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, London, UK
| |
Collapse
|
8
|
Rose AM, Shah AZ, Venturini G, Krishna A, Chakravarti A, Rivolta C, Bhattacharya SS. Transcriptional regulation of PRPF31 gene expression by MSR1 repeat elements causes incomplete penetrance in retinitis pigmentosa. Sci Rep 2016; 6:19450. [PMID: 26781568 PMCID: PMC4725990 DOI: 10.1038/srep19450] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 12/14/2015] [Indexed: 11/26/2022] Open
Abstract
PRPF31-associated retinitis pigmentosa presents a fascinating enigma: some mutation carriers are blind, while others are asymptomatic. We identify the major molecular cause of this incomplete penetrance through three cardinal features: (1) there is population variation in the number (3 or 4) of a minisatellite repeat element (MSR1) adjacent to the PRPF31 core promoter; (2) in vitro, 3-copies of the MSR1 element can repress gene transcription by 50 to 115-fold; (3) the higher-expressing 4-copy allele is not observed among symptomatic PRPF31 mutation carriers and correlates with the rate of asymptomatic carriers in different populations. Thus, a linked transcriptional modifier decreases PRPF31 gene expression that leads to haploinsufficiency. This result, taken with other identified risk alleles, allows precise genetic counseling for the first time. We also demonstrate that across the human genome, the presence of MSR1 repeats in the promoters or first introns of genes is associated with greater population variability in gene expression indicating that copy number variation of MSR1s is a generic controller of gene expression and promises to provide new insights into our understanding of gene expression regulation.
Collapse
Affiliation(s)
- Anna M. Rose
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Amna Z. Shah
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
| | - Giulia Venturini
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
| | - Abhay Krishna
- Department of Cell Therapy and Regenerative Medicine, CABIMER, 41092 Seville, Spain
| | - Aravinda Chakravarti
- Johns Hopkins University School of Medicine, Institute of Genetic Medicine, 733 N. Broadway MRB 579 Baltimore, MD 21287, USA
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, 1005 Lausanne, Switzerland
| | | |
Collapse
|
9
|
Coppieters F, Todeschini AL, Fujimaki T, Baert A, De Bruyne M, Van Cauwenbergh C, Verdin H, Bauwens M, Ongenaert M, Kondo M, Meire F, Murakami A, Veitia RA, Leroy BP, De Baere E. Hidden Genetic Variation in LCA9-Associated Congenital Blindness Explained by 5'UTR Mutations and Copy-Number Variations of NMNAT1. Hum Mutat 2015; 36:1188-96. [PMID: 26316326 PMCID: PMC5054839 DOI: 10.1002/humu.22899] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
Leber congenital amaurosis (LCA) is a severe autosomal‐recessive retinal dystrophy leading to congenital blindness. A recently identified LCA gene is NMNAT1, located in the LCA9 locus. Although most mutations in blindness genes are coding variations, there is accumulating evidence for hidden noncoding defects or structural variations (SVs). The starting point of this study was an LCA9‐associated consanguineous family in which no coding mutations were found in the LCA9 region. Exploring the untranslated regions of NMNAT1 revealed a novel homozygous 5′UTR variant, c.‐70A>T. Moreover, an adjacent 5′UTR variant, c.‐69C>T, was identified in a second consanguineous family displaying a similar phenotype. Both 5′UTR variants resulted in decreased NMNAT1 mRNA abundance in patients’ lymphocytes, and caused decreased luciferase activity in human retinal pigment epithelial RPE‐1 cells. Second, we unraveled pseudohomozygosity of a coding NMNAT1 mutation in two unrelated LCA patients by the identification of two distinct heterozygous partial NMNAT1 deletions. Molecular characterization of the breakpoint junctions revealed a complex Alu‐rich genomic architecture. Our study uncovered hidden genetic variation in NMNAT1‐associated LCA and emphasized a shift from coding to noncoding regulatory mutations and repeat‐mediated SVs in the molecular pathogenesis of heterogeneous recessive disorders such as hereditary blindness.
Collapse
Affiliation(s)
| | | | - Takuro Fujimaki
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Annelot Baert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | | | | | - Hannah Verdin
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Maté Ongenaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie, Japan
| | - Françoise Meire
- Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Reiner A Veitia
- Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| |
Collapse
|
10
|
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.”
Collapse
Affiliation(s)
- Anna M Rose
- Department of Genetics, UCL Institute of Ophthalmology, London, United Kingdom
| | | | | | | | | | | |
Collapse
|
11
|
Utz VM, Beight CD, Marino MJ, Hagstrom SA, Traboulsi EI. Autosomal dominant retinitis pigmentosa secondary to pre-mRNA splicing-factor gene PRPF31 (RP11): review of disease mechanism and report of a family with a novel 3-base pair insertion. Ophthalmic Genet 2013; 34:183-8. [PMID: 23343310 DOI: 10.3109/13816810.2012.762932] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Several forms of autosomal dominant retinitis pigmentosa (adRP) are caused by mutations in genes encoding proteins that are ubiquitously expressed and involved in the pre-mRNA spliceosome such as PRPF31. This paper provides an overview of the molecular genetics, pathophysiology, and mechanism for incomplete penetrance and retina-specific disease in pedigrees of families who harbor mutations in PRPF31 (RP11). The molecular and clinical features of a family with a novel 3-base insertion, c.914_915insTGT (p.Val305_Asp306insVal) in exon 9 of PRPF31 are described to illustrate the salient clinical features of mutations in this gene.
Collapse
Affiliation(s)
- Virginia M Utz
- Cole Eye Institute, Cleveland Clinic , Cleveland, OH , USA , and
| | | | | | | | | |
Collapse
|
12
|
Venturini G, Rose AM, Shah AZ, Bhattacharya SS, Rivolta C. CNOT3 is a modifier of PRPF31 mutations in retinitis pigmentosa with incomplete penetrance. PLoS Genet 2012; 8:e1003040. [PMID: 23144630 PMCID: PMC3493449 DOI: 10.1371/journal.pgen.1003040] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/05/2012] [Indexed: 01/23/2023] Open
Abstract
Heterozygous mutations in the PRPF31 gene cause autosomal dominant retinitis pigmentosa (adRP), a hereditary disorder leading to progressive blindness. In some cases, such mutations display incomplete penetrance, implying that certain carriers develop retinal degeneration while others have no symptoms at all. Asymptomatic carriers are protected from the disease by a higher than average expression of the PRPF31 allele that is not mutated, mainly through the action of an unknown modifier gene mapping to chromosome 19q13.4. We investigated a large family with adRP segregating an 11-bp deletion in PRPF31. The analysis of cell lines derived from asymptomatic and affected individuals revealed that the expression of only one gene among a number of candidates within the 19q13.4 interval significantly correlated with that of PRPF31, both at the mRNA and protein levels, and according to an inverse relationship. This gene was CNOT3, encoding a subunit of the Ccr4-not transcription complex. In cultured cells, siRNA–mediated silencing of CNOT3 provoked an increase in PRPF31 expression, confirming a repressive nature of CNOT3 on PRPF31. Furthermore, chromatin immunoprecipitation revealed that CNOT3 directly binds to a specific PRPF31 promoter sequence, while next-generation sequencing of the CNOT3 genomic region indicated that its variable expression is associated with a common intronic SNP. In conclusion, we identify CNOT3 as the main modifier gene determining penetrance of PRPF31 mutations, via a mechanism of transcriptional repression. In asymptomatic carriers CNOT3 is expressed at low levels, allowing higher amounts of wild-type PRPF31 transcripts to be produced and preventing manifestation of retinal degeneration. Retinitis pigmentosa (RP) is an inherited disorder of the retina that is caused by mutations in more than 50 genes. Dominant mutations in one of these, PRPF31, can be non-penetrant. That is, some carriers of mutations suffer from the disease while others do not display any symptoms. In these particular individuals, functional PRPF31 transcripts are expressed at higher levels compared to affected persons, thus compensating for the deleterious effects of the mutated allele. Up to now, the nature of such a stochastic and protective effect was unknown. In this work, we identify CNOT3 as the modifier gene responsible for penetrance of PRPF31 mutations. We show that CNOT3 is a negative regulator of PRPF31 expression and modulates PRPF31 transcription by directly binding to its promoter. In asymptomatic carriers of mutations, CNOT3 expression is lower, allowing higher amounts of PRPF31 to be produced and therefore inhibiting the development of symptoms. Finally, we find that a polymorphism within a CNOT3 intronic region is associated with the clinical manifestation of the disease.
Collapse
Affiliation(s)
- Giulia Venturini
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Anna M. Rose
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Amna Z. Shah
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Shomi S. Bhattacharya
- Department of Genetics, UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- * E-mail:
| |
Collapse
|