1
|
Leenders M, Gaastra M, Jayagopal A, Malone KE. Prevalence estimates and genetic diversity for autosomal dominant retinitis pigmentosa due to RHO, c.68C>A (p.P23H) variant. Am J Ophthalmol 2024:S0002-9394(24)00404-5. [PMID: 39278389 DOI: 10.1016/j.ajo.2024.08.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/18/2024]
Abstract
OBJECTIVE To provide the most up-to-date clinical prevalence estimate for autosomal dominant retinitis pigmentosa (adRP) patients due to RHO c.68C>A, (p.P23H) in the United States, supported by two independent approaches; literature based meta-analysis of reported patients and population genetics modeling. DESIGN Systematic review and meta-analysis plus population genetics modeling. METHODS Systematic review of the literature describing RP patients attributed to RHO variants was conducted to support a meta-analysis used to estimate the clinical prevalence of the RHO P23H patients diagnosed in the US. In parallel, large-scale genetic diversity studies describing the US population and non-European cohorts of the Americas (PAGE II), were evaluated to ascertain the allele frequencies of variant RHO c.68C>A, (p.P23H). The genetic prevalence for variant RHO c.68C>A, (p.P23H) was calculated using Hardy-Weinberg equilibrium. Further demographic data, including age and average age of onset for visual impairment were incorporated into a basic distribution model to estimate clinical prevalence of genetically predisposed persons. RESULTS The estimated clinical prevalence of adRP due to RHO P23H based on literature review was approximately 2000-3000 patients. In comparison the genetic prevalence of persons with RHO c.68C>A, (p.P23H) in the United States was an estimated 6176 (90% CI: 3333-11398) and only half of them are expected to cluster with European genetic ancestry. This variant was found enriched in subgroups of African American or other non-European biogeographic ancestries. Of the estimated 6200 persons carrying this variant in the US, ∼3500 (estimate range: 1900-6500) are expected to show clinical signs of visual impairment as modeled by average age of onset previously reported for patients with this variant. CONCLUSIONS We utilized two independent approaches to estimate the total number of adRP patients due to RHO c.68C>A, (p.P23H) in the United States; systematic literature review based meta-analysis and population genetics modeling. Both approaches yielded similar, overlapping estimates of adRP patients due to RHO P23H. However, comparison of these estimates provides some indication for a diagnosis gap. Unexpectedly, this variant is present at relatively higher frequency in some predominantly non-European genetic ancestries in the US. While this genetic analysis supports our estimates of clinical prevalence of adRP due to RHO P23H in the United States, it also has implications for diagnosing potential adRP patients due to this variant, raising questions of genotype-phenotype correlation and access to genetic testing.
Collapse
Affiliation(s)
- Matthijs Leenders
- TU Delft, Mekelweg 5, 2628 CD Delft, the Netherlands; Erasmus MC, Dr. Molewaterplein 40, 3015 GD Rotterdam, the Netherlands; GeneScape, Leiden, the Netherlands
| | | | - Ash Jayagopal
- Opus Genetics, 8 Davis Drive Suite 220, Durham, NC 27709; Ocuphire Pharma, 37000 Grand River Ave., Suite 120, Farmington Hills, MI 48335
| | | |
Collapse
|
2
|
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.
Collapse
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.
| |
Collapse
|
3
|
Eid AT, Eid KT, Odom JV, Hinkle D, Leys M. Autosomal Dominant Retinitis Pigmentosa Secondary to TOPORS Mutations: A Report of a Novel Mutation and Clinical Findings. J Clin Med 2024; 13:1498. [PMID: 38592336 PMCID: PMC10934045 DOI: 10.3390/jcm13051498] [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: 01/03/2024] [Revised: 02/19/2024] [Accepted: 02/20/2024] [Indexed: 04/10/2024] Open
Abstract
Purpose: Mutations in Topoisomerase I-binding RS protein (TOPORS) have been previously documented and have been described to result in pathological autosomal dominant retinitis pigmentosa (adRP). In our study, we describe the various genotypes and clinical/phenotypic manifestations of TOPORS-related mutations of our unique patient population in Rural Appalachia. Methods: The medical records of 416 patients with inherited retinal disease at the West Virginia University Eye Institute who had undergone genetic testing between the years of 2015-2022 were reviewed. Patients found to have pathologic RP and mutations related to TOPORS were then analyzed. Results: In total, 7 patients (ages 12-70) were identified amongst three unique families. All patients were female in our study. The average follow-up period was 7.7 years. A mother (70 yr) and daughter (51 yr) had a novel heterozygous nonsense point mutation in TOPORS c.2431C > T, p.Gln811X (Exon 3) that led to premature termination of the desired protein resulting in early onset vision loss, cataract formation, and visual field restriction. The mother developed a full-thickness macular hole which was successfully repaired. Five other patients were found to have previously described TOPORS mutations. Visual field loss was progressive with age in both cohorts. Conclusions: Seven patients at our institution were identified to have mutations in TOPORS resulting in autosomal dominant retinitis pigmentosa. Two patients were found to have novel truncating mutations in the TOPORS gene resulting in profound night blindness and visual field loss, recurrent macular edema, and in one individual, epiretinal membrane formation leading to a macular hole which was able to be successfully repaired.
Collapse
Affiliation(s)
- Alen T. Eid
- Department of Ophthalmology and Visual Sciences, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| | - Kevin Toni Eid
- Department of Ophthalmology and Visual Sciences, John A. Moran Eye Center, University of Utah, Salt Lake City, UT 84112, USA;
| | - James Vernon Odom
- Department of Ophthalmology and Visual Sciences, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| | - David Hinkle
- Tulane University School of Medicine, New Orleans, LA 70112, USA;
| | - Monique Leys
- Department of Ophthalmology and Visual Sciences, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| |
Collapse
|
4
|
Lee TJ, Sasaki Y, Ruzycki PA, Ban N, Lin JB, Wu HT, Santeford A, Apte RS. Catalytic isoforms of AMP-activated protein kinase differentially regulate IMPDH activity and photoreceptor neuron function. JCI Insight 2024; 9:e173707. [PMID: 38227383 PMCID: PMC11143937 DOI: 10.1172/jci.insight.173707] [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: 07/10/2023] [Accepted: 01/10/2024] [Indexed: 01/17/2024] Open
Abstract
AMP-activated protein kinase (AMPK) plays a crucial role in maintaining ATP homeostasis in photoreceptor neurons. AMPK is a heterotrimeric protein consisting of α, β, and γ subunits. The independent functions of the 2 isoforms of the catalytic α subunit, PRKAA1 and PRKAA2, are uncharacterized in specialized neurons, such as photoreceptors. Here, we demonstrate in mice that rod photoreceptors lacking PRKAA2, but not PRKAA1, showed altered levels of cGMP, GTP, and ATP, suggesting isoform-specific regulation of photoreceptor metabolism. Furthermore, PRKAA2-deficient mice displayed visual functional deficits on electroretinography and photoreceptor outer segment structural abnormalities on transmission electron microscopy consistent with neuronal dysfunction, but not neurodegeneration. Phosphoproteomics identified inosine monophosphate dehydrogenase (IMPDH) as a molecular driver of PRKAA2-specific photoreceptor dysfunction, and inhibition of IMPDH improved visual function in Prkaa2 rod photoreceptor-knockout mice. These findings highlight a therapeutically targetable PRKAA2 isoform-specific function of AMPK in regulating photoreceptor metabolism and function through a potentially previously uncharacterized mechanism affecting IMPDH activity.
Collapse
Affiliation(s)
- Tae Jun Lee
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology; and
| | - Yo Sasaki
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Philip A. Ruzycki
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Genetics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Norimitsu Ban
- Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Joseph B. Lin
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
| | | | - Andrea Santeford
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
| | - Rajendra S. Apte
- John F. Hardesty, MD Department of Ophthalmology and Visual Sciences
- Department of Developmental Biology; and
- Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| |
Collapse
|
5
|
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
|
6
|
Sakti DH, Cornish EE, Nash BM, Jamieson RV, Grigg JR. IMPDH1-associated autosomal dominant retinitis pigmentosa: natural history of novel variant Lys314Gln and a comprehensive literature search. Ophthalmic Genet 2023; 44:437-455. [PMID: 37259572 DOI: 10.1080/13816810.2023.2215310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 05/11/2023] [Accepted: 05/14/2023] [Indexed: 06/02/2023]
Abstract
BACKGROUND Inosine monophosphate dehydrogenase (IMPDH) is a key regulatory enzyme in the de novo synthesis of the purine base guanine. Mutations in the inosine monophosphate dehydrogenase 1 gene (IMPDH1) are causative for RP10 autosomal dominant retinitis pigmentosa (adRP). This study reports a novel variant in a family with IMPDH1-associated retinopathy. We also performed a comprehensive review of all reported IMPDH1 disease causing variants with their associated phenotype. MATERIALS AND METHODS Multimodal imaging and functional studies documented the phenotype including best-corrected visual acuity (BCVA), fundus photograph, fundus autofluorescence (FAF), full field electroretinogram (ffERG), optical coherence tomography (OCT) and visual field (VF) data were collected. A literature search was performed in the PubMed and LOVD repositories. RESULTS We report 3 cases from a 2-generation family with a novel heterozygous likely pathogenic variant p. (Lys314Gln) (exon 10). The ophthalmic phenotype showed diffuse outer retinal atrophy with mild pigmentary changes with sparse pigmentary changes. FAF showed early macular involvement with macular hyperautofluorescence (hyperAF) surrounded by hypoAF. Foveal ellipsoid zone island can be found in the youngest patient but not in the older ones. The literature review identified a further 56 heterozygous, 1 compound heterozygous, and 2 homozygous variant. The heterozygous group included 43 missense, 3 in-frame, 1 nonsense, 2 frameshift, 1 synonymous, and 6 intronic variants. Exon 10 was noted as a hotspot harboring 18 variants. CONCLUSIONS We report a novel IMPDH1 variant. IMPDH1-associated retinopathy presents most frequently in the first decade of life with early macular involvement.
Collapse
Affiliation(s)
- Dhimas H Sakti
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Department of Ophthalmology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Elisa E Cornish
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - Benjamin M Nash
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
- Sydney Genome Diagnostics, Western Sydney Genetics Program, Sydney Children's Hospitals Network, Sydney, New South Wales, Australia
| | - Robyn V Jamieson
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| | - John R Grigg
- Save Sight Institute, University of Sydney, Sydney, New South Wales, Australia
- Eye Genetics Research Unit, Children's Medical Research Institute, The Children's Hospital at Westmead, Sydney, New South Wales, Australia
| |
Collapse
|
7
|
Keppeke GD, Chang CC, Zhang Z, Liu JL. Effect on cell survival and cytoophidium assembly of the adRP-10-related IMPDH1 missense mutation Asp226Asn. Front Cell Dev Biol 2023; 11:1234592. [PMID: 37731818 PMCID: PMC10507268 DOI: 10.3389/fcell.2023.1234592] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/17/2023] [Indexed: 09/22/2023] Open
Abstract
Introduction: Inosine monophosphate dehydrogenase 1 (IMPDH1) is a critical enzyme in the retina, essential for the correct functioning of photoreceptor cells. Mutations in IMPDH1 have been linked to autosomal dominant retinitis pigmentosa subtype 10 (adRP-10), a genetic eye disorder. Some of these mutations such as the Asp226Asn (D226N) lead to the assembly of large filamentous structures termed cytoophidia. D226N also gives IMPDH1 resistance to feedback inhibition by GDP/GTP. This study aims to emulate the adRP-10 condition with a long-term expression of IMPDH1-D226N in vitro and explore cytoophidium assembly and cell survival. We also assessed whether the introduction of an additional mutation (Y12C) to disrupt the cytoophidium has an attenuating effect on the toxicity caused by the D226N mutation. Results: Expression of IMPDH1-D226N in HEp-2 cells resulted in cytoophidium assembly in ∼70% of the cells, but the presence of the Y12C mutation disrupted the filaments. Long-term cell survival was significantly affected by the presence of the D226N mutation, with a decrease of ∼40% in the cells expressing IMPDH1-D226N when compared to IMPDH1-WT; however, survival was significantly recovered in IMPDH1-Y12C/D226N, with only a ∼10% decrease when compared to IMPDH1-WT. On the other hand, the IMPDH1 expression level in the D226N-positive cells was <30% of that of the IMPDH1-WT-positive cells and only slightly higher in the Y12C/D226N, suggesting that although cell survival in Y12C/D226N was recovered, higher expression levels of the mutated IMPDH1 were not tolerated by the cells in the long term. Conclusion: The IMPDH1-D226N effect on photoreceptor cell survival may be the result of a sum of problems: nucleotide unbalance plus a toxic long-life cytoophidium, supported by the observation that by introducing Y12C in IMPDH1 the cytoophidium was disrupted and cell survival significantly recovered, but not the sensibility to GDP/GTP regulation since higher expression levels of IMPDH1-D226N were not tolerated.
Collapse
Affiliation(s)
- Gerson Dierley Keppeke
- Departamento de Ciencias Biomédicas, Facultad de Medicina, Universidad Católica del Norte, Coquimbo, Chile
- Rheumatology Division, Escola Paulista de Medicina, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Chia-Chun Chang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Ziheng Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ji-Long Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
8
|
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.
Collapse
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
| |
Collapse
|
9
|
Micevych PS, Wong J, Zhou H, Wang RK, Porco TC, Carroll J, Roorda A, Duncan JL. Cone Structure and Function in RPGR- and USH2A-Associated Retinal Degeneration. Am J Ophthalmol 2023; 250:1-11. [PMID: 36646238 PMCID: PMC10308738 DOI: 10.1016/j.ajo.2023.01.006] [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: 10/12/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
PURPOSE To compare cone structure and function between RPGR- and USH2A-associated retinal degeneration. DESIGN Retrospective, observational, cross-sectional study. METHODS This multicenter study included 13 eyes (9 participants) with RPGR-related X-linked retinitis pigmentosa (RPGR), 15 eyes (10 participants) with USH2A-related Usher syndrome type 2 (USH2), 16 eyes (9 participants) with USH2A-related autosomal recessive retinitis pigmentosa (ARRP), and 7 normal eyes (6 participants). Structural measures included cone spacing and density from adaptive optics scanning laser ophthalmoscopy and photoreceptor inner segment (IS), outer segment (OS), and outer nuclear layer (ONL) thickness from optical coherence tomography (OCT) images. OCT angiography images were used to study choriocapillaris flow deficit percent (CCFD). Cone function was assessed by fundus-guided microperimetry. Measures were compared at designated regions using analysis of variance with pairwise comparisons among disease groups, adjusted for disease duration and eccentricity. RESULTS OCT segmentation revealed shorter OS and IS, with reduced ONL thickness in RPGR compared to normal (OS: P < .001, IS: P = .001, ONL: P = .005), USH2 (OS: P = .01, IS: P = .03, ONL: P = .03), or ARRP (OS: P = .001, ONL: P = .03). Increased cone spacing was observed in both RPGR (P = .03) and USH2 compared with normal (P = .048). The mean CCFD in RPGR was greater than in USH2 (P = .02). Microperimetry demonstrated below-normal regional sensitivity in RPGR (P = .004), USH2 (P = .02), and ARRP (P = .009), without significant intergroup differences. CONCLUSIONS Outer retinal structure and choriocapillaris perfusion were more abnormal in RPGR- than USH2A-related retinal degenerations, whereas there were no significant differences in below-normal regional sensitivity between each rod-cone degeneration associated with variants in these 2 genes expressed at the photoreceptor-connecting cilium.
Collapse
Affiliation(s)
- Paul S Micevych
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California
| | - Jessica Wong
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California
| | - Hao Zhou
- Department of Bioengineering, University of Washington (H.Z., R.K.W.), Seattle, Washington
| | - Ruikang K Wang
- Department of Bioengineering, University of Washington (H.Z., R.K.W.), Seattle, Washington
| | - Travis C Porco
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California; Francis I. Proctor Foundation, Department of Ophthalmology, University of California (T.C.P.), San Francisco, California
| | - Joseph Carroll
- Department of Ophthalmology & Visual Sciences, Medical College of Wisconsin Eye Institute (J.C.), Milwaukee, Wisconsin
| | - Austin Roorda
- Herbert Wertheim School of Optometry & Vision Science, University of California Berkeley (A.R.), Berkeley, California, USA
| | - Jacque L Duncan
- From the Department of Ophthalmology, University of California (P.S.M., J.W., T.C.P., J.L.D.), San Francisco, California.
| |
Collapse
|
10
|
Justin GA, Girach A, Maldonado RS. Antisense oligonucleotide therapy for proline-23-histidine autosomal dominant retinitis pigmentosa. Curr Opin Ophthalmol 2023; 34:226-231. [PMID: 36924362 DOI: 10.1097/icu.0000000000000947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
PURPOSE OF REVIEW To discuss antisense oligonucleotide (ASON) therapy for autosomal dominant retinitis pigmentosa (adRP) caused by the proline-23-histidine (P23H) mutation in the rhodopsin gene. RECENT FINDINGS Viral and nonviral therapies to treat adRP are currently under investigation. A promising therapeutic option is a nonviral approach using ASONs. This form of genetic therapy has demonstrated a dose-dependent and highly selective reduction of P23H mutant rhodopsin mRNA in animal models, and it is currently being investigated as a human phase 1/2 clinical trial. SUMMARY There are promising new therapies to treat adRP. ASON has shown encouraging results in animal models and has undergone a phase 1 clinical trial. ASON does not use a viral vector, is delivered with standard intravitreal injection, and its effects are reversible.
Collapse
Affiliation(s)
- Grant A Justin
- Department of Ophthalmology, Duke University, Durham, North Carolina, USA
| | | | - Ramiro S Maldonado
- Department of Ophthalmology, Duke University, Durham, North Carolina, USA
| |
Collapse
|
11
|
Zhen F, Zou T, Wang T, Zhou Y, Dong S, Zhang H. Rhodopsin-associated retinal dystrophy: Disease mechanisms and therapeutic strategies. Front Neurosci 2023; 17:1132179. [PMID: 37077319 PMCID: PMC10106759 DOI: 10.3389/fnins.2023.1132179] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/13/2023] [Indexed: 04/05/2023] Open
Abstract
Rhodopsin is a light-sensitive G protein-coupled receptor that initiates the phototransduction cascade in rod photoreceptors. Mutations in the rhodopsin-encoding gene RHO are the leading cause of autosomal dominant retinitis pigmentosa (ADRP). To date, more than 200 mutations have been identified in RHO. The high allelic heterogeneity of RHO mutations suggests complicated pathogenic mechanisms. Here, we discuss representative RHO mutations as examples to briefly summarize the mechanisms underlying rhodopsin-related retinal dystrophy, which include but are not limited to endoplasmic reticulum stress and calcium ion dysregulation resulting from protein misfolding, mistrafficking, and malfunction. Based on recent advances in our understanding of disease mechanisms, various treatment methods, including adaptation, whole-eye electrical stimulation, and small molecular compounds, have been developed. Additionally, innovative therapeutic treatment strategies, such as antisense oligonucleotide therapy, gene therapy, optogenetic therapy, and stem cell therapy, have achieved promising outcomes in preclinical disease models of rhodopsin mutations. Successful translation of these treatment strategies may effectively ameliorate, prevent or rescue vision loss related to rhodopsin mutations.
Collapse
Affiliation(s)
- Fangyuan Zhen
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Tongdan Zou
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Ting Wang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Yongwei Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
| | - Shuqian Dong
- Department of Ophthalmology, The First Affiliated Hospital of Zhengzhou University, Henan Provincial Ophthalmic Hospital, Zhengzhou, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
| | - Houbin Zhang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Institute of Laboratory Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Research Unit for Blindness Prevention, Chinese Academy of Medical Sciences (2019RU026), Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, Sichuan, China
- *Correspondence: Shuqian Dong, ; Houbin Zhang,
| |
Collapse
|
12
|
Buckley TM, Cehajic-Kapetanovic J, Shanks M, Clouston P, MacLaren RE. Compound dominant-null heterozygosity in a family with RP1-related retinal dystrophy. Am J Ophthalmol Case Rep 2022; 28:101698. [PMID: 36393903 PMCID: PMC9650022 DOI: 10.1016/j.ajoc.2022.101698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/15/2022] [Accepted: 09/01/2022] [Indexed: 11/20/2022] Open
Abstract
Purpose To report on the presence of autosomal dominant and compound dominant-null RP1-related retinitis pigmentosa in the same non-consanguineous family. Observation The father was minimally symptomatic and referred by his optometrist aged 38. He was diagnosed with rod-cone dystrophy, confirmed to be caused by the previously reported RP1 c.2613dupA mutation. He was reassured that his 11-year-old daughter had a 50% chance of inheriting the same mutation and that the condition, if she had it, would most likely be similar. Clinical phenotyping of his daughter however revealed an early onset cone-rod dystrophy. The mother was entirely asymptomatic and clinically normal. Sanger sequencing of the RP1 gene in the daughter confirmed the presence of biallelic mutations - the dominant c.2613dupA variant from her father and a c.3843dupT truncating variant inherited from her mother, both located in exon 4 of the RP1 gene. The maternal c.3843dupT has previously been reported. Conclusions and importance Pathogenic variants in exon 4 of RP1 are known to cause differential dominant and recessive disease. The presence of both phenotypes in a single family has not yet been reported. The father, being minimally symptomatic, is affected by a known dominant variant which truncates the RP1 protein more proximally. However, inheritance of both variants in a compound heterozygous state in the daughter resulted in a much more severe, early onset cone-rod phenotype in a pattern akin to recessive disease. This raises challenges for genetic counselling and development of gene-based therapies for RP1 mutations.
Collapse
Affiliation(s)
- Thomas M.W. Buckley
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, UK
| | | | - Morag Shanks
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, UK
| | - Penny Clouston
- Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Headley Way, OX3 9DU, UK
| | - Robert E. MacLaren
- Nuffield Laboratory of Ophthalmology, Level 6, West Wing, John Radcliffe Hospital, Headley Way, OX3 9DU, UK
| |
Collapse
|
13
|
Wang J, Xiao X, Li S, Jiang H, Sun W, Wang P, Zhang Q. Landscape of pathogenic variants in six pre-mRNA processing factor genes for retinitis pigmentosa based on large in-house data sets and database comparisons. Acta Ophthalmol 2022; 100:e1412-e1425. [PMID: 35138024 DOI: 10.1111/aos.15104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 12/31/2021] [Accepted: 01/20/2022] [Indexed: 12/29/2022]
Abstract
PURPOSE Variants in six genes encoding pre-mRNA processing factors (PRPFs) are a common cause of autosomal dominant retinitis pigmentosa (ADRP). This study aims to determine the characteristics of potential pathogenic variants (PPVs) in the six genes. METHODS Variants in six PRPF genes were identified from in-house exome sequencing data. PPVs were identified based on comparative bioinformatics analysis, clinical phenotypes and the ACMG/AMP guidelines. The features of PPVs were revealed by comparative analysis of in-house data set, gnomAD and previously published literature. RESULTS Totally, 36 heterozygous PPVs, including 19 novels, were detected from 45 families, which contributed to 4.4% (45/1019) of RP cases. These PPVs were distributed in PRPF31 (17/45, 37.8%), SNRNP200 (12/45, 26.7%), PRPF8 (10/45, 22.2%) and PRPF3 (6/45, 13.3%) but not in PRPF6 or PRPF4. Different types of PPVs were predominant in different PRPF genes, such as loss-of-function variants in PRPF31 and missense variants in the five remaining genes. The clustering of PPVs in specific regions was observed in SNRNP200, PRPF8 and PRPF3. The pathogenicity for certain classes of variants in these genes, such as loss-of-function variants in PRPF6 and missense variants in PRPF31 and PRPF4, requires careful consideration and further validation. The predominant fundus changes were early macular involvement, widespread RPE atrophy and pigmentation in the mid- and far-peripheral retina. CONCLUSION Systemic comparative analysis may shed light on the characterization of PPVs in these genes. Our findings provide a brief landscape of PPVs in PRPF genes and the associated phenotypes and emphasize the careful classification of pathogenicity for certain types of variants that warrant further characterization.
Collapse
Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Hongmei Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
14
|
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: 16] [Impact Index Per Article: 8.0] [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.
Collapse
|
15
|
Wang J, Wang Y, Jiang Y, Li X, Xiao X, Li S, Jia X, Sun W, Wang P, Zhang Q. Autosomal Dominant Retinitis Pigmentosa-Associated TOPORS Protein Truncating Variants Are Exclusively Located in the Region of Amino Acid Residues 807 to 867. Invest Ophthalmol Vis Sci 2022; 63:19. [PMID: 35579903 PMCID: PMC9123486 DOI: 10.1167/iovs.63.5.19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Heterozygous truncating variants of TOPORS have been reported to cause autosomal dominant retinitis pigmentosa (adRP). The purpose of this study was to investigate whether all heterozygous truncating variants, including copy number variants (CNVs), are pathogenic. Methods TOPORS truncating variants were collected and reviewed through an in-house dataset and existing databases. Individuals with truncating variants underwent ophthalmological evaluation. Results Six truncating variants were detected in seven families. Three N-terminus truncating variants were detected in three families without RP, and the other three were identified in four unrelated families with typical RP. Based on the in-house dataset and published literature, 17 truncating variants were identified in 47 families with RP. All RP-associated truncating alleles, except one, were distributed in the last exon of TOPORS and clustered in amino acid residues 807 to 867 (46/47, 97.9%). Conversely, in the gnomAD database, only one truncating allele (1/27, 3.7%) was in this region, and the others were outside (26/27, 96.3%), suggesting that the pathogenic truncating variants were significantly clustered in residues 807 to 867 (χ2 = 65.6, P = 1.1 × 10–17). Additionally, three CNVs involving the N-terminus of TOPORS were recorded in control populations but were absent in affected patients. Conclusions This study suggests that all pathogenic truncating variants of TOPORS were clustered in residues 807 to 867, whereas the truncating variants outside this region and the CNVs involving the N-terminus were not associated with RP. A dominant-negative effect, rather than haploinsufficiency, is speculated to be the underlying pathogenesis. These findings provide valuable information for interpreting variation in TOPORS and other genes in similar situations, especially for CNVs.
Collapse
Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yingwei Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Yi Jiang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueqing Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Xiaoyun Jia
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| |
Collapse
|
16
|
He K, Zhou Y, Li N. Mutations of TOPORS identified in families with retinitis pigmentosa. Ophthalmic Genet 2022; 43:371-377. [PMID: 35254173 DOI: 10.1080/13816810.2022.2039721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Kaiwen He
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
| | - Yunyu Zhou
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
| | - Ningdong Li
- Department of Ophthalmology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, China 100045
| |
Collapse
|
17
|
Perkins BD. Zebrafish models of inherited retinal dystrophies. JOURNAL OF TRANSLATIONAL GENETICS AND GENOMICS 2022; 6:95-110. [PMID: 35693295 PMCID: PMC9186516 DOI: 10.20517/jtgg.2021.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Inherited retinal degenerations (IRDs) cause permanent vision impairment or vision loss due to the death of rod and cone photoreceptors. Animal models of IRDs have been instrumental in providing knowledge of the pathological mechanisms that cause photoreceptor death and in developing successful approaches that could slow or prevent vision loss. Zebrafish models of IRDs represent an ideal model system to study IRDs in a cone-rich retina and to test strategies that exploit the natural ability to regenerate damaged neurons. This review highlights those zebrafish mutants and transgenic lines that exhibit adult-onset retinal degeneration and serve as models of retinitis pigmentosa, cone-rod dystrophy, and ciliopathies.
Collapse
Affiliation(s)
- Brian D. Perkins
- Department of Ophthalmic Research, Cole Eye Institute, Cleveland Clinic, OH 44195, USA
- Department of Ophthalmology, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, OH 44195, USA
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH 44195, USA
| |
Collapse
|
18
|
Yang J, Zhou L, Ouyang J, Xiao X, Sun W, Li S, Zhang Q. Genotype-Phenotype Analysis of RPGR Variations: Reporting of 62 Chinese Families and a Literature Review. Front Genet 2021; 12:600210. [PMID: 34745198 PMCID: PMC8565807 DOI: 10.3389/fgene.2021.600210] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Accepted: 04/27/2021] [Indexed: 02/05/2023] Open
Abstract
Purpose RPGR is the most common cause of X-linked retinitis pigmentosa (RP), of which female carriers are also frequently affected. The aim of the current study was to explore the RPGR variation spectrum and associated phenotype based on the data from our lab and previous studies. Methods Variants in RPGR were selected from exome sequencing data of 7,092 probands with different eye conditions. The probands and their available family members underwent comprehensive ocular examinations. Similar data were collected from previous reports through searches in PubMed, Web of Science, and Google Scholar. Systematic analyses of genotypes, phenotypes and their correlations were performed. Results A total of 46 likely pathogenic variants, including nine missense and one in-frame variants in RCC1-like domain and 36 truncation variants, in RPGR were detected in 62 unrelated families in our in-house cohort. In addition, a total of 585 variants, including 491 (83.9%) truncation variants, were identified from the literature. Systematic analysis of variants from our in-house dataset, literature, and gnomAD suggested that most of the pathogenic variants of RPGR were truncation variants while pathogenic missense and in-frame variants were enriched in the RCC1-like domain. Phenotypic variations were present between males and female carriers, including more severe refractive error but better best corrected visual acuity (BCVA) in female carriers than those in males. The male patients showed a significant reduction of BCVA with increase of age and males with exon1-14 variants presented a better BCVA than those with ORF15 variants. For female carriers, the BCVA also showed significant reduction with increase of age, but BCVA in females with exon1-14 variants was not significant difference compared with those with ORF15 variants. Conclusion Most pathogenic variants of RPGR are truncations. Missense and in-frame variants located outside of the RCC1-like domain might be benign and the pathogenicity criteria for these variants should be considered with greater caution. The BCVA and refractive error are different between males and female carriers. Increase of age and location of variants in ORF15 contribute to the reduction of BCVA in males. These results are valuable for understanding genotypes and phenotypes of RPGR.
Collapse
Affiliation(s)
- Junxing Yang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Lin Zhou
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China.,Department of Ophthalmology, West China Hospital, Sichuan University, Chengdu, China
| | - Jiamin Ouyang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
19
|
Biswas P, Villanueva AL, Soto-Hermida A, Duncan JL, Matsui H, Borooah S, Kurmanov B, Richard G, Khan SY, Branham K, Huang B, Suk J, Bakall B, Goldberg JL, Gabriel L, Khan NW, Raghavendra PB, Zhou J, Devalaraja S, Huynh A, Alapati A, Zawaydeh Q, Weleber RG, Heckenlively JR, Hejtmancik JF, Riazuddin S, Sieving PA, Riazuddin SA, Frazer KA, Ayyagari R. Deciphering the genetic architecture and ethnographic distribution of IRD in three ethnic populations by whole genome sequence analysis. PLoS Genet 2021; 17:e1009848. [PMID: 34662339 PMCID: PMC8589175 DOI: 10.1371/journal.pgen.1009848] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 11/12/2021] [Accepted: 09/29/2021] [Indexed: 12/12/2022] Open
Abstract
Patients with inherited retinal dystrophies (IRDs) were recruited from two understudied populations: Mexico and Pakistan as well as a third well-studied population of European Americans to define the genetic architecture of IRD by performing whole-genome sequencing (WGS). Whole-genome analysis was performed on 409 individuals from 108 unrelated pedigrees with IRDs. All patients underwent an ophthalmic evaluation to establish the retinal phenotype. Although the 108 pedigrees in this study had previously been examined for mutations in known IRD genes using a wide range of methodologies including targeted gene(s) or mutation(s) screening, linkage analysis and exome sequencing, the gene mutations responsible for IRD in these 108 pedigrees were not determined. WGS was performed on these pedigrees using Illumina X10 at a minimum of 30X depth. The sequence reads were mapped against hg19 followed by variant calling using GATK. The genome variants were annotated using SnpEff, PolyPhen2, and CADD score; the structural variants (SVs) were called using GenomeSTRiP and LUMPY. We identified potential causative sequence alterations in 61 pedigrees (57%), including 39 novel and 54 reported variants in IRD genes. For 57 of these pedigrees the observed genotype was consistent with the initial clinical diagnosis, the remaining 4 had the clinical diagnosis reclassified based on our findings. In seven pedigrees (12%) we observed atypical causal variants, i.e. unexpected genotype(s), including 4 pedigrees with causal variants in more than one IRD gene within all affected family members, one pedigree with intrafamilial genetic heterogeneity (different affected family members carrying causal variants in different IRD genes), one pedigree carrying a dominant causative variant present in pseudo-recessive form due to consanguinity and one pedigree with a de-novo variant in the affected family member. Combined atypical and large structural variants contributed to about 20% of cases. Among the novel mutations, 75% were detected in Mexican and 50% found in European American pedigrees and have not been reported in any other population while only 20% were detected in Pakistani pedigrees and were not previously reported. The remaining novel IRD causative variants were listed in gnomAD but were found to be very rare and population specific. Mutations in known IRD associated genes contributed to pathology in 63% Mexican, 60% Pakistani and 45% European American pedigrees analyzed. Overall, contribution of known IRD gene variants to disease pathology in these three populations was similar to that observed in other populations worldwide. This study revealed a spectrum of mutations contributing to IRD in three populations, identified a large proportion of novel potentially causative variants that are specific to the corresponding population or not reported in gnomAD and shed light on the genetic architecture of IRD in these diverse global populations.
Collapse
Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
| | - Adda L. Villanueva
- Retina and Genomics Institute, Yucatán, México
- Laboratoire de Diagnostic Moleculaire, Hôpital Maisonneuve Rosemont, Montreal, Quebec, Canada
| | - Angel Soto-Hermida
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Jacque L. Duncan
- Ophthalmology, University of California San Francisco, San Francisco, California, United States of America
| | - Hiroko Matsui
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Berzhan Kurmanov
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | | | - Shahid Y. Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kari Branham
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Bonnie Huang
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - John Suk
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Benjamin Bakall
- Ophthalmology, University of Arizona College of Medicine Phoenix, Phoenix, Arizona, United States of America
| | - Jeffrey L. Goldberg
- Byers Eye Institute, Stanford, Palo Alto, California, United States of America
| | - Luis Gabriel
- Genetics and Ophthalmology, Genelabor, Goiânia, Brazil
| | - Naheed W. Khan
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - Pongali B. Raghavendra
- School of Biotechnology, REVA University, Bengaluru, Karnataka, India
- School of Regenerative Medicine, Manipal University, Bengaluru, Karnataka, India
| | - Jason Zhou
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Sindhu Devalaraja
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Andrew Huynh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Akhila Alapati
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Qais Zawaydeh
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| | - Richard G. Weleber
- Casey Eye Institute, Oregon Health & Science University, Portland, Oregon, United States of America
| | - John R. Heckenlively
- Ophthalmology & Visual Science, University of Michigan Kellogg Eye Center, Ann Arbor, Michigan, United States of America
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan
| | - Paul A. Sieving
- National Eye Institute, Bethesda, Maryland, United States of America
- Ophthalmology & Vision Science, UC Davis Medical Center, California, United States of America
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelly A. Frazer
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, California, United States of America
- Department of Pediatrics, Rady Children’s Hospital, Division of Genome Information Sciences, San Diego, California, United States of America
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
| |
Collapse
|
20
|
Peeters MHCA, Khan M, Rooijakkers AAMB, Mulders T, Haer-Wigman L, Boon CJF, Klaver CCW, van den Born LI, Hoyng CB, Cremers FPM, den Hollander AI, Dhaenens CM, Collin RWJ. PRPH2 mutation update: In silico assessment of 245 reported and 7 novel variants in patients with retinal disease. Hum Mutat 2021; 42:1521-1547. [PMID: 34411390 PMCID: PMC9290825 DOI: 10.1002/humu.24275] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/22/2021] [Accepted: 08/16/2021] [Indexed: 01/31/2023]
Abstract
Mutations in PRPH2, encoding peripherin-2, are associated with the development of a wide variety of inherited retinal diseases (IRDs). To determine the causality of the many PRPH2 variants that have been discovered over the last decades, we surveyed all published PRPH2 variants up to July 2020, describing 720 index patients that in total carried 245 unique variants. In addition, we identified seven novel PRPH2 variants in eight additional index patients. The pathogenicity of all variants was determined using the ACMG guidelines. With this, 107 variants were classified as pathogenic, 92 as likely pathogenic, one as benign, and two as likely benign. The remaining 50 variants were classified as variants of uncertain significance. Interestingly, of the total 252 PRPH2 variants, more than half (n = 137) were missense variants. All variants were uploaded into the Leiden Open source Variation and ClinVar databases. Our study underscores the need for experimental assays for variants of unknown significance to improve pathogenicity classification, which would allow us to better understand genotype-phenotype correlations, and in the long-term, hopefully also support the development of therapeutic strategies for patients with PRPH2-associated IRD.
Collapse
Affiliation(s)
- Manon H C A Peeters
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | | | - Timo Mulders
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Amsterdam UMC, Academic Medical Center, Amsterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Ophthalmology, Erasmus University Medical Centre, Rotterdam, The Netherlands.,Institute of Molecular and Clinical Ophthalmology, Basel, Switzerland
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands.,Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Biochemistry and Molecular Biology, Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, Lille, France
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Human Genetics and Ophthalmology, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, The Netherlands
| |
Collapse
|
21
|
Roshandel D, Thompson JA, Heath Jeffery RC, Zhang D, Lamey TM, McLaren TL, De Roach JN, McLenachan S, Mackey DA, Chen FK. Clinical Evidence for the Importance of the Wild-Type PRPF31 Allele in the Phenotypic Expression of RP11. Genes (Basel) 2021; 12:genes12060915. [PMID: 34198599 PMCID: PMC8232116 DOI: 10.3390/genes12060915] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/09/2021] [Accepted: 06/12/2021] [Indexed: 11/16/2022] Open
Abstract
PRPF31-associated retinopathy (RP11) is a common form of autosomal dominant retinitis pigmentosa (adRP) that exhibits wide variation in phenotype ranging from non-penetrance to early-onset RP. Herein, we report inter-familial and intra-familial variation in the natural history of RP11 using multimodal imaging and microperimetry. Patients were recruited prospectively. The age of symptom onset, best-corrected visual acuity, microperimetry mean sensitivity (MS), residual ellipsoid zone span and hyperautofluorescent ring area were recorded. Genotyping was performed using targeted next-generation and Sanger sequencing and copy number variant analysis. PRPF31 mutations were found in 14 individuals from seven unrelated families. Four disease patterns were observed: (A) childhood onset with rapid progression (N = 4), (B) adult-onset with rapid progression (N = 4), (C) adult-onset with slow progression (N = 4) and (D) non-penetrance (N = 2). Four different patterns were observed in a family harbouring c.267del; patterns B, C and D were observed in a family with c.772_773delins16 and patterns A, B and C were observed in 3 unrelated individuals with large deletions. Our findings suggest that the RP11 phenotype may be related to the wild-type PRPF31 allele rather than the type of mutation. Further studies that correlate in vitro wild-type PRPF31 allele expression level with the disease patterns are required to investigate this association.
Collapse
Affiliation(s)
- Danial Roshandel
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Rachael C. Heath Jeffery
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
| | - Dan Zhang
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - Tina M. Lamey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Terri L. McLaren
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - John N. De Roach
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Samuel McLenachan
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
| | - David A. Mackey
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Perth, WA 6009, Australia; (D.R.); (R.C.H.J.); (T.M.L.); (T.L.M.); (J.N.D.R.); (S.M.); (D.A.M.)
- Ocular Tissue Engineering Laboratory, Lions Eye Institute, Nedlands, WA 6009, Australia;
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia;
- Department of Ophthalmology, Royal Perth Hospital, Perth, WA 6000, Australia
- Department of Ophthalmology, Perth Children’s Hospital, Nedlands, WA 6009, Australia
- Correspondence: ; Tel.: +61-08-9381-0777
| |
Collapse
|
22
|
Wang J, Xiao X, Li S, Wang P, Sun W, Zhang Q. Dominant RP in the Middle While Recessive in Both the N- and C-Terminals Due to RP1 Truncations: Confirmation, Refinement, and Questions. Front Cell Dev Biol 2021; 9:634478. [PMID: 33681214 PMCID: PMC7935555 DOI: 10.3389/fcell.2021.634478] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 01/19/2021] [Indexed: 11/13/2022] Open
Abstract
RP1 truncation variants, including frameshift, nonsense, and splicing, are a common cause of retinitis pigmentosa (RP). RP1 is a unique gene where truncations cause either autosomal dominant RP (adRP) or autosomal recessive RP (arRP) depending on the location of the variants. This study aims to clarify the boundaries between adRP and arRP caused by RP1 truncation variants based on a systemic analysis of 165 RP1 variants from our in-house exome-sequencing data of 7,092 individuals as well as a thorough review of 185 RP1 variants from published literature. In our cohort, potential pathogenic variants were detected in 16 families, including 11 new and five previously described families. Of the 16, seven families with adRP had heterozygous truncations in the middle portion, while nine families with either arRP (eight) or macular degeneration had biallelic variants in the N- and C-terminals, involving 10 known and seven novel variants. In the literature, 147 truncations in RP1 were reported to be responsible for either arRP (85) or adRP (58) or both (four). An overall evaluation of RP1 causative variants suggested three separate regions, i.e., the N-terminal from c.1 (p.1) to c.1837 (p.613), the middle portion from c.1981 (p.661) to c.2749 (p.917), and the C-terminal from c.2816 (p.939) to c.6471 (p.2157), where truncations in the middle portion were associated with adRP, while those in the N- and C-terminals were responsible for arRP. Heterozygous truncations alone in the N- and C- terminals were unlikely pathogenic. However, conflict reports with reverse situation were present for 13 variants, suggesting a complicated pathogenicity awaiting to be further elucidated. In addition, pathogenicity for homozygous truncations around c.5797 and thereafter might also need to be further clarified, so as for missense variants and for truncations located in the two gaps. Our data not only confirmed and refined the boundaries between dominant and recessive RP1 truncations but also revealed unsolved questions valuable for further investigation. These findings remind us that great care is needed in interpreting the results of RP1 variants in clinical gene testing as well as similar features may also be present in some other genes.
Collapse
Affiliation(s)
- Junwen Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Panfeng Wang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
23
|
Xiao T, Xie Y, Zhang X, Xu K, Zhang X, Jin ZB, Li Y. Variant Profiling of a Large Cohort of 138 Chinese Families With Autosomal Dominant Retinitis Pigmentosa. Front Cell Dev Biol 2021; 8:629994. [PMID: 33598457 PMCID: PMC7882618 DOI: 10.3389/fcell.2020.629994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy, and 15–25% of RP is transmitted as an autosomal dominant (ad) trait. The objectives of this study were to establish the variant profile in a large cohort of adRP families and to elucidate the variant spectrum of each adRP gene in Chinese patients. A total of 138 probands clinically diagnosed with RP as a presumed autosomal dominant trait were recruited. All probands underwent ophthalmic examinations by specialists. A combination of molecular screening methods, including targeted next-generation sequencing, Sanger DNA sequencing, and multiplex ligation probe amplification assay, was used to detect variants. We identified heterozygous variants of 11 adRP genes in 73 probands, hemizygous, or heterozygous variants of X-linked RP genes in six patients, compound heterozygous variants of autosomal recessive RP genes in three pseudodominant families, and one heterozygous variant of one ad cone and rod dystrophy gene in one proband. One proband was found carrying both variants in RPGR and FAM161A. The overall detection rate was 59.4% (82/138). We detected 72 distinct disease-causing variants involving 16 RP genes and one cone-rod dystrophy gene; 33 of these variants have not been reported previously. Disease-causing variants were identified in the adRP genes in 52.9% of the families, followed by 4.3% in the X-linked RP genes, and 2.2% in the autosomal recessive genes. The most frequent mutant genes were RHO, PRPF31, RP1, SNRNP200, and PRPF8, which explained up to 78.0% of the genetically diagnosed families. Most of the variants identified in adRP genes were missense, and copy number variations were common (7/20) in the PRPF31 gene. We established the profile of the mutated genes and the variant spectrum of adRP genes in a large cohort of Chinese patients, providing essential information for genetic counseling and future development of therapeutics for retinal dystrophy inherited as a dominant trait.
Collapse
Affiliation(s)
- Ting Xiao
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yue Xie
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xin Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Ke Xu
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xiaohui Zhang
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zi-Bing Jin
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Li
- Beijing Ophthalmology & Visual Sciences Key Lab, Beijing Tongren Eye Center, Beijing Institute of Ophthalmology, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
24
|
de Bruijn SE, Fiorentino A, Ottaviani D, Fanucchi S, Melo US, Corral-Serrano JC, Mulders T, Georgiou M, Rivolta C, Pontikos N, Arno G, Roberts L, Greenberg J, Albert S, Gilissen C, Aben M, Rebello G, Mead S, Raymond FL, Corominas J, Smith CEL, Kremer H, Downes S, Black GC, Webster AR, Inglehearn CF, van den Born LI, Koenekoop RK, Michaelides M, Ramesar RS, Hoyng CB, Mundlos S, Mhlanga MM, Cremers FPM, Cheetham ME, Roosing S, Hardcastle AJ. Structural Variants Create New Topological-Associated Domains and Ectopic Retinal Enhancer-Gene Contact in Dominant Retinitis Pigmentosa. Am J Hum Genet 2020; 107:802-814. [PMID: 33022222 PMCID: PMC7675008 DOI: 10.1016/j.ajhg.2020.09.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 09/02/2020] [Indexed: 01/07/2023] Open
Abstract
The cause of autosomal-dominant retinitis pigmentosa (adRP), which leads to loss of vision and blindness, was investigated in families lacking a molecular diagnosis. A refined locus for adRP on Chr17q22 (RP17) was delineated through genotyping and genome sequencing, leading to the identification of structural variants (SVs) that segregate with disease. Eight different complex SVs were characterized in 22 adRP-affected families with >300 affected individuals. All RP17 SVs had breakpoints within a genomic region spanning YPEL2 to LINC01476. To investigate the mechanism of disease, we reprogrammed fibroblasts from affected individuals and controls into induced pluripotent stem cells (iPSCs) and differentiated them into photoreceptor precursor cells (PPCs) or retinal organoids (ROs). Hi-C was performed on ROs, and differential expression of regional genes and a retinal enhancer RNA at this locus was assessed by qPCR. The epigenetic landscape of the region, and Hi-C RO data, showed that YPEL2 sits within its own topologically associating domain (TAD), rich in enhancers with binding sites for retinal transcription factors. The Hi-C map of RP17 ROs revealed creation of a neo-TAD with ectopic contacts between GDPD1 and retinal enhancers, and modeling of all RP17 SVs was consistent with neo-TADs leading to ectopic retinal-specific enhancer-GDPD1 accessibility. qPCR confirmed increased expression of GDPD1 and increased expression of the retinal enhancer that enters the neo-TAD. Altered TAD structure resulting in increased retinal expression of GDPD1 is the likely convergent mechanism of disease, consistent with a dominant gain of function. Our study highlights the importance of SVs as a genomic mechanism in unsolved Mendelian diseases.
Collapse
Affiliation(s)
- Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Alessia Fiorentino
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | | | - Stephanie Fanucchi
- Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Uirá S Melo
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | | | - Timo Mulders
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michalis Georgiou
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK; Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, 4031, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, 4001, Switzerland
| | - Nikolas Pontikos
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Lisa Roberts
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Jacquie Greenberg
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Marco Aben
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - George Rebello
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Simon Mead
- MRC Prion Unit at UCL, UCL Institute of Prion Disease, London, W1W 7FF, UK
| | - F Lucy Raymond
- NIHR BioResource, Cambridge University Hospitals, Cambridge, CB2 0QQ, UK; Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 OXY, UK
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Claire E L Smith
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | - Hannie Kremer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Susan Downes
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Oxford Eye Hospital, Oxford University Hospitals NHS Trust and Nuffield Laboratory of Ophthalmology, University of Oxford, Oxford, OX3 9DU, UK
| | - Graeme C Black
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester, M13 9WL, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Chris F Inglehearn
- UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, LS2 9JT, UK
| | | | - Robert K Koenekoop
- Department of Paediatric Surgery, Human Genetics and Ophthalmology, McGill University, Montréal, QC H4A 3J1, Canada
| | - Michel Michaelides
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership; Moorfields Eye Hospital, London, EC1V 2PD, UK
| | - Raj S Ramesar
- University of Cape Town/MRC Genomic and Precision Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa
| | - Carel B Hoyng
- Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Stefan Mundlos
- Max Planck Institute for Molecular Genetics, RG Development & Disease, Berlin, 14195, Germany; Institute for Medical and Human Genetics, Charité - Universitätsmedizin, Berlin, 10117, Germany
| | - Musa M Mhlanga
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Gene Expression and Biophysics Group, Division of Chemical, Systems and Synthetic Biology, Department of Integrative Biomedical Science, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, 7935, South Africa; Gene Expression and Biophysics Unit, Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, Lisbon, 1649-028, Portugal; Epigenomics & Single Cell Biophysics Group, Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University, Nijmegen, 6525 GA, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands
| | - Michael E Cheetham
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands; Donders Institute for Brain Cognition and Behaviour, Radboud University Medical Center, Nijmegen, 6500 HB, the Netherlands.
| | - Alison J Hardcastle
- UCL Institute of Ophthalmology, London, EC1V 9EL, UK; UK Inherited Retinal Disease Consortium; Genomics England Clinical Interpretation Partnership
| |
Collapse
|
25
|
Al-khuzaei S, Broadgate S, Halford S, Jolly JK, Shanks M, Clouston P, Downes SM. Novel Pathogenic Sequence Variants in NR2E3 and Clinical Findings in Three Patients. Genes (Basel) 2020; 11:E1288. [PMID: 33138239 PMCID: PMC7716234 DOI: 10.3390/genes11111288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 10/21/2020] [Accepted: 10/28/2020] [Indexed: 01/08/2023] Open
Abstract
A retrospective review of the clinical records of patients seen at the Oxford Eye Hospital identified as having NR2E3 mutations was performed. The data included symptoms, best-corrected visual acuity, multimodal retinal imaging, visual fields and electrophysiology testing. Three participants were identified with biallelic NR2E3 pathogenic sequence variants detected using a targeted NGS gene panel, two of which were novel. Participant I was a Nepalese male aged 68 years, and participants II and III were white Caucasian females aged 69 and 10 years old, respectively. All three had childhood onset nyctalopia, a progressive decrease in central vision, and visual field loss. Patients I and III had photopsia, patient II had photosensitivity and patient III also had photophobia. Visual acuities in patients I and II were preserved even into the seventh decade, with the worst visual acuity measured at 6/36. Visual field constriction was severe in participant I, less so in II, and fields were full to bright targets targets in participant III. Electrophysiology testing in all three demonstrated loss of rod function. The three patients share some of the typical distinctive features of NR2E3 retinopathies, as well as a novel clinical observation of foveal ellipsoid thickening.
Collapse
Affiliation(s)
- Saoud Al-khuzaei
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
| | - Suzanne Broadgate
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Stephanie Halford
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Jasleen K. Jolly
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| | - Morag Shanks
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; (M.S.); (P.C.)
| | - Penny Clouston
- Oxford Medical Genetics Laboratory, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK; (M.S.); (P.C.)
| | - Susan M. Downes
- Oxford Eye Hospital, John Radcliffe Hospital, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 9DU, UK; (S.A.-k.); (J.K.J.)
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neuroscience, University of Oxford, Level 6 John Radcliffe Hospital, Headley Way, Oxford OX3 9DU, UK; (S.B.); (S.H.)
| |
Collapse
|
26
|
A CRISPR and high-content imaging assay compliant with ACMG/AMP guidelines for clinical variant interpretation in ciliopathies. Hum Genet 2020; 140:593-607. [PMID: 33095315 PMCID: PMC7981318 DOI: 10.1007/s00439-020-02228-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 10/14/2020] [Indexed: 11/04/2022]
Abstract
Ciliopathies are a broad range of inherited developmental and degenerative diseases associated with structural or functional defects in motile or primary non-motile cilia. There are around 200 known ciliopathy disease genes and whilst genetic testing can provide an accurate diagnosis, 24–60% of ciliopathy patients who undergo genetic testing do not receive a genetic diagnosis. This is partly because following current guidelines from the American College of Medical Genetics and the Association for Molecular Pathology, it is difficult to provide a confident clinical diagnosis of disease caused by missense or non-coding variants, which account for more than one-third of cases of disease. Mutations in PRPF31 are the second most common cause of the degenerative retinal ciliopathy autosomal dominant retinitis pigmentosa. Here, we present a high-throughput high-content imaging assay providing quantitative measure of effect of missense variants in PRPF31 which meets the recently published criteria for a baseline standard in vitro test for clinical variant interpretation. This assay utilizes a new PRPF31+/– human retinal cell line generated using CRISPR gene editing to provide a stable cell line with significantly fewer cilia in which novel missense variants are expressed and characterised. We show that high-content imaging of cells expressing missense variants in a ciliopathy gene on a null background can allow characterisation of variants according to the cilia phenotype. We hope that this will be a useful tool for clinical characterisation of PRPF31 variants of uncertain significance, and can be extended to variant classification in other ciliopathies.
Collapse
|
27
|
Cao L, Peng C, Yu J, Jiang W, Yang J. Identification of two novel PRPF31 mutations in Chinese families with non-syndromic autosomal dominant retinitis pigmentosa. Mol Genet Genomic Med 2020; 8:e1537. [PMID: 33085829 PMCID: PMC7767543 DOI: 10.1002/mgg3.1537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/30/2020] [Accepted: 10/02/2020] [Indexed: 12/05/2022] Open
Abstract
Background Retinitis pigmentosa is a heterogeneous group of inherited retinal diseases leading to progressive vision loss. It has been estimated that the etiology is still unclear in 22%‐40% of cases, indicating that many novel pathogenic variations related to RP remain unidentified in many patients. In this study, our aim was to investigate the disease‐causing variants and function of the variants in two Chinese families with non‐syndromic autosomal dominant retinitis pigmentosa (adRP). Methods Clinical data and peripheral blood DNA samples were collected. Whole exome sequencing (WES) was conducted to screen for variations. Then, the expression of green fluorescent protein (GFP)‐fused wild‐type PRPF31 protein and its variants was evaluated via western blotting and GFP fluorescence detection in vitro. Results Two novel heterozygous variants of PRPF31 (NM_015629.4): c.855+5G>A and c.849_855del (p.Pro284Ilefs*35) were identified respectively in two families. The variant c.855+5G>A is co‐segregated with the disease in adRP‐01 family. The pedigree analysis result for c.849_855del (p. Pro284Ilefs*35) shows an inheritance pattern with incomplete penetrance for adRP‐02 family. The RT‐PCR analysis shows the PRPF31 gene c.855+5G>A leading to the missing from the 997th to the 1405th positions of the PRPF31 gene (NM_015629.4) cDNA. The expressions of the mutant GFP‐fused PRPF31 protein were not detected in HEK293 cells or Cos7 cells via western blotting and immunofluorescence. Conclusions Our findings identified two novel variants in PRPF31 in two Chinese families with adRP, expanding the mutational spectrum of this gene. Functional analysis reveals that these variants lead to the truncation of the PRPF31 protein.
Collapse
Affiliation(s)
- Li Cao
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Chunyan Peng
- The Key Laboratory for Human Disease Gene Study of Sichuan Province, Prenatal Diagnosis Center, Sichuan Provincial People's Hospital, the University of Electronic Science and Technology of China, Chengdu, PR China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China
| | - Jing Yu
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, PR China
| | - Wei Jiang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province, Prenatal Diagnosis Center, Sichuan Provincial People's Hospital, the University of Electronic Science and Technology of China, Chengdu, PR China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China
| | - Jiyun Yang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province, Prenatal Diagnosis Center, Sichuan Provincial People's Hospital, the University of Electronic Science and Technology of China, Chengdu, PR China.,School of Medicine, University of Electronic Science and Technology of China, Chengdu, PR China
| |
Collapse
|
28
|
Foote KG, Wong JJ, Boehm AE, Bensinger E, Porco TC, Roorda A, Duncan JL. Comparing Cone Structure and Function in RHO- and RPGR-Associated Retinitis Pigmentosa. Invest Ophthalmol Vis Sci 2020; 61:42. [PMID: 32343782 PMCID: PMC7401955 DOI: 10.1167/iovs.61.4.42] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Purpose To study cone structure and function in patients with retinitis pigmentosa (RP) owing to mutations in rhodopsin (RHO), expressed in rod outer segments, and mutations in the RP-GTPase regulator (RPGR) gene, expressed in the connecting cilium of rods and cones. Methods Four eyes of 4 patients with RHO mutations, 5 eyes of 5 patients with RPGR mutations, and 4 eyes of 4 normal subjects were studied. Cone structure was studied with confocal and split-detector adaptive optics scanning laser ophthalmoscopy (AOSLO) and spectral-domain optical coherence tomography. Retinal function was measured using a 543-nm AOSLO-mediated adaptive optics microperimetry (AOMP) stimulus. The ratio of sensitivity to cone density was compared between groups using the Wilcoxon rank-sum test. Results AOMP sensitivity/cone density in patients with RPGR mutations was significantly lower than normal (P< 0.001) and lower than patients with RHO mutations (P< 0.015), whereas patients with RHO mutations were similar to normal (P> 0.9). Conclusions Retinal sensitivity/cone density was lower in patients with RPGR mutations than normal and lower than patients with RHO mutations, perhaps because cones express RPGR and degenerate primarily, whereas cones in eyes with RHO mutations die secondary to rod degeneration. High-resolution microperimetry can reveal differences in cone degeneration in patients with different forms of RP.
Collapse
|
29
|
Plana-Bonamaisó A, López-Begines S, Fernández-Justel D, Junza A, Soler-Tapia A, Andilla J, Loza-Alvarez P, Rosa JL, Miralles E, Casals I, Yanes O, de la Villa P, Buey RM, Méndez A. Post-translational regulation of retinal IMPDH1 in vivo to adjust GTP synthesis to illumination conditions. eLife 2020; 9:56418. [PMID: 32254022 PMCID: PMC7176436 DOI: 10.7554/elife.56418] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 03/30/2020] [Indexed: 02/06/2023] Open
Abstract
We report the in vivo regulation of Inosine-5´-monophosphate dehydrogenase 1 (IMPDH1) in the retina. IMPDH1 catalyzes the rate-limiting step in the de novo synthesis of guanine nucleotides, impacting the cellular pools of GMP, GDP and GTP. Guanine nucleotide homeostasis is central to photoreceptor cells, where cGMP is the signal transducing molecule in the light response. Mutations in IMPDH1 lead to inherited blindness. We unveil a light-dependent phosphorylation of retinal IMPDH1 at Thr159/Ser160 in the Bateman domain that desensitizes the enzyme to allosteric inhibition by GDP/GTP. When exposed to bright light, living mice increase the rate of GTP and ATP synthesis in their retinas; concomitant with IMPDH1 aggregate formation at the outer segment layer. Inhibiting IMPDH activity in living mice delays rod mass recovery. We unveil a novel mechanism of regulation of IMPDH1 in vivo, important for understanding GTP homeostasis in the retina and the pathogenesis of adRP10 IMPDH1 mutations.
Collapse
Affiliation(s)
- Anna Plana-Bonamaisó
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut de Neurociències, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Santiago López-Begines
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - David Fernández-Justel
- Metabolic Engineering Group, Department of Microbiology and Genetics. University of Salamanca, Salamanca, Spain
| | - Alexandra Junza
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
| | - Ariadna Soler-Tapia
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Jordi Andilla
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Castelldefels, Spain
| | - Jose Luis Rosa
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| | - Esther Miralles
- Centres Cientifics i Tecnològics (CCiTUB), University of Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Isidre Casals
- Centres Cientifics i Tecnològics (CCiTUB), University of Barcelona, Parc Científic de Barcelona, Barcelona, Spain
| | - Oscar Yanes
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering, Universitat Rovira i Virgili, Tarragona, Spain
| | - Pedro de la Villa
- Physiology Unit, Dept of Systems Biology, School of Medicine, University of Alcalá, Madrid, Spain.,Visual Neurophysiology Group-IRYCIS, Madrid, Spain
| | - Ruben M Buey
- Metabolic Engineering Group, Department of Microbiology and Genetics. University of Salamanca, Salamanca, Spain
| | - Ana Méndez
- Department of Physiological Sciences, School of Medicine, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut de Neurociències, Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain.,Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), Campus Universitari de Bellvitge, University of Barcelona, Barcelona, Spain
| |
Collapse
|
30
|
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
|
31
|
Chen ZJ, Lin KH, Lee SH, Shen RJ, Feng ZK, Wang XF, Huang XF, Huang ZQ, Jin ZB. Mutation spectrum and genotype-phenotype correlation of inherited retinal dystrophy in Taiwan. Clin Exp Ophthalmol 2020; 48:486-499. [PMID: 31872526 DOI: 10.1111/ceo.13708] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/15/2019] [Accepted: 12/15/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Inherited retinal dystrophy (IRD) is a group of irreversible retinal degenerative disorders with significant genotypic and phenotypic heterogeneity, which cause difficulty in making a precise clinical diagnosis. Furthermore, the mutation spectrum of IRD in Taiwan remains unknown. Therefore, our study focused on investigating the spectrum of mutations among Taiwanese families with IRD using targeted exome sequencing (TES) technology. METHODS We recruited a total of 60 unrelated Taiwanese families with IRD; most of them were retinitis pigmentosa. We employed TES to investigate 284 candidate genes. Bioinformatics analysis, Sanger sequencing-based co-segregation testing, and computational assessment were performed to validate each mutation and its pathogenicity. The genotype-phenotype correlation was analysed in all patients with mutations defined in the guidelines provided by the American College of Medical Genetics. RESULTS We successfully identified genetic causes in 32 families (detection rate of 53.3%). Among them, 16 had a sporadic inheritance (16/36, 44.4%); eight had an autosomal recessive inheritance (8/14, 57.1%); four had an autosomal dominant inheritance (4/5, 80%); four had an X-linked inheritance (4/5, 80%). Among 38 pathological mutations in 19 known genes, 20 mutations are reported here for the first time. Novel mutation spectrum and genotype-phenotype correlations were revealed as well. CONCLUSION Here we achieved a detection rate of 53.3% and elucidated the mutation spectrum in Taiwanese families with IRD for the first time. The results indicated that CYP4V2 and USH2A might be the most common pathogenic genes in IRD patients in Taiwan.
Collapse
Affiliation(s)
- Zhen-Ji Chen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Keng-Hung Lin
- Department of Ophthalmology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Shi-Huang Lee
- Department of Ophthalmology, Taichung Tzu Chi Hospital, Taichung, Taiwan
| | - Ren-Juan Shen
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhuo-Kun Feng
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiao-Fang Wang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Xiu-Feng Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zhi-Qin Huang
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| | - Zi-Bing Jin
- Division of Ophthalmic Genetics, The Eye Hospital, Wenzhou Medical University, Wenzhou, China.,Lab for Stem Cell & Retinal Regeneration, Institute of Stem Cell Research, Wenzhou Medical University, Wenzhou, China.,National Center for International Research in Regenerative Medicine and Neurogenetics, Wenzhou Medical University, Wenzhou, China.,State Key Laboratory of Ophthalmology, Optometry and Visual Science, National Clinical Research Center for Ocular Diseases, Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
32
|
Yau EH, Taggart RT, Zuber M, Trujillo AJ, Fayazi ZS, Butler MC, Sheflin LG, Breen JB, Yu D, Sullivan JM. Systematic Screening, Rational Development, and Initial Optimization of Efficacious RNA Silencing Agents for Human Rod Opsin Therapeutics. Transl Vis Sci Technol 2019; 8:28. [PMID: 31853424 PMCID: PMC6908138 DOI: 10.1167/tvst.8.6.28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 07/15/2019] [Indexed: 12/13/2022] Open
Abstract
Purpose To systematically evaluate human rod opsin (hRHO) mRNA for potential target sites sensitive to posttranscriptional gene silencing (PTGS) by hammerhead ribozyme (hhRz) or RNA interference (RNAi) in human cells. To develop a comprehensive strategy to identify and optimize lead candidate agents for PTGS gene therapeutics. Methods In multidisciplinary RNA drug discovery, computational mRNA accessibility and in vitro experimental methods using reverse transcription–polymerase chain reaction (RT-PCR) were used to map accessibility in full-length hRHO transcripts. HhRzs targeted predicted accessible and inaccessible sites and were screened for cellular knockdown using a bicistronic reporter construct. Lead hhRz and RNAi PTGS agents were rationally optimized for target knockdown in human cells. Results Systematic screening of hRHO mRNA targeting agents resulted in lead candidate identification of a novel hhRz embedded in an RNA scaffold. Rational optimization strategies identified a minimal 725 hhRz as the most active agent. Recently identified tertiary accessory elements did not enhance activity. A 725-short-hairpin RNA (shRNA) agent exerts log-order knockdown. Silent modulation of the 725-hhRz target site in hRHO mRNA resulted in resistance to knockdown. Conclusions Combining rational RNA drug design with cell-based screening allowed rapid identification of lead agents targeting hRHO. Optimization strategies identified the agent with highest intracellular activity. These agents have therapeutic potential in a mutation-independent strategy for adRP, or other degenerations where hRHO is a target. This approach can be broadly applied to any validated target mRNA, regardless of the disease. Translational Relevance This work establishes a platform approach to develop RNA biologicals for the treatment of human disease.
Collapse
Affiliation(s)
- Edwin H Yau
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Department of Medicine, Department of Cancer Genetics and Genomics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Robert T Taggart
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Mohammed Zuber
- Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Current affiliation: Biologist, Office of Pesticide Programs, Environmental Protection Agency, Arlington, VA, USA
| | - Alexandria J Trujillo
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Zahra S Fayazi
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA
| | - Mark C Butler
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Current affiliation: Custom ColLABorators, Buffalo, NY, USA
| | - Lowell G Sheflin
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA
| | - Jennifer B Breen
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Research Analyst II, Athenex, Buffalo, NY, USA
| | - Dian Yu
- Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Current affiliation: Washington National Eye Center, Medstar Georgetown University Hospital/Medstar Washington Hospital, Washington, DC, USA
| | - Jack M Sullivan
- Department of Pharmacology/Toxicology, University at Buffalo-SUNY, Buffalo, NY, USA.,Department of Ophthalmology (Ross Eye Institute), University at Buffalo-SUNY, Buffalo, NY, USA.,Research Service, VA Western New York Healthcare System, Buffalo, NY, USA.,Department of Physiology/Biophysics, University at Buffalo-SUNY, Buffalo, NY, USA.,Neuroscience Program, University at Buffalo-SUNY, Buffalo, NY, USA.,SUNY Eye Institute, Albany, NY, USA.,RNA Institute at University at Albany-SUNY, Albany, NY, USA
| |
Collapse
|
33
|
Kelch-like proteins: Physiological functions and relationships with diseases. Pharmacol Res 2019; 148:104404. [DOI: 10.1016/j.phrs.2019.104404] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 02/07/2023]
|
34
|
Genome Editing as a Treatment for the Most Prevalent Causative Genes of Autosomal Dominant Retinitis Pigmentosa. Int J Mol Sci 2019; 20:ijms20102542. [PMID: 31126147 PMCID: PMC6567127 DOI: 10.3390/ijms20102542] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 05/15/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023] Open
Abstract
: Inherited retinal dystrophies (IRDs) are a clinically and genetically heterogeneous group of diseases with more than 250 causative genes. The most common form is retinitis pigmentosa. IRDs lead to vision impairment for which there is no universal cure. Encouragingly, a first gene supplementation therapy has been approved for an autosomal recessive IRD. However, for autosomal dominant IRDs, gene supplementation therapy is not always pertinent because haploinsufficiency is not the only cause. Disease-causing mechanisms are often gain-of-function or dominant-negative, which usually require alternative therapeutic approaches. In such cases, genome-editing technology has raised hopes for treatment. Genome editing could be used to i) invalidate both alleles, followed by supplementation of the wild type gene, ii) specifically invalidate the mutant allele, with or without gene supplementation, or iii) to correct the mutant allele. We review here the most prevalent genes causing autosomal dominant retinitis pigmentosa and the most appropriate genome-editing strategy that could be used to target their different causative mutations.
Collapse
|
35
|
Talib M, van Schooneveld MJ, Van Cauwenbergh C, Wijnholds J, Ten Brink JB, Florijn RJ, Schalij-Delfos NE, Dagnelie G, van Genderen MM, De Baere E, Meester-Smoor MA, De Zaeytijd J, Cremers FPM, van den Born LI, Thiadens AA, Hoyng CB, Klaver CC, Leroy BP, Bergen AA, Boon CJF. The Spectrum of Structural and Functional Abnormalities in Female Carriers of Pathogenic Variants in the RPGR Gene. Invest Ophthalmol Vis Sci 2019; 59:4123-4133. [PMID: 30105367 DOI: 10.1167/iovs.17-23453] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The purpose of this study was to investigate the phenotype and long-term clinical course of female carriers of RPGR mutations. Methods This was a retrospective cohort study of 125 heterozygous RPGR mutation carriers from 49 families. Results Eighty-three heterozygotes were from retinitis pigmentosa (RP) pedigrees, 37 were from cone-/cone-rod dystrophy (COD/CORD) pedigrees, and 5 heterozygotes were from pedigrees with mixed RP/CORD or unknown diagnosis. Mutations were located in exon 1-14 and in ORF15 in 42 of 125 (34%) and 83 of 125 (66%) subjects, respectively. The mean age at the first examination was 34.4 years (range, 2.1 to 86.0 years). The median follow-up time in heterozygotes with longitudinal data (n = 62) was 12.2 years (range, 1.1 to 52.2 years). Retinal pigmentary changes were present in 73 (58%) individuals. Visual symptoms were reported in 51 (40%) cases. Subjects with both symptoms and pigmentary fundus changes were older than the other heterozygotes (P = 0.01) and had thinner foveal outer retinas (P = 0.006). Complete expression of the RP or CORD phenotype was observed in 29 (23%) heterozygotes, although usually in milder forms than in affected male relatives. Best-corrected visual acuity (BCVA) was <20/40 and <20/400 in at least one eye in 45 of 116 (39%) and 11 of 116 (9%) heterozygotes, respectively. Myopia was observed in 74 of 101 (73%) subjects and was associated with lower BCVA (P = 0.006). Increasing age was associated with lower BCVA (P = 0.002) and decreasing visual field size (P = 0.012; I4e isopter). Conclusions RPGR mutations lead to a phenotypic spectrum in female carriers, with myopia as a significantly aggravating factor. Complete disease expression is observed in some individuals, who may benefit from future (gene) therapeutic options.
Collapse
Affiliation(s)
- Mays Talib
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Caroline Van Cauwenbergh
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jan Wijnholds
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jacoline B Ten Brink
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands
| | - Ralph J Florijn
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands
| | | | - Gislin Dagnelie
- Wilmer Eye Institute, Johns Hopkins University, Baltimore, Maryland, United States
| | - Maria M van Genderen
- Bartiméus, Diagnostic Centre for Complex Visual Disorders, Zeist, The Netherlands
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Frans P M Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Alberta A Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Caroline C Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart P Leroy
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium.,Ophthalmic Genetics & Visual Electrophysiology, Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States
| | - Arthur A Bergen
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Amsterdam UMC, University of Amsterdam, The Netherlands
| |
Collapse
|
36
|
Wheway G, Nazlamova L, Meshad N, Hunt S, Jackson N, Churchill A. A Combined in silico, in vitro and Clinical Approach to Characterize Novel Pathogenic Missense Variants in PRPF31 in Retinitis Pigmentosa. Front Genet 2019; 10:248. [PMID: 30967900 PMCID: PMC6438860 DOI: 10.3389/fgene.2019.00248] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 03/05/2019] [Indexed: 11/30/2022] Open
Abstract
At least six different proteins of the spliceosome, including PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, and SNRNP200, are mutated in autosomal dominant retinitis pigmentosa (adRP). These proteins have recently been shown to localize to the base of the connecting cilium of the retinal photoreceptor cells, elucidating this form of RP as a retinal ciliopathy. In the case of loss-of-function variants in these genes, pathogenicity can easily be ascribed. In the case of missense variants, this is more challenging. Furthermore, the exact molecular mechanism of disease in this form of RP remains poorly understood. In this paper we take advantage of the recently published cryo EM-resolved structure of the entire human spliceosome, to predict the effect of a novel missense variant in one component of the spliceosome; PRPF31, found in a patient attending the genetics eye clinic at Bristol Eye Hospital. Monoallelic variants in PRPF31 are a common cause of autosomal dominant retinitis pigmentosa (adRP) with incomplete penetrance. We use in vitro studies to confirm pathogenicity of this novel variant PRPF31 c.341T > A, p.Ile114Asn. This work demonstrates how in silico modeling of structural effects of missense variants on cryo-EM resolved protein complexes can contribute to predicting pathogenicity of novel variants, in combination with in vitro and clinical studies. It is currently a considerable challenge to assign pathogenic status to missense variants in these proteins.
Collapse
Affiliation(s)
- Gabrielle Wheway
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Liliya Nazlamova
- Centre for Research in Biosciences, University of the West of England, Bristol, United Kingdom
| | - Nervine Meshad
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Samantha Hunt
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Nicola Jackson
- Clinical Genetics Service, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| | - Amanda Churchill
- Bristol Eye Hospital, University Hospitals Bristol NHS Foundation Trust, Bristol, United Kingdom
| |
Collapse
|
37
|
Foote KG, Loumou P, Griffin S, Qin J, Ratnam K, Porco TC, Roorda A, Duncan JL. Relationship Between Foveal Cone Structure and Visual Acuity Measured With Adaptive Optics Scanning Laser Ophthalmoscopy in Retinal Degeneration. Invest Ophthalmol Vis Sci 2019; 59:3385-3393. [PMID: 30025078 PMCID: PMC6038831 DOI: 10.1167/iovs.17-23708] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Purpose To evaluate foveal function in patients with inherited retinal degenerations (IRD) by measuring visual acuity (VA) after correction of higher-order aberrations. Methods Adaptive optics scanning laser ophthalmoscopy (AOSLO) was used to image cones in 4 healthy subjects and 15 patients with IRD. The 840-nm scanning laser delivered an "E" optotype to measure AOSLO-mediated VA (AOSLO-VA). Cone spacing was measured at the preferred retinal locus by two independent graders and the percentage of cones below the average density of 47 age-similar healthy subjects was computed. Cone spacing was correlated with best-corrected VA measured with the Early Treatment of Diabetic Retinopathy Study protocol (ETDRS-VA), AOSLO-VA, and foveal sensitivity. Results ETDRS-VA significantly correlated with AOSLO-VA (ρ = 0.79, 95% confidence interval [CI] 0.5-0.9). Cone spacing correlated with AOSLO-VA (ρ = 0.54, 95% CI 0.02-0.7), and negatively correlated with ETDRS letters read (ρ = -0.64, 95% CI -0.8 to -0.2). AOSLO-VA remained ≥20/20 until cones decreased to 40.2% (CI 31.1-45.5) below normal. Similarly, ETDRS-VA remained ≥20/20 until cones were 42.0% (95% CI 36.5-46.1) below normal. Cone spacing z scores negatively correlated with foveal sensitivity (ρ = -0.79, 95% CI -0.9 to -0.4) and foveal sensitivity was ≥35 dB until cones were 43.1% (95% CI 39.3-46.6) below average. Conclusions VA and foveal cone spacing were weakly correlated until cones were reduced by 40% to 43% below normal. The relationship suggests that VA is an insensitive measure of foveal cone survival; cone spacing may be a more sensitive measure of cone loss.
Collapse
Affiliation(s)
- Katharina G Foote
- School of Optometry and Vision Science Graduate Group, University of California, Berkeley, California, United States.,Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Panagiota Loumou
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Shane Griffin
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Jia Qin
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| | - Kavitha Ratnam
- School of Optometry and Vision Science Graduate Group, University of California, Berkeley, California, United States
| | - Travis C Porco
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States.,Proctor Foundation, University of California, San Francisco, California, United States
| | - Austin Roorda
- School of Optometry and Vision Science Graduate Group, University of California, Berkeley, California, United States
| | - Jacque L Duncan
- Department of Ophthalmology, University of California, San Francisco, San Francisco, California, United States
| |
Collapse
|
38
|
Mutation-independent rhodopsin gene therapy by knockdown and replacement with a single AAV vector. Proc Natl Acad Sci U S A 2018; 115:E8547-E8556. [PMID: 30127005 DOI: 10.1073/pnas.1805055115] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Inherited retinal degenerations are caused by mutations in >250 genes that affect photoreceptor cells or the retinal pigment epithelium and result in vision loss. For autosomal recessive and X-linked retinal degenerations, significant progress has been achieved in the field of gene therapy as evidenced by the growing number of clinical trials and the recent commercialization of the first gene therapy for a form of congenital blindness. However, despite significant efforts to develop a treatment for the most common form of autosomal dominant retinitis pigmentosa (adRP) caused by >150 mutations in the rhodopsin (RHO) gene, translation to the clinic has stalled. Here, we identified a highly efficient shRNA that targets human (and canine) RHO in a mutation-independent manner. In a single adeno-associated viral (AAV) vector we combined this shRNA with a human RHO replacement cDNA made resistant to RNA interference and tested this construct in a naturally occurring canine model of RHO-adRP. Subretinal vector injections led to nearly complete suppression of endogenous canine RHO RNA, while the human RHO replacement cDNA resulted in up to 30% of normal RHO protein levels. Noninvasive retinal imaging showed photoreceptors in treated areas were completely protected from retinal degeneration. Histopathology confirmed retention of normal photoreceptor structure and RHO expression in rod outer segments. Long-term (>8 mo) follow-up by retinal imaging and electroretinography indicated stable structural and functional preservation. The efficacy of this gene therapy in a clinically relevant large-animal model paves the way for treating patients with RHO-adRP.
Collapse
|
39
|
Long-term clinical course of 2 Japanese patients with PRPF31-related retinitis pigmentosa. Jpn J Ophthalmol 2018; 62:186-193. [PMID: 29305715 DOI: 10.1007/s10384-017-0560-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 11/28/2017] [Indexed: 12/17/2022]
Abstract
PURPOSE To assess the long-term clinical course of 2 patients with PRPF31-related retinitis pigmentosa (RP). PATIENTS AND METHODS We clinically examined 2 unrelated patients with RP and collected peripheral blood samples from them. Ophthalmic examinations, including best-corrected visual acuity measurements, Goldmann perimetry, full-field electroretinography, fundus autofluorescence imaging, and optical coherence tomography, were also performed. The visual acuity and visual field were continuously monitored. To identify the causative mutations, 74 genes known to cause RP or Leber congenital amaurosis were examined via targeted next-generation sequencing. RESULTS The clinical courses of both patients were similar. The onset of nyctalopia occurred in the first decade. Fundus examination showed typical RP. Although the patients' visual acuity was relatively preserved even into the fourth decade, the visual field area exhibited rapid deterioration in the mid-teens, with severe concentric constriction in the third decade. Mutation analysis revealed PRPF31 mutations as the cause for autosomal dominant RP in both patients. CONCLUSIONS To the best of our knowledge, few reports of long-term observations pertaining to patients with PRPF31-related RP have been published. The findings reported herein, especially those relating to the progressive degeneration of the visual field, may ultimately play a role in the provision of high-quality counseling for patients with this condition.
Collapse
|
40
|
Daiger SP, Bowne SJ, Sullivan LS, Branham K, Wheaton DK, Jones KD, Avery CE, Cadena ED, Heckenlively JR, Birch DG. Molecular Findings in Families with an Initial Diagnose of Autosomal Dominant Retinitis Pigmentosa (adRP). ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1074:237-245. [PMID: 29721949 DOI: 10.1007/978-3-319-75402-4_29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Genetic testing of probands in families with an initial diagnosis of autosomal dominant retinitis pigmentosa (adRP) usually confirms the diagnosis, but there are exceptions. We report results of genetic testing in a large cohort of adRP families with an emphasis on exceptional cases including X-linked RP with affected females; homozygous affected individuals in families with heterozygous, dominant disease; and independently segregating mutations in the same family. Genetic testing was conducted in more than 700 families with a provisional or probable diagnosis of adRP. Exceptions to the proposed mode of inheritance were extracted from our comprehensive patient and family database. In a subset of 300 well-characterized families with a probable diagnosis of adRP, 195 (70%) have dominant mutations in known adRP genes but 25 (8%) have X-linked mutations, 3 (1%) have multiple segregating mutations, and 3 (1%) have dominant-acting mutations in genes previously associated with recessive disease. It is currently possible to determine the underlying disease-causing gene and mutation in approximately 80% of families with an initial diagnosis of adRP, but 10% of "adRP" families have a variant mode of inheritance. Informed genetic diagnosis requires close collaboration between clinicians, genetic counselors, and laboratory scientists.
Collapse
Affiliation(s)
- Stephen P Daiger
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA. .,Ruiz Department of Ophthalmology and Visual Science, UTHealth, Houston, TX, USA.
| | - Sara J Bowne
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Kari Branham
- Kellogg Eye Center, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Cheryl E Avery
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | - Elizabeth D Cadena
- Human Genetics Center, School of Public Health, The University of Texas Health Science Center (UTHealth), Houston, TX, USA
| | | | - David G Birch
- The Retina Foundation of the Southwest, Dallas, TX, USA
| |
Collapse
|
41
|
Hariri AH, Gui W, Datoo O'Keefe GA, Ip MS, Sadda SR, Gorin MB. Ultra-Widefield Fundus Autofluorescence Imaging of Patients with Retinitis Pigmentosa: A Standardized Grading System in Different Genotypes. Ophthalmol Retina 2017; 2:735-745. [PMID: 31047384 DOI: 10.1016/j.oret.2017.10.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 10/18/2022]
Abstract
PURPOSE To report a genotype-phenotype correlation study of patients with retinitis pigmentosa (RP) based on ultra-widefield (UWF) fundus autofluorescence (FAF) imaging. DESIGN Case series. PARTICIPANTS Thirty-four patients with RP. METHODS This retrospective study included RP patients with confirmed causative genetic variants and UWF FAF imaging data. Qualitative grading criteria including the pattern of macular abnormal autofluorescence, decreased autofluorescence (DAF), and its extent and distribution were applied to evaluate the genotype-phenotype correlation. MAIN OUTCOME MEASURES The main parameters measured were increased or decreased patterns and extent of autofluorescence. RESULTS Thirty-four unrelated patients 38±19 years of age (range, 9-82 years) were enrolled. Mutations in 17 different genes were detected in patients, including 7 patients having mutations in USH2A, 4 in DHDDS, 4 in RPGR, 3 in PRPF31, and 3 in RP1. Patients with nummular DAF and widespread DAF were significantly older (59±14 years and 56±19 years, respectively). All 3 patients with PRPF31 mutations showed an abnormal macular ring hyperautofluorescence and a circular pattern of coarse DAF distributed in Early Treatment Diabetic Retinopathy Study fields 1, 2, and 3 with sparing of the far periphery. In other genotypes, no specific DAF or macular abnormal autofluorescence pattern could be discerned. CONCLUSIONS Specific UWF FAF characteristics in RP patients were correlated strongly with patient age and stage of the disease. Particular UWF FAF characteristics were found to be more prominent in a unique genotype.
Collapse
Affiliation(s)
- Amir H Hariri
- Doheny Image Reading Center, Doheny Eye Institute, Los Angeles, California; Department of Ophthalmology, David Geffen School of Medicine of the University of California, Los Angeles, Los Angeles, California
| | - Wei Gui
- Department of Ophthalmology, David Geffen School of Medicine of the University of California, Los Angeles, Los Angeles, California.
| | | | - Michael S Ip
- Doheny Image Reading Center, Doheny Eye Institute, Los Angeles, California; Department of Ophthalmology, David Geffen School of Medicine of the University of California, Los Angeles, Los Angeles, California
| | - SriniVas R Sadda
- Doheny Image Reading Center, Doheny Eye Institute, Los Angeles, California; Department of Ophthalmology, David Geffen School of Medicine of the University of California, Los Angeles, Los Angeles, California
| | - Michael B Gorin
- Department of Ophthalmology, David Geffen School of Medicine of the University of California, Los Angeles, Los Angeles, California
| |
Collapse
|
42
|
Opposing Effects of Valproic Acid Treatment Mediated by Histone Deacetylase Inhibitor Activity in Four Transgenic X. laevis Models of Retinitis Pigmentosa. J Neurosci 2017; 37:1039-1054. [PMID: 28490005 DOI: 10.1523/jneurosci.1647-16.2016] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 10/18/2016] [Accepted: 11/22/2016] [Indexed: 12/19/2022] Open
Abstract
Retinitis pigmentosa (RP) is an inherited retinal degeneration (RD) that leads to blindness for which no treatment is available. RP is frequently caused by mutations in Rhodopsin; in some animal models, RD is exacerbated by light. Valproic acid (VPA) is a proposed treatment for RP and other neurodegenerative disorders, with a phase II trial for RP under way. However, the therapeutic mechanism is unclear, with minimal research supporting its use in RP. We investigated the effects of VPA on Xenopus laevis models of RP expressing human P23H, T17M, T4K, and Q344ter rhodopsins, which are associated with RP in humans. VPA ameliorated RD associated with P23H rhodopsin and promoted clearing of mutant rhodopsin from photoreceptors. The effect was equal to that of dark rearing, with no additive effect observed. Rescue of visual function was confirmed by electroretinography. In contrast, VPA exacerbated RD caused by T17M rhodopsin in light, but had no effect in darkness. Effects in T4K and Q344ter rhodopsin models were also negative. These effects of VPA were paralleled by treatment with three additional histone deacetylase (HDAC) inhibitors, but not other antipsychotics, chemical chaperones, or VPA structural analogues. In WT retinas, VPA treatment increased histone H3 acetylation. In addition, electron microscopy showed increased autophagosomes in rod inner segments with HDAC inhibitor (HDACi) treatment, potentially linking the therapeutic effects in P23H rhodopsin animals and negative effects in other models with autophagy. Our results suggest that the success or failure of VPA treatment is dependent on genotype and that HDACi treatment is contraindicated for some RP cases.SIGNIFICANCE STATEMENT Retinitis pigmentosa (RP) is an inherited, degenerative retinal disease that leads to blindness for which no therapy is available. We determined that valproic acid (VPA), currently undergoing a phase II trial for RP, has both beneficial and detrimental effects in animal models of RP depending on the underlying disease mechanism and that both effects are due to histone deacetylase (HDAC) inhibition possibly linked to autophagy regulation. Off-label use of VPA and other HDAC inhibitors for the treatment of RP should be limited to the research setting until this effect is understood and can be predicted. Our study suggests that, unless genotype is accounted for, clinical trials for RP treatments may give negative results due to multiple disease mechanisms with differential responses to therapeutic interventions.
Collapse
|
43
|
Ramkumar HL, Gudiseva HV, Kishaba KT, Suk JJ, Verma R, Tadimeti K, Thorson JA, Ayyagari R. A Report on Molecular Diagnostic Testing for Inherited Retinal Dystrophies by Targeted Genetic Analyses. Genet Test Mol Biomarkers 2016; 21:66-73. [PMID: 28005406 DOI: 10.1089/gtmb.2016.0251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM To test the utility of targeted sequencing as a method of clinical molecular testing in patients diagnosed with inherited retinal degeneration (IRD). METHODS After genetic counseling, peripheral blood was drawn from 188 probands and 36 carriers of IRD. Single gene testing was performed on each patient in a Clinical Laboratory Improvement Amendment (CLIA) certified laboratory. DNA was isolated, and all exons in the gene of interest were analyzed along with 20 base pairs of flanking intronic sequence. Genetic testing was most often performed on ABCA4, CTRP5, ELOV4, BEST1, CRB1, and PRPH2. Pathogenicity of novel sequence changes was predicted by PolyPhen2 and sorting intolerant from tolerant (SIFT). RESULTS Of the 225 genetic tests performed, 150 were for recessive IRD, and 75 were for dominant IRD. A positive molecular diagnosis was made in 70 (59%) of probands with recessive IRD and 19 (26%) probands with dominant IRD. Analysis confirmed 12 (34%) of individuals as carriers of familial mutations associated with IRD. Thirty-two novel variants were identified; among these, 17 sequence changes in four genes were predicted to be possibly or probably damaging including: ABCA4 (14), BEST1 (2), PRPH2 (1), and TIMP3 (1). CONCLUSIONS Targeted analysis of clinically suspected genes in 225 subjects resulted in a positive molecular diagnosis in 26% of patients with dominant IRD and 59% of patients with recessive IRD. Novel damaging mutations were identified in four genes. Single gene screening is not an ideal method for diagnostic testing given the phenotypic and genetic heterogeneity among IRD cases. High-throughput sequencing of all genes associated with retinal degeneration may be more efficient for molecular diagnosis.
Collapse
Affiliation(s)
- Hema L Ramkumar
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - Harini V Gudiseva
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - Kameron T Kishaba
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - John J Suk
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - Rohan Verma
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - Keerti Tadimeti
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| | - John A Thorson
- 2 Department of Pathology, University of California , San Diego, La Jolla, California
| | - Radha Ayyagari
- 1 Shiley Eye Institute, Jacobs Retina Center, University of California , San Diego, La Jolla, California
| |
Collapse
|
44
|
Zhong Z, Yan M, Sun W, Wu Z, Han L, Zhou Z, Zheng F, Chen J. Two novel mutations in PRPF3 causing autosomal dominant retinitis pigmentosa. Sci Rep 2016; 6:37840. [PMID: 27886254 PMCID: PMC5122955 DOI: 10.1038/srep37840] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 11/02/2016] [Indexed: 11/10/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous set of hereditary eye diseases, characterized by selective death of photoreceptor cells in the retina, resulting in progressive visual impairment. Approximately 20–40% of RP cases are autosomal dominant RP (ADRP). In this study, a Chinese ADRP family previously localized to the region between D1S2819 and D1S2635 was sequenced via whole-exome sequencing and a variant c.1345C > G (p.R449G) was identified in PRPF3. The Sanger sequencing was performed in probands of additional 95 Chinese ADRP families to investigate the contribution of PRPF3 to ADRP in Chinese population and another variant c.1532A > C (p.H511P) was detected in one family. These two variants, co-segregate with RP in two families respectively and both variants are predicted to be pathological. This is the first report about the spectrum of PRPF3 mutations in Chinese population, leading to the identification of two novel PRPF3 mutations. Only three clustered mutations in PRPF3 have been identified so far in several populations and all are in exon 11. Our study expands the spectrum of PRPF3 mutations in RP. We also demonstrate that PRPF3 mutations are responsible for 2.08% of ADRP families in this cohort indicating that PRPF3 mutations might be relatively rare in Chinese ADRP patients.
Collapse
Affiliation(s)
- Zilin Zhong
- Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Ming Yan
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wan Sun
- Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Zehua Wu
- Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Liyun Han
- Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fang Zheng
- Center for Gene Diagnosis, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Jianjun Chen
- Department of Ophthalmology of Shanghai Tenth People's Hospital, and Tongji Eye Institute, Tongji University School of Medicine, Shanghai, China.,Department of Medical Genetics, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
45
|
Ellingford JM, Barton S, Bhaskar S, O'Sullivan J, Williams SG, Lamb JA, Panda B, Sergouniotis PI, Gillespie RL, Daiger SP, Hall G, Gale T, Lloyd IC, Bishop PN, Ramsden SC, Black GCM. Molecular findings from 537 individuals with inherited retinal disease. J Med Genet 2016; 53:761-767. [PMID: 27208204 PMCID: PMC5106339 DOI: 10.1136/jmedgenet-2016-103837] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/14/2016] [Indexed: 01/12/2023]
Abstract
BACKGROUND Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. METHODS We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). RESULTS Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. CONCLUSIONS Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.
Collapse
Affiliation(s)
- Jamie M Ellingford
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephanie Barton
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Sanjeev Bhaskar
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - James O'Sullivan
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Simon G Williams
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Janine A Lamb
- Institute of Population Health, University of Manchester, Manchester, UK
| | - Binay Panda
- Ganit Labs, Bio-IT Centre, Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Panagiotis I Sergouniotis
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Rachel L Gillespie
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
| | - Stephen P Daiger
- School of Public Health, University of Texas Health Science Center, Houston, Texas, USA
| | - Georgina Hall
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Theodora Gale
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - I Christopher Lloyd
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Paul N Bishop
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Simon C Ramsden
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
| | - Graeme C M Black
- Manchester Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, St Mary's Hospital, Manchester, UK
- Institute of Human Development, University of Manchester, Manchester, UK
- Manchester Royal Eye Hospital, Manchester Academic Health Sciences Centre, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| |
Collapse
|
46
|
Hafler BP, Comander J, Weigel DiFranco C, Place EM, Pierce EA. Course of Ocular Function in PRPF31 Retinitis Pigmentosa. Semin Ophthalmol 2016; 31:49-52. [PMID: 26959129 DOI: 10.3109/08820538.2015.1114856] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Mutations in pre-mRNA splicing factors are the second most common cause of autosomal dominant retinitis pigmentosa, and a major cause of vision loss. The development of gene augmentation therapy for disease caused by mutations in PRPF31 necessitates defining pretreatment characteristics and disease progression of patients with PRPF31-related retinitis pigmentosa. We show rates of decline of visual field area -6.9% per year and 30-Hz flicker cone response of -9.2% per year, which are both similar to observed rates for retinitis pigmentosa. We hypothesize that RNA splicing factor retinitis pigmentosa will be amenable to treatment by AAV-mediated gene therapy, and that understanding the clinical progression rates of PRPF31 retinitis pigmentosa will help with the design of gene therapy clinical trials.
Collapse
Affiliation(s)
- Brian P Hafler
- a Department of Ophthalmology , Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| | - Jason Comander
- a Department of Ophthalmology , Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| | - Carol Weigel DiFranco
- a Department of Ophthalmology , Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| | - Emily M Place
- a Department of Ophthalmology , Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| | - Eric A Pierce
- a Department of Ophthalmology , Massachusetts Eye and Ear Infirmary , Boston , Massachusetts , USA
| |
Collapse
|
47
|
Kabir F, Ullah I, Ali S, Gottsch AD, Naeem MA, Assir MZ, Khan SN, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases. Mol Vis 2016; 22:610-25. [PMID: 27307693 PMCID: PMC4901054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 06/08/2016] [Indexed: 10/31/2022] Open
Abstract
PURPOSE This study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families. METHODS Large consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation. RESULTS The ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples. CONCLUSIONS These results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families.
Collapse
Affiliation(s)
- Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Inayat Ullah
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahbaz Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Shaheen N. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Radha Ayyagari
- Shiley Eye Institute, University of California, San Diego, CA
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| |
Collapse
|
48
|
Abdulridha-Aboud W, Kjellström U, Andréasson S, Ponjavic V. Characterization of macular structure and function in two Swedish families with genetically identified autosomal dominant retinitis pigmentosa. Mol Vis 2016; 22:362-73. [PMID: 27212874 PMCID: PMC4860447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/20/2016] [Indexed: 10/31/2022] Open
Abstract
PURPOSE To study the phenotype in two families with genetically identified autosomal dominant retinitis pigmentosa (adRP) focusing on macular structure and function. METHODS Clinical data were collected at the Department of Ophthalmology, Lund University, Sweden, for affected and unaffected family members from two pedigrees with adRP. Examinations included optical coherence tomography (OCT), full-field electroretinography (ffERG), and multifocal electroretinography (mfERG). Molecular genetic screening was performed for known mutations associated with adRP. RESULTS The mode of inheritance was autosomal dominant in both families. The members of the family with a mutation in the PRPF31 (p.IVS6+1G>T) gene had clinical features characteristic of RP, with severely reduced retinal rod and cone function. The degree of deterioration correlated well with increasing age. The mfERG showed only centrally preserved macular function that correlated well with retinal thinning on OCT. The family with a mutation in the RHO (p.R135W) gene had an extreme intrafamilial variability of the phenotype, with more severe disease in the younger generations. OCT showed pathology, but the degree of morphological changes was not correlated with age or with the mfERG results. The mother, with a de novo mutation in the RHO (p.R135W) gene, had a normal ffERG, and her retinal degeneration was detected merely with the reduced mfERG. CONCLUSIONS These two families demonstrate the extreme inter- and intrafamilial variability in the clinical phenotype of adRP. This is the first Swedish report of the clinical phenotype associated with a mutation in the PRPF31 (p.IVS6+1G>T) gene. Our results indicate that methods for assessment of the central retinal structure and function may improve the detection and characterization of the RP phenotype.
Collapse
|
49
|
Iwabe S, Ying GS, Aguirre GD, Beltran WA. Assessment of visual function and retinal structure following acute light exposure in the light sensitive T4R rhodopsin mutant dog. Exp Eye Res 2016; 146:341-353. [PMID: 27085210 DOI: 10.1016/j.exer.2016.04.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2016] [Revised: 04/08/2016] [Accepted: 04/11/2016] [Indexed: 01/12/2023]
Abstract
The effect of acute exposure to various intensities of white light on visual behavior and retinal structure was evaluated in the T4R RHO dog, a naturally-occurring model of autosomal dominant retinitis pigmentosa due to a mutation in the Rhodopsin gene. A total of 14 dogs (ages: 4-5.5 months) were used in this study: 3 homozygous mutant RHO(T4R/T4R), 8 heterozygous mutant RHO(T4R/+), and 3 normal wild-type (WT) dogs. Following overnight dark adaptation, the left eyes were acutely exposed to bright white light with a monocular Ganzfeld dome, while the contralateral right eye was shielded. Each of the 3 homozygous (RHO(T4R/T4R)) mutant dogs had a single unilateral light exposure (LE) to a different (low, moderate, and high) dose of white light (corneal irradiance/illuminance: 0.1 mW/cm(2), 170 lux; 0.5 mW/cm(2), 820 lux; or 1 mW/cm(2), 1590 lux) for 1 min. All 8 heterozygous (RHO(T4R/+)) mutant dogs were exposed once to the same moderate dose of light. The 3 WT dogs had their left eyes exposed 1, 2, or 3 times to the same highest dose of light. Visual function prior to LE and at 2 weeks and 33 weeks after exposure was objectively assessed in the RHO(T4R/T4R) and WT dogs by using an obstacle-avoidance course. Transit time through the obstacle course was measured under different scotopic to photopic ambient illuminations. Morphological retinal changes were evaluated by non-invasive in vivo cSLO/sdOCT imaging and histology before and at several time-points (2-36 weeks) after light exposure. The analysis of the transit time through the obstacle course showed that no differences were observed in any of mutant or WT dogs at 2 weeks and 33 weeks post LE. The RHO(T4R/T4R) retina exposed to the lowest dose of white light showed no obvious changes in ONL thickness at 2 weeks, but mild decrease was noted 36 weeks after LE. The RHO(T4R/T4R) retina that received a moderate dose (showed an obvious decrease in ONL thickness along the superior and temporal meridians at 2 weeks post LE with more severe damage at 36 weeks post LE in all four meridians. The RHO(T4R/T4R) retina exposed to the high dose showed at 2 weeks after LE extensive ONL damage in all four meridians. This light intensity did not cause any retinal damage in WT dogs even after repeated (up to 3) LE. Analysis of ONL thickness in heterozygous mutant dogs exposed to the moderate dose of light confirmed the increased sensitivity to light damage of the superior/tapetal retina, and the occurrence of an ongoing cell death process several weeks after the acute LE. In conclusion, a short single exposure to a dose of white light that is not retinotoxic in WT dogs causes in the T4R RHO retina an acute loss of ONL in the central to mid peripheral region that keeps progressing over the course of several weeks. However, this severe retinal damage does not affect visual behavior presumably because of islands of surviving photoreceptors found in the area centralis including the newly discovered canine fovea-like area, and the lack of damage to peripheral photoreceptors.
Collapse
Affiliation(s)
- Simone Iwabe
- Section of Ophthalmology, Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Gui-Shuang Ying
- Scheie Eye Institute, Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, USA
| | - Gustavo D Aguirre
- Section of Ophthalmology, Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - William A Beltran
- Section of Ophthalmology, Department of Clinical Studies, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
| |
Collapse
|
50
|
Strom SP, Clark MJ, Martinez A, Garcia S, Abelazeem AA, Matynia A, Parikh S, Sullivan LS, Bowne SJ, Daiger SP, Gorin MB. De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa. PLoS One 2016; 11:e0150944. [PMID: 26964041 PMCID: PMC4786330 DOI: 10.1371/journal.pone.0150944] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/22/2016] [Indexed: 11/19/2022] Open
Abstract
Background Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa. Methods Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing. Results and Conclusions A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in ARL3. Follow-up testing established that this variant occurred de novo in the index case. No additional putative causal variants in ARL3 were identified in the follow-up cohort, suggesting that if ARL3 variants can cause adRP it is an extremely rare phenomenon.
Collapse
Affiliation(s)
- Samuel P. Strom
- Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California, United States of America
- * E-mail:
| | - Michael J. Clark
- Personalis Inc., Menlo Park, California, United States of America
| | - Ariadna Martinez
- Department of Cardiology, Cedars-Sinai Medical Center, Los Angeles, California, United States of America
| | - Sarah Garcia
- Personalis Inc., Menlo Park, California, United States of America
| | | | - Anna Matynia
- Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Sachin Parikh
- Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America
| | - Lori S. Sullivan
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Sara J. Bowne
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Stephen P. Daiger
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Michael B. Gorin
- Jules Stein Eye Institute and Department of Ophthalmology, University of California Los Angeles, Los Angeles, California, United States of America
| |
Collapse
|