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Basharat R, de Bruijn SE, Zahid M, Rodenburg K, Hitti-Malin RJ, Rodríguez-Hidalgo M, Boonen EGM, Jarral A, Mahmood A, Corominas J, Khalil S, Zai JA, Ali G, Ruiz-Ederra J, Gilissen C, Cremers FPM, Ansar M, Panneman DM, Roosing S. Next-generation sequencing to genetically diagnose a diverse range of inherited eye disorders in 15 consanguineous families from Pakistan. Exp Eye Res 2024; 244:109945. [PMID: 38815792 DOI: 10.1016/j.exer.2024.109945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 04/19/2024] [Accepted: 05/27/2024] [Indexed: 06/01/2024]
Abstract
Inherited retinal dystrophies (IRDs) are characterized by photoreceptor dysfunction or degeneration. Clinical and phenotypic overlap between IRDs makes the genetic diagnosis very challenging and comprehensive genomic approaches for accurate diagnosis are frequently required. While there are previous studies on IRDs in Pakistan, causative genes and variants are still unknown for a significant portion of patients. Therefore, there is a need to expand the knowledge of the genetic spectrum of IRDs in Pakistan. Here, we recruited 52 affected and 53 normal individuals from 15 consanguineous Pakistani families presenting non-syndromic and syndromic forms of IRDs. We employed single molecule Molecular Inversion Probes (smMIPs) based panel sequencing and whole genome sequencing to identify the probable disease-causing variants in these families. Using this approach, we obtained a 93% genetic solve rate and identified 16 (likely) causative variants in 14 families, of which seven novel variants were identified in ATOH7, COL18A1, MERTK, NDP, PROM1, PRPF8 and USH2A while nine recurrent variants were identified in CNGA3, CNGB1, HGSNAT, NMNAT1, SIX6 and TULP1. The novel MERTK variant and one recurrent TULP1 variant explained the intra-familial locus heterogeneity in one of the screened families while two recurrent CNGA3 variants explained compound heterozygosity in another family. The identification of variants in known disease-associated genes emphasizes the utilization of time and cost-effective screening approaches for rapid diagnosis. The timely genetic diagnosis will not only identify any associated systemic issues in case of syndromic IRDs, but will also aid in the acceleration of personalized medicine for patients affected with IRDs.
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Affiliation(s)
- Rabia Basharat
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan; Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Suzanne E de Bruijn
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Zahid
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rebekkah J Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - María Rodríguez-Hidalgo
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Erica G M Boonen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Afeefa Jarral
- Department of Biotechnology, Mirpur University of Science and Technology, Mirpur, (AJK), Pakistan
| | - Arif Mahmood
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jordi Corominas
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Sharqa Khalil
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jawaid Ahmed Zai
- Department of Physiology and MLT, University of Sindh, Jamshoro, Pakistan
| | - Ghazanfar Ali
- Department of Biotechnology, University of Azad Jammu and Kashmir, Muzaffarabad, Pakistan
| | - Javier Ruiz-Ederra
- Department of Neuroscience, Biogipuzkoa Health Research Institute, Donostia-San Sebastián, Spain; Department of Dermatology, Ophthalmology, and Otorhinolaryngology, University of the Basque Country (UPV/EHU), Donostia-San Sebastián, Spain
| | - Christian Gilissen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Muhammad Ansar
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Daan M Panneman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands.
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Daich Varela M, Jeste M, de Guimaraes TAC, Mahroo OA, Arno G, Webster AR, Michaelides M. Clinical, Ophthalmic and Genetic Characterization of RPGRIP1-Associated Leber Congenital Amaurosis/Early Onset Severe Retinal Dystrophy. Am J Ophthalmol 2024:S0002-9394(24)00207-1. [PMID: 38768745 DOI: 10.1016/j.ajo.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 05/06/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
PURPOSE To present the clinical characteristics, retinal features, natural history, and genetics of RPGRIP1-Associated Early Onset Severe Retinal Dystrophy (EOSRD)/Leber Congenital Amaurosis (LCA). DESIGN Retrospective case series. METHODS Review of clinical notes, multi-modal retinal imaging, and molecular diagnosis of 18 patients (17 families) with EOSRD/LCA and disease-causing variants in RPGRIP1. RESULTS The mean age of visual symptoms onset was 0.87 ± 1 year (birth-3 years) and the mean age at baseline visit was 11.4 ± 10.2 years (1-39 years). At the baseline visit, 44% of patients were legally blind (range= 2-39 years) and there was no significant association found between age and best corrected visual acuity (BCVA) in cross sectional analysis. Retinal evaluation showed an abolished electroretinogram or a cone-rod dystrophy pattern, none or minimal pigment deposits, a hyperautofluorescent ring at the posterior pole, and a largely preserved central macular architecture, with retained outer nuclear layer and ellipsoid zone island into adulthood. Eleven variants (48%) were previously unreported, and 13 families (76%) had a double null genotype (DN). Twelve patients (67%) had follow up assessments over a 15.7 ± 9.5 year period. The rate of BCVA decline was 0.02 LogMAR (1 letter)/year. CONCLUSIONS RPGRIP1-EOSRD/LCA often presents at birth or early infancy, with nystagmus, decreased VA, hyperopia, and photophobia. Patients with a DN genotype may develop symptoms earlier and have worse vision. Multimodal imaging may show a hyperautofluorescent posterior pole ring, and relatively preserved central macular architecture, suggesting that the condition is a promising candidate for gene supplementation.
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Affiliation(s)
- Malena Daich Varela
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | | | - Thales A C de Guimaraes
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Omar A Mahroo
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom.; St Thomas' Hospital, London, United Kingdom
| | - Gavin Arno
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Andrew R Webster
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom
| | - Michel Michaelides
- Moorfields Eye Hospital, London, United Kingdom.; UCL Institute of Ophthalmology, University College London, London, United Kingdom..
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3
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Munir A, Afsar S, Rehman AU. A systematic review of inherited retinal dystrophies in Pakistan: updates from 1999 to April 2023. BMC Ophthalmol 2024; 24:55. [PMID: 38317096 PMCID: PMC10840256 DOI: 10.1186/s12886-024-03319-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 01/19/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Inherited retinal degenerations (IRDs) are a group of rare genetic conditions affecting retina of the eye that range in prevalence from 1 in 2000 to 1 in 4000 people globally. This review is based on a retrospective analysis of research articles reporting IRDs associated genetic findings in Pakistani families between 1999 and April 2023. METHODS Articles were retrieved through survey of online sources, notably, PubMed, Google Scholar, and Web of Science. Following a stringent selection criterion, a total of 126 research articles and conference abstracts were considered. All reported variants were cross-checked and validated for their correct genomic nomenclature using different online resources/databases, and their pathogenicity scores were explained as per ACMG guidelines. RESULTS A total of 277 unique sequence variants in 87 distinct genes, previously known to cause IRDs, were uncovered. In around 70% cases, parents of the index patient were consanguineously married, and approximately 88.81% of the detected variants were found in a homozygous state. Overall, more than 95% of the IRDs cases were recessively inherited. Missense variants were predominant (41.88%), followed by Indels/frameshift (26.35%), nonsense (19.13%), splice site (12.27%) and synonymous change (0.36%). Non-syndromic IRDs were significantly higher than syndromic IRDs (77.32% vs. 22.68%). Retinitis pigmentosa (RP) was the most frequently observed IRD followed by Leber's congenital amaurosis (LCA). Altogether, mutations in PDE6A gene was the leading cause of IRDs in Pakistani families followed by mutations in TULP1 gene. CONCLUSION In summary, Pakistani families are notable in expressing recessively inherited monogenic disorders including IRDs likely due to the highest prevalence of consanguinity in the country that leads to expression of rare pathogenic variants in homozygous state.
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Affiliation(s)
- Asad Munir
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Salma Afsar
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University, Mansehra, 21300, Khyber Pakhtunkhwa, Pakistan.
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Muñoz-Barrera A, Rubio-Rodríguez LA, Díaz-de Usera A, Jáspez D, Lorenzo-Salazar JM, González-Montelongo R, García-Olivares V, Flores C. From Samples to Germline and Somatic Sequence Variation: A Focus on Next-Generation Sequencing in Melanoma Research. Life (Basel) 2022; 12:1939. [PMID: 36431075 PMCID: PMC9695713 DOI: 10.3390/life12111939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/12/2022] [Accepted: 11/16/2022] [Indexed: 11/24/2022] Open
Abstract
Next-generation sequencing (NGS) applications have flourished in the last decade, permitting the identification of cancer driver genes and profoundly expanding the possibilities of genomic studies of cancer, including melanoma. Here we aimed to present a technical review across many of the methodological approaches brought by the use of NGS applications with a focus on assessing germline and somatic sequence variation. We provide cautionary notes and discuss key technical details involved in library preparation, the most common problems with the samples, and guidance to circumvent them. We also provide an overview of the sequence-based methods for cancer genomics, exposing the pros and cons of targeted sequencing vs. exome or whole-genome sequencing (WGS), the fundamentals of the most common commercial platforms, and a comparison of throughputs and key applications. Details of the steps and the main software involved in the bioinformatics processing of the sequencing results, from preprocessing to variant prioritization and filtering, are also provided in the context of the full spectrum of genetic variation (SNVs, indels, CNVs, structural variation, and gene fusions). Finally, we put the emphasis on selected bioinformatic pipelines behind (a) short-read WGS identification of small germline and somatic variants, (b) detection of gene fusions from transcriptomes, and (c) de novo assembly of genomes from long-read WGS data. Overall, we provide comprehensive guidance across the main methodological procedures involved in obtaining sequencing results for the most common short- and long-read NGS platforms, highlighting key applications in melanoma research.
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Affiliation(s)
- Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), 38600 Santa Cruz de Tenerife, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, 35450 Las Palmas de Gran Canaria, Spain
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Tehreem R, Chen I, Shah MR, Li Y, Khan MA, Afshan K, Chen R, Firasat S. Exome Sequencing Identified Molecular Determinants of Retinal Dystrophies in Nine Consanguineous Pakistani Families. Genes (Basel) 2022; 13:genes13091630. [PMID: 36140798 PMCID: PMC9498396 DOI: 10.3390/genes13091630] [Citation(s) in RCA: 2] [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: 06/03/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 11/16/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) are a heterogeneous group of degenerative disorders of the retina. Retinitis Pigmentosa (RP) is a common type of IRD that causes night blindness and loss of peripheral vision and may progress to blindness. Mutations in more than 300 genes have been associated with syndromic and non-syndromic IRDs. Recessive forms are more frequent in populations where endogamy is a social preference, such as Pakistan. The aim of this study was to identify molecular determinants of IRDs with the common presentation of night blindness in consanguineous Pakistani families. This study included nine consanguineous IRD-affected families that presented autosomal recessive inheritance of the night blindness phenotype. DNA was extracted from blood samples. Targeted exome sequencing of 344 known genes for retinal dystrophies was performed. Screening of nine affected families revealed two novel (c.5571_5576delinsCTAGATand c.471dup in EYS and SPATA7 genes, respectively) and six reported pathogenic mutations (c.304C>A, c.187C>T, c.1560C>A, c.547C>T, c.109del and c.9911_11550del in PDE6A, USH2A, USH2A, NMNAT1, PAX6 and ALMS1 genes, respectively) segregating with disease phenotype in each respective family. Molecular determinants of hereditary retinal dystrophies were identified in all screened families. Identification of novel variants aid future diagnosis of retinal dystrophies and help to provide genetic counseling to affected families.
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Affiliation(s)
- Raeesa Tehreem
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Iris Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mudassar Raza Shah
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muzammil Ahmad Khan
- Gomal Center of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan 29111, Pakistan
- Department of Human Genetics, Sidra Medicine, Doha P.O. Box 26999, Qatar
| | - Kiran Afshan
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
| | - Sabika Firasat
- Department of Zoology, Faculty of Biological Sciences, Quaid-i-Azam University, University Road, Islamabad 45320, Pakistan
- Correspondence: (R.C.); (S.F.); Tel.: +(713)-798-5194 (R.C.); +92-51-9064-4410 (S.F.)
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Dawood M, Lin S, Din TU, Shah IU, Khan N, Jan A, Marwan M, Sultan K, Nowshid M, Tahir R, Ahmed AN, Yasin M, Baple EL, Crosby AH, Saleha S. Novel mutations in PDE6A and CDHR1 cause retinitis pigmentosa in Pakistani families. Int J Ophthalmol 2021; 14:1843-1851. [PMID: 34926197 PMCID: PMC8640774 DOI: 10.18240/ijo.2021.12.06] [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: 02/10/2021] [Accepted: 08/11/2021] [Indexed: 11/23/2022] Open
Abstract
AIM To investigate the genetic basis of autosomal recessive retinitis pigmentosa (arRP) in two consanguineous/ endogamous Pakistani families. METHODS Whole exome sequencing (WES) was performed on genomic DNA samples of patients with arRP to identify disease causing mutations. Sanger sequencing was performed to confirm familial segregation of identified mutations, and potential pathogenicity was determined by predictions of the mutations' functions. RESULTS A novel homozygous frameshift mutation [NM_000440.2:c.1054delG, p. (Gln352Argfs*4); Chr5:g.149286886del (GRCh37)] in the PDE6A gene in an endogamous family and a novel homozygous splice site mutation [NM_033100.3:c.1168-1G>A, Chr10:g.85968484G>A (GRCh37)] in the CDHR1 gene in a consanguineous family were identified. The PDE6A variant p. (Gln352Argfs*4) was predicted to be deleterious or pathogenic, whilst the CDHR1 variant c.1168-1G>A was predicted to result in potential alteration of splicing. CONCLUSION This study expands the spectrum of genetic variants for arRP in Pakistani families.
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Affiliation(s)
- Muhammad Dawood
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Siying Lin
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Taj Ud Din
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Irfan Ullah Shah
- Department of Ophthalmology, KMU Institute of Medical Sciences (KIMS) Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Niamat Khan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Abid Jan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Marwan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Komal Sultan
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Maha Nowshid
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Raheel Tahir
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Asif Naveed Ahmed
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Yasin
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
| | - Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre (Level 4), Royal Devon and Exeter NHS Foundation Trust, Exeter, Devon EX2 5DW, UK
| | - Shamim Saleha
- Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology (KUST), Kohat 26000, Khyber Pakhtunkhwa, Pakistan
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Beryozkin A, Aweidah H, Carrero Valenzuela RD, Berman M, Iguzquiza O, Cremers FPM, Khan MI, Swaroop A, Amer R, Khateb S, Ben-Yosef T, Sharon D, Banin E. Retinal Degeneration Associated With RPGRIP1: A Review of Natural History, Mutation Spectrum, and Genotype-Phenotype Correlation in 228 Patients. Front Cell Dev Biol 2021; 9:746781. [PMID: 34722527 PMCID: PMC8551679 DOI: 10.3389/fcell.2021.746781] [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: 07/24/2021] [Accepted: 09/15/2021] [Indexed: 12/03/2022] Open
Abstract
Purpose:RPGRIP1 encodes a ciliary protein expressed in the photoreceptor connecting cilium. Mutations in this gene cause ∼5% of Leber congenital amaurosis (LCA) worldwide, but are also associated with cone–rod dystrophy (CRD) and retinitis pigmentosa (RP) phenotypes. Our purpose was to clinically characterize RPGRIP1 patients from our cohort, collect clinical data of additional RPGRIP1 patients reported previously in the literature, identify common clinical features, and seek genotype–phenotype correlations. Methods: Clinical data were collected from 16 patients of our cohort and 212 previously reported RPGRIP1 patients and included (when available) family history, best corrected visual acuity (BCVA), refraction, comprehensive ocular examination, optical coherence tomography (OCT) imaging, visual fields (VF), and full-field electroretinography (ffERG). Results: Out of 228 patients, the majority (197, 86%) were diagnosed with LCA, 18 (7%) with RP, and 13 (5%) with CRD. Age of onset was during early childhood (n = 133, average of 1.7 years). All patients but 6 had moderate hyperopia (n = 59, mean of 4.8D), and average BCVA was 0.06 Snellen (n = 124; only 10 patients had visual acuity [VA] > 0.10 Snellen). On funduscopy, narrowing of blood vessels was noted early in life. Most patients had mild bone spicule-like pigmentation starting in the midperiphery and later encroaching upon the posterior pole. OCT showed thinning of the outer nuclear layer (ONL), while cystoid changes and edema were relatively rare. VF were usually very constricted from early on. ffERG responses were non-detectable in the vast majority of cases. Most of the mutations are predicted to be null (363 alleles), and 93 alleles harbored missense mutations. Missense mutations were identified only in two regions: the RPGR-interacting domain and the C2 domains. Biallelic null mutations are mostly associated with a severe form of the disease, whereas biallelic missense mutations usually cause a milder disease (mostly CRD). Conclusion: Our results indicate that RPGRIP1 biallelic mutations usually cause severe retinal degeneration at an early age with a cone–rod pattern. However, most of the patients exhibit preservation of some (usually low) BCVA for a long period and can potentially benefit from gene therapy. Missense changes appear only in the conserved domains and are associated with a milder phenotype.
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Affiliation(s)
- Avigail Beryozkin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hamzah Aweidah
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | | | - Myriam Berman
- Ophthalmology, Clinical Department, Faculty of Medicine, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Oscar Iguzquiza
- Neurology, Clinical Department, Faculty of Medicine, Universidad Nacional de Tucumán, Tucumán, Argentina
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Anand Swaroop
- Neurobiology-Neurodegeneration and Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, MD, United States
| | - Radgonde Amer
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Samer Khateb
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- The Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
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8
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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: 11] [Impact Index Per Article: 3.7] [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. The study was performed to identify the underlying cause of inherited retinal degeneration (IRD) in 409 individuals from 108 families. Primarily, these families were recruited from three different geographic regions: Mexico, Pakistan and European Americans from the United States. Blood samples were collected from all individuals for genome analysis. This analysis detected causative variants in 61 out of the 108 pedigrees. A total of 93 gene variants were found in the 61 families. Among these, 54 were previously reported as causative variants and the remaining 39 have not been reported in IRD pedigrees. Interestingly, 54% of these novel variants were not listed in gnomAD. In addition to these findings, complex causative genotypes were observed in 20% of pedigrees. Overall, causative variants were detected in 63% Mexican, 60% Pakistani and 45% European American pedigrees. This study revealed the distribution of IRD causative variants in pedigrees with diverse ethnic and geographic backgrounds.
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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
- * E-mail: (RA); (KAF); (SAR)
| | - 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
- * E-mail: (RA); (KAF); (SAR)
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, California, United States of America
- * E-mail: (RA); (KAF); (SAR)
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9
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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10
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Homozygosity mapping coupled with whole-exome sequencing and protein modelling identified a novel missense mutation in GUCY2D in a consanguineous Pakistani family with Leber congenital amaurosis. J Genet 2021. [DOI: 10.1007/s12041-021-01310-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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11
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Nassisi M, Smirnov VM, Solis Hernandez C, Mohand‐Saïd S, Condroyer C, Antonio A, Kühlewein L, Kempf M, Kohl S, Wissinger B, Nasser F, Ragi SD, Wang N, Sparrow JR, Greenstein VC, Michalakis S, Mahroo OA, Ba‐Abbad R, Michaelides M, Webster AR, Degli Esposti S, Saffren B, Capasso J, Levin A, Hauswirth WW, Dhaenens C, Defoort‐Dhellemmes S, Tsang SH, Zrenner E, Sahel J, Petersen‐Jones SM, Zeitz C, Audo I. CNGB1-related rod-cone dystrophy: A mutation review and update. Hum Mutat 2021; 42:641-666. [PMID: 33847019 PMCID: PMC8218941 DOI: 10.1002/humu.24205] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/26/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Cyclic nucleotide-gated channel β1 (CNGB1) encodes the 240-kDa β subunit of the rod photoreceptor cyclic nucleotide-gated ion channel. Disease-causing sequence variants in CNGB1 lead to autosomal recessive rod-cone dystrophy/retinitis pigmentosa (RP). We herein present a comprehensive review and analysis of all previously reported CNGB1 sequence variants, and add 22 novel variants, thereby enlarging the spectrum to 84 variants in total, including 24 missense variants (two of which may also affect splicing), 21 nonsense, 19 splicing defects (7 at noncanonical positions), 10 small deletions, 1 small insertion, 1 small insertion-deletion, 7 small duplications, and 1 gross deletion. According to the American College of Medical Genetics and Genomics classification criteria, 59 variants were considered pathogenic or likely pathogenic and 25 were variants of uncertain significance. In addition, we provide further phenotypic data from 34 CNGB1-related RP cases, which, overall, are in line with previous findings suggesting that this form of RP has long-term retention of useful central vision despite the early onset of night blindness, which is valuable for patient counseling, but also has implications for it being considered a priority target for gene therapy trials.
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Affiliation(s)
- Marco Nassisi
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- Department of Clinical Sciences and Community HealthUniversity of MilanMilanItaly
- Ophthalmological Unit, Fondazione IRCCS Ca' GrandaOspedale Maggiore PoliclinicoMilanItaly
| | - Vasily M. Smirnov
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Exploration de la vision et Neuro‐Ophthalmologie, CHU de LilleLilleFrance
- Faculté de MédecineUniversité de LilleLilleFrance
| | - Cyntia Solis Hernandez
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Saddek Mohand‐Saïd
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
| | - Christel Condroyer
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Aline Antonio
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Laura Kühlewein
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Melanie Kempf
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Bernd Wissinger
- Institute for Ophthalmic Research, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Fadi Nasser
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Sara D. Ragi
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | - Nan‐Kai Wang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- College of MedicineChang Gung UniversityTaoyuanTaiwan
- Department of Ophthalmology, Chang Gung Memorial HospitalLinkou Medical CenterTaoyuanTaiwan
| | - Janet R. Sparrow
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
| | | | | | - Omar A. Mahroo
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Rola Ba‐Abbad
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Michel Michaelides
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Andrew R. Webster
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Simona Degli Esposti
- Moorfields Eye HospitalLondonUK
- UCL Institute of Ophthalmology, University College LondonLondonUK
| | - Brooke Saffren
- Philadelphia College of Osteopathic MedicinePhiladelphiaPennsylvaniaUSA
| | | | - Alex Levin
- Pediatric Ophthalmology and Ocular Genetics, Flaum Eye Institute, Pediatric Genetics, Golisano Children's HospitalUniversity of RochesterRochesterNew YorkUSA
| | | | - Claire‐Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172‐LilNCog‐Lille Neuroscience & CognitionLilleFrance
| | | | - Stephen H. Tsang
- Department of OphthalmologyColumbia University, New YorkNew YorkUSA
- Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma LaboratoryNew YorkNew YorkUSA
- Department of Pathology and Cell BiologyColumbia UniversityNew YorkNew YorkUSA
- Stem Cell Initiative (CSCI), Institute of Human Nutrition, Vagelos College of Physicians and SurgeonsNew YorkNew YorkUSA
| | - Eberhart Zrenner
- University Eye Hospital, Centre for OphthalmologyUniversity of TübingenTübingenGermany
| | - Jose‐Alain Sahel
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Department of OphthalmologyThe University of Pittsburgh School of MedicinePittsburghPennsylvaniaUSA
- Fondation Ophtalmologique Adolphe de RothschildParisFrance
| | - Simon M. Petersen‐Jones
- Department of Small Animal Clinical SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Christina Zeitz
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
| | - Isabelle Audo
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche ScientifiqueInstitut de la VisionParisFrance
- Centre Hospitalier National d'Ophtalmologie des Quinze‐Vingts, INSERM‐DGOS CIC1423ParisFrance
- University College London Institute of OphthalmologyLondonUK
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12
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Tian W, Li X, Li Y, Wang L, Yang Y, Sun K, Liu W, Zhou B, Lei B, Zhu X. Identification of Novel EYS Mutations by Targeted Sequencing Analysis. Genet Test Mol Biomarkers 2020; 24:745-753. [PMID: 33058741 DOI: 10.1089/gtmb.2020.0186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Purpose: Retinitis pigmentosa (RP) is an inherited and progressive degenerative retinal disease that often results in severe vision loss and blindness. However, mutations in known RP disease genes account for only 60% of RP cases, indicating that there are additional pathogenic mutations are yet to be identified. We aimed to identify the causative mutations in the eyes shut homolog (EYS) gene in a cohort of Chinese RP and rod-cone dystrophy families. Materials and Methods: Targeted next-generation sequencing was applied to identify novel mutations in these patients. Candidate variants were evaluated using bioinformatics tools. Mutations were confirmed by Sanger sequencing. Results: We identified eight heterozygous mutations in the EYS gene in the four probands, including a novel frameshift deletion mutation, c.8242_8243del (p.L2748fs); a novel insertion mutation, c.5802_5803insT (p.I1935YfsX6); a novel splicing mutation, c.1300-1G>A; two heterozygous stop-gain mutations, c.1750G>T (p.E584X) and c.8805C>A (p.Y2935X); and three novel missense mutations, c.8269G>A (p.V2757I), c.2545C>T (p.R849C) and c.7506C>A (p.S2502R). Only c.8805C>A had been reported previously in RP patients. None of these mutations were present in 1000 control individuals. Conclusions: We identified seven novel mutations in the EYS gene, expanding the mutational specra of EYS in Chinese patients with RP and rod-cone dystrophy.
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Affiliation(s)
- Wanli Tian
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiao Li
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Ya Li
- People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, China
| | - Luyao Wang
- Psychosomatic Medicine Center, Sichuan Academy of Medicine and Sichuan Provincial People's Hospital, Chengdu, China
| | - Yeming Yang
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Kuanxiang Sun
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Wenjing Liu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| | - Bo Zhou
- Psychosomatic Medicine Center, Sichuan Academy of Medicine and Sichuan Provincial People's Hospital, Chengdu, China
| | - Bo Lei
- People's Hospital of Zhengzhou University, Henan Provincial People's Hospital, Henan Eye Institute, Henan Eye Hospital, Zhengzhou, China
| | - Xianjun Zhu
- The Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Laboratory Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.,Department of Ophthalmology, First People's Hospital of Shangqiu, Shangqiu, China
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13
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Exploring the Genetic Landscape of Retinal Diseases in North-Western Pakistan Reveals a High Degree of Autozygosity and a Prevalent Founder Mutation in ABCA4. Genes (Basel) 2019; 11:genes11010012. [PMID: 31877759 PMCID: PMC7017091 DOI: 10.3390/genes11010012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022] Open
Abstract
Variants in more than 271 different genes have been linked to hereditary retinal diseases, making comprehensive genomic approaches mandatory for accurate diagnosis. We explored the genetic landscape of retinal disorders in consanguineous families from North-Western Pakistan, harboring a population of approximately 35 million inhabitants that remains relatively isolated and highly inbred (~50% consanguinity). We leveraged on the high degree of consanguinity by applying genome-wide high-density single-nucleotide polymorphism (SNP) genotyping followed by targeted Sanger sequencing of candidate gene(s) lying inside autozygous intervals. In addition, we performed whole-exome sequencing (WES) on at least one proband per family. We identified 7 known and 4 novel variants in a total of 10 genes (ABCA4, BBS2, CNGA1, CNGA3, CNGB3, MKKS, NMNAT1, PDE6B, RPE65, and TULP1) previously known to cause inherited retinal diseases. In spite of all families being consanguineous, compound heterozygosity was detected in one family. All homozygous pathogenic variants resided in autozygous intervals ≥2.0 Mb in size. Putative founder variants were observed in the ABCA4 (NM_000350.2:c.214G>A; p.Gly72Arg; ten families) and NMNAT1 genes (NM_022787.3:c.25G>A; p.Val9Met; two families). We conclude that geographic isolation and sociocultural tradition of intrafamilial mating in North-Western Pakistan favor both the clinical manifestation of rare “generic” variants and the prevalence of founder mutations.
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14
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Riaz M, Tiller J, Ajmal M, Azam M, Qamar R, Lacaze P. Implementation of public health genomics in Pakistan. Eur J Hum Genet 2019; 27:1485-1492. [PMID: 31101884 PMCID: PMC6777461 DOI: 10.1038/s41431-019-0428-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 02/10/2019] [Accepted: 04/30/2019] [Indexed: 02/06/2023] Open
Abstract
There has been considerable recent progress in the implementation of public health genomics policy throughout the developed world. However, in the developing world, genetic services still remain limited, or unavailable to most. Here, we discuss challenges and opportunities related to the implementation of public health genomics in developing countries. We focus on Pakistan, a country with one of the world's highest rates of inter-family marriages and prevalence of inherited genetic conditions. Pakistan still lacks a national newborn screening programme, clinical genetic testing services, or public health genomics framework. The medical infrastructure in Pakistan, characterized by limited publicly-funded health services and a significant burden of infectious disease, may contribute to de-prioritization of genetic health services. In addition, there are a number of societal, cultural and religious factors to consider. Recently a number of large research studies have been conducted in populations of Pakistani descent, mostly in collaboration with major US, UK and European institutions. Some of these have yielded high-impact scientific findings, but have yet to translate into public health outcomes in Pakistan. Before the benefits of genomics can be realized in developing countries, the first initial steps towards strategic prioritization, resourcing, and long-term goal setting are required. We propose some practical recommendations and possible first steps forward.
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Affiliation(s)
- Moeen Riaz
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia.
| | - Jane Tiller
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
| | - Muhammad Ajmal
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Maleeha Azam
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Raheel Qamar
- Translational Genomics Laboratory, Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
- Pakistan Academy of Sciences, Islamabad, Pakistan
| | - Paul Lacaze
- Public Health Genomics, Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC, Australia
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15
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Charbel Issa P, Reuter P, Kühlewein L, Birtel J, Gliem M, Tropitzsch A, Whitcroft KL, Bolz HJ, Ishihara K, MacLaren RE, Downes SM, Oishi A, Zrenner E, Kohl S, Hummel T. Olfactory Dysfunction in Patients With CNGB1-Associated Retinitis Pigmentosa. JAMA Ophthalmol 2019; 136:761-769. [PMID: 29800053 DOI: 10.1001/jamaophthalmol.2018.1621] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Importance Co-occurrence of retinitis pigmentosa (RP) and olfactory dysfunction may have a common genetic cause. Objective To report olfactory function and the retinal phenotype in patients with biallelic mutations in CNGB1, a gene coding for a signal transduction channel subunit expressed in rod photoreceptors and olfactory sensory neurons. Design, Setting, and Participants This case series was conducted from August 2015 through July 2017. The setting was a multicenter study involving 4 tertiary referral centers for inherited retinal dystrophies. Participants were 9 patients with CNGB1-associated RP. Main Outcomes and Measures Results of olfactory testing, ocular phenotyping, and molecular genetic testing using targeted next-generation sequencing. Results Nine patients were included in the study, 3 of whom were female. Their ages ranged between 34 and 79 years. All patients had an early onset of night blindness but were usually not diagnosed as having RP before the fourth decade because of slow retinal degeneration. Retinal features were characteristic of a rod-cone dystrophy. Olfactory testing revealed reduced or absent olfactory function, with all except one patient scoring in the lowest quartile in relation to age-related norms. Brain magnetic resonance imaging and electroencephalography measurements in response to olfactory stimulation were available for 1 patient and revealed no visible olfactory bulbs and reduced responses to odor, respectively. Molecular genetic testing identified 5 novel (c.1312C>T, c.2210G>A, c.2492+1G>A, c.2763C>G, and c.3044_3050delGGAAATC) and 5 previously reported mutations in CNGB1. Conclusions and Relevance Mutations in CNGB1 may cause an autosomal recessive RP-olfactory dysfunction syndrome characterized by a slow progression of retinal degeneration and variable anosmia or hyposmia.
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Affiliation(s)
- Peter Charbel Issa
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.,Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Peggy Reuter
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Laura Kühlewein
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Johannes Birtel
- Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Martin Gliem
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Department of Ophthalmology, University of Bonn, Bonn, Germany
| | - Anke Tropitzsch
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Tübingen, Tübingen, Germany
| | - Katherine L Whitcroft
- University College London (UCL) Ear Institute and Royal National Throat, Nose and Ear Hospital, London, United Kingdom.,Centre for the Study of the Senses, Institute of Philosophy, School of Advanced Study, University of London, London, United Kingdom.,Smell and Taste Clinic, Department of Otorhinolaryngology-Head and Neck Surgery, Technische Universität Dresden, Dresden, Germany
| | - Hanno J Bolz
- Bioscientia Center for Human Genetics, Ingelheim, Germany.,Institute of Human Genetics, University Hospital of Cologne, Cologne, Germany
| | - Kenji Ishihara
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Robert E MacLaren
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Susan M Downes
- Oxford Eye Hospital, Oxford University Hospitals National Health Service (NHS) Foundation Trust, Oxford, United Kingdom.,Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom
| | - Akio Oishi
- Department of Ophthalmology and Visual Sciences, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Eberhart Zrenner
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Susanne Kohl
- Centre for Ophthalmology, Institute for Ophthalmic Research, University of Tübingen, Tübingen, Germany
| | - Thomas Hummel
- Smell and Taste Clinic, Department of Otorhinolaryngology-Head and Neck Surgery, Technische Universität Dresden, Dresden, Germany
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16
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Identification of a CNGB1 Frameshift Mutation in a Han Chinese Family with Retinitis Pigmentosa. Optom Vis Sci 2019; 95:1155-1161. [PMID: 30451805 DOI: 10.1097/opx.0000000000001305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
SIGNIFICANCE Retinitis pigmentosa (RP) is a severe hereditary retinal disorder characterized by progressive degeneration of rod and cone photoreceptors. This study identified a novel frameshift mutation, c.385delC, p.(L129WfsTer148), in the cyclic nucleotide-gated channel beta 1 (CNGB1) gene of a consanguineous Han Chinese family with autosomal recessive RP (arRP). This expands the spectrum of CNGB1 gene variants in RP cases and possibly refines future genetic counseling. PURPOSE The present study sought to identify potential pathogenetic gene mutations in a five-generation consanguineous Han Chinese family with RP. METHODS Two members of a five-generation consanguineous Han Chinese pedigree with arRP and 100 normal individuals were enrolled in this study. Exome sequencing was performed on the 70-year-old male proband from a consanguineous family to screen potential pathogenic mutations according to the American College of Medical Genetics and Genomics for the interpretation of sequence variants. Sanger sequencing was performed on the proband, the proband's unaffected son, and 100 normal individuals to verify the disease-causing mutation. RESULTS A novel frameshift mutation, c.385delC, p.(L129WfsTer148), with homozygous status in the CNGB1 gene was identified in the proband of the family with arRP, and the mutation with heterozygous status was carried by the asymptomatic son. CONCLUSIONS The c.385delC (p.(L129WfsTer148)) mutation in the CNGB1 gene screened by exome sequencing is probably responsible for the RP phenotype in this family. The result expands the spectrum of CNGB1 gene variants in RP cases and possibly refines future genetic counseling.
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17
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Maryam A, Vedithi SC, Khalid RR, Alsulami AF, Torres PHM, Siddiqi AR, Blundell TL. The Molecular Organization of Human cGMP Specific Phosphodiesterase 6 (PDE6): Structural Implications of Somatic Mutations in Cancer and Retinitis Pigmentosa. Comput Struct Biotechnol J 2019; 17:378-389. [PMID: 30962868 PMCID: PMC6434069 DOI: 10.1016/j.csbj.2019.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/24/2019] [Accepted: 03/03/2019] [Indexed: 01/12/2023] Open
Abstract
In the cyclic guanosine monophosphate (cGMP) signaling pathway, phosphodiesterase 6 (PDE6) maintains a critical balance of the intracellular concentration of cGMP by catalyzing it to 5′ guanosine monophosphate (5′-GMP). To gain insight into the mechanistic impacts of the PDE6 somatic mutations that are implicated in cancer and retinitis pigmentosa, we first defined the structure and organization of the human PDE6 heterodimer using computational comparative modelling. Each subunit of PDE6αβ possesses three domains connected through long α-helices. The heterodimer model indicates that the two chains are likely related by a pseudo two-fold axis. The N-terminal region of each subunit is comprised of two allosteric cGMP-binding domains (Gaf-A & Gaf-B), oriented in the same way and interacting with the catalytic domain present at the C-terminal in a way that would allow the allosteric cGMP-binding domains to influence catalytic activity. Subsequently, we applied an integrated knowledge-driven in silico mutation analysis approach to understand the structural and functional implications of experimentally identified mutations that cause various cancers and retinitis pigmentosa, as well as computational saturation mutagenesis of the dimer interface and cGMP-binding residues of both Gaf-A, and the catalytic domains. We studied the impact of mutations on the stability of PDE6αβ structure, subunit-interfaces and Gaf-cGMP interactions. Further, we discussed the changes in interatomic interactions of mutations that are destabilizing in Gaf-A (R93L, V141 M, F162 L), catalytic domain (D600N, F742 L, F776 L) and at the dimer interface (F426A, F248G, F424 N). This study establishes a possible link of change in PDE6αβ structural stability to the experimentally observed disease phenotypes.
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Affiliation(s)
- Arooma Maryam
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan.,Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Rana Rehan Khalid
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan
| | - Ali F Alsulami
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Abdul Rauf Siddiqi
- Department of Biosciences, COMSATS University Islamabad (CUI), Park Road, Islamabad, Pakistan
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, UK
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18
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Chen X, Sheng X, Liu Y, Li Z, Sun X, Jiang C, Qi R, Yuan S, Wang X, Zhou G, Zhen Y, Xie P, Liu Q, Yan B, Zhao C. Distinct mutations with different inheritance mode caused similar retinal dystrophies in one family: a demonstration of the importance of genetic annotations in complicated pedigrees. J Transl Med 2018; 16:145. [PMID: 29843741 PMCID: PMC5975579 DOI: 10.1186/s12967-018-1522-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 05/17/2018] [Indexed: 12/03/2022] Open
Abstract
Background Retinitis pigmentosa (RP) is the most common form of inherited retinal dystrophy presenting remarkable genetic heterogeneity. Genetic annotations would help with better clinical assessments and benefit gene therapy, and therefore should be recommended for RP patients. This report reveals the disease causing mutations in two RP pedigrees with confusing inheritance patterns using whole exome sequencing (WES). Methods Twenty-five participants including eight patients from two families were recruited and received comprehensive ophthalmic evaluations. WES was applied for mutation identification. Bioinformatics annotations, intrafamilial co-segregation tests, and in silico analyses were subsequently conducted for mutation verification. Results All patients were clinically diagnosed with RP. The first family included two siblings born to parents with consanguineous marriage; however, no potential pathogenic variant was found shared by both patients. Further analysis revealed that the female patient carried a recurrent homozygous C8ORF37 p.W185*, while the male patient had hemizygous OFD1 p.T120A. The second family was found to segregate mutations in two genes, TULP1 and RP1. Two patients born to consanguineous marriage carried homozygous TULP1 p.R419W, while a recurrent heterozygous RP1 p.L762Yfs*17 was found in another four patients presenting an autosomal dominant inheritance pattern. Crystal structural analysis further indicated that the substitution from arginine to tryptophan at the highly conserved residue 419 of TULP1 could lead to the elimination of two hydrogen bonds between residue 419 and residues V488 and S534. All four genes, including C8ORF37, OFD1, TULP1 and RP1, have been previously implicated in RP etiology. Conclusions Our study demonstrates the coexistence of diverse inheritance modes and mutations affecting distinct disease causing genes in two RP families with consanguineous marriage. Our data provide novel insights into assessments of complicated pedigrees, reinforce the genetic complexity of RP, and highlight the need for extensive molecular evaluations in such challenging families with diverse inheritance modes and mutations. Electronic supplementary material The online version of this article (10.1186/s12967-018-1522-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue Chen
- Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China.,Key Laboratory of Myopia of State Health Ministry (Fudan University) and Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China
| | - Xunlun Sheng
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Yani Liu
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Zili Li
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Xiantao Sun
- Department of Ophthalmology, Children's Hospital of Zhengzhou, Zhengzhou, China
| | - Chao Jiang
- Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Rui Qi
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Shiqin Yuan
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Xuhui Wang
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Ge Zhou
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Yanyan Zhen
- Department of Ophthalmology, Ningxia Eye Hospital, People Hospital of Ningxia Hui Autonomous Region (First Affiliated Hospital of Northwest University for Nationalities), Yinchuan, China
| | - Ping Xie
- Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Qinghuai Liu
- Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Biao Yan
- Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China. .,Key Laboratory of Myopia of State Health Ministry (Fudan University) and Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China.
| | - Chen Zhao
- Department of Ophthalmology, State Key Laboratory of Reproductive Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China. .,Department of Ophthalmology and Vision Science, Eye & ENT Hospital, Shanghai Medical College, Fudan University, Shanghai, China. .,Key Laboratory of Myopia of State Health Ministry (Fudan University) and Shanghai Key Laboratory of Visual Impairment and Restoration, Shanghai, China. .,Department of Ophthalmology, Children's Hospital of Zhengzhou, Zhengzhou, China.
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19
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Sharon D, Wimberg H, Kinarty Y, Koch KW. Genotype-functional-phenotype correlations in photoreceptor guanylate cyclase (GC-E) encoded by GUCY2D. Prog Retin Eye Res 2018; 63:69-91. [DOI: 10.1016/j.preteyeres.2017.10.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 01/09/2023]
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20
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Petersen-Jones SM, Occelli LM, Winkler PA, Lee W, Sparrow JR, Tsukikawa M, Boye SL, Chiodo V, Capasso JE, Becirovic E, Schön C, Seeliger MW, Levin AV, Michalakis S, Hauswirth WW, Tsang SH. Patients and animal models of CNGβ1-deficient retinitis pigmentosa support gene augmentation approach. J Clin Invest 2017; 128:190-206. [PMID: 29202463 PMCID: PMC5749539 DOI: 10.1172/jci95161] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/10/2017] [Indexed: 01/07/2023] Open
Abstract
Retinitis pigmentosa (RP) is a major cause of blindness that affects 1.5 million people worldwide. Mutations in cyclic nucleotide-gated channel β 1 (CNGB1) cause approximately 4% of autosomal recessive RP. Gene augmentation therapy shows promise for treating inherited retinal degenerations; however, relevant animal models and biomarkers of progression in patients with RP are needed to assess therapeutic outcomes. Here, we evaluated RP patients with CNGB1 mutations for potential biomarkers of progression and compared human phenotypes with those of mouse and dog models of the disease. Additionally, we used gene augmentation therapy in a CNGβ1-deficient dog model to evaluate potential translation to patients. CNGB1-deficient RP patients and mouse and dog models had a similar phenotype characterized by early loss of rod function and slow rod photoreceptor loss with a secondary decline in cone function. Advanced imaging showed promise for evaluating RP progression in human patients, and gene augmentation using adeno-associated virus vectors robustly sustained the rescue of rod function and preserved retinal structure in the dog model. Together, our results reveal an early loss of rod function in CNGB1-deficient patients and a wide window for therapeutic intervention. Moreover, the identification of potential biomarkers of outcome measures, availability of relevant animal models, and robust functional rescue from gene augmentation therapy support future work to move CNGB1-RP therapies toward clinical trials.
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Affiliation(s)
- Simon M Petersen-Jones
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Laurence M Occelli
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Paige A Winkler
- Department of Small Animal Clinical Sciences, Michigan State University, East Lansing, Michigan, USA
| | - Winston Lee
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Janet R Sparrow
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Mai Tsukikawa
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Sanford L Boye
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Vince Chiodo
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Jenina E Capasso
- Ocular Genetics, Wills Eye Hospital (WEH), Philadelphia, Pennsylvania, USA
| | - Elvir Becirovic
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Christian Schön
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Mathias W Seeliger
- Division of Ocular Neurodegeneration, Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Alex V Levin
- Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,Ocular Genetics, Wills Eye Hospital (WEH), Philadelphia, Pennsylvania, USA
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich (CIPSM), Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - William W Hauswirth
- Department of Ophthalmology, University of Florida, Gainesville, Florida, USA
| | - Stephen H Tsang
- Department of Ophthalmology Pathology & Cell Biology, College of Physicians and Surgeons, Columbia University, New York, New York, USA.,Edward S. Harkness Eye Institute, New York-Presbyterian Hospital, New York, New York, USA.,Jonas Children's Vision Care and Bernard & Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia University Medical Center (CUMC), Edward S. Harkness Eye Institute, New York, New York, USA
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21
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Abstract
There have been major advances in genetic testing especially over the last 10 years. We have advanced from looking at simple chromosomes under a microscope to more sophisticated analysis of the DNA makeup of chromosomes and from testing a single gene to sequencing almost all of our genetic material. Similarly, in the field of prenatal testing we have made great strides in screening and diagnostic testing in the hope of detecting significant abnormalities in the fetus while decreasing the risk to the pregnancy. In this article the major types of genetic screening and diagnostic testing, both prenatal and postnatal, will be reviewed. [Pediatr Ann. 2017;46(11):e423-e427.].
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22
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Chakraborty D, Conley SM, Pittler SJ, Naash MI. Role of RDS and Rhodopsin in Cngb1-Related Retinal Degeneration. Invest Ophthalmol Vis Sci 2016; 57:787-97. [PMID: 26934134 PMCID: PMC4777275 DOI: 10.1167/iovs.15-18516] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose Rod photoreceptor outer segment (OS) morphogenesis, structural integrity, and proper signal transduction rely on critical proteins found in the different OS membrane domains (e.g., plasma, disc, and disc rim membrane). Among these key elements are retinal degeneration slow (RDS, also known as peripherin-2), rhodopsin, and the beta subunit of the cyclic nucleotide gated channel (CNGB1a), which have been found to interact in a complex. The purpose of this study was to evaluate the potential interplay between these three proteins by examining retinal disease phenotypes in animal models expressing varying amounts of CNGB1a, rhodopsin, and RDS. Methods Outer segment trafficking, retinal function, and photoreceptor structure were evaluated using knockout mouse lines. Results Eliminating Cngb1 and reducing RDS leads to additive defects in RDS expression levels and rod electroretinogram (ERG) function, (e.g., Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−) but not to additive defects in rod ultrastructure. These additive effects also manifested in cone function: Photopic ERG responses were significantly lower in the Cngb1−/−/rds+/− versus rds+/− or Cngb1−/−, suggesting that eliminating Cngb1 can accelerate the cone degeneration that usually presents later in the rds+/−. This was not the case with rhodopsin; reducing rhodopsin levels in concert with eliminating CNGB1a did not lead to phenotypes more severe than those observed in the Cngb1 knockout alone. Conclusions These data support a role for RDS as the core component of a multiprotein plasma membrane-rim-disc complex that has both a structural role in photoreceptor OS formation and maintenance and a functional role in orienting proteins for optimal signal transduction.
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Affiliation(s)
- Dibyendu Chakraborty
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Shannon M Conley
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
| | - Steven J Pittler
- Department of Vision Sciences, School of Optometry, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | - Muna I Naash
- Department of Biomedical Engineering, University of Houston, Houston, Texas, United States
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23
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Ullah I, Kabir F, Iqbal M, Gottsch CBS, Naeem MA, Assir MZ, Khan SN, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Pathogenic mutations in TULP1 responsible for retinitis pigmentosa identified in consanguineous familial cases. Mol Vis 2016; 22:797-815. [PMID: 27440997 PMCID: PMC4947966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 07/14/2016] [Indexed: 11/16/2022] Open
Abstract
PURPOSE To identify pathogenic mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous familial cases. METHODS Seven large familial cases with multiple individuals diagnosed with retinitis pigmentosa were included in the study. Affected individuals in these families underwent ophthalmic examinations to document the symptoms and confirm the initial diagnosis. Blood samples were collected from all participating members, and genomic DNA was extracted. An exclusion analysis with microsatellite markers spanning the TULP1 locus on chromosome 6p was performed, and two-point logarithm of odds (LOD) scores were calculated. All coding exons along with the exon-intron boundaries of TULP1 were sequenced bidirectionally. We constructed a single nucleotide polymorphism (SNP) haplotype for the four familial cases harboring the K489R allele and estimated the likelihood of a founder effect. RESULTS The ophthalmic examinations of the affected individuals in these familial cases were suggestive of RP. Exclusion analyses confirmed linkage to chromosome 6p harboring TULP1 with positive two-point LOD scores. Subsequent Sanger sequencing identified the single base pair substitution in exon14, c.1466A>G (p.K489R), in four families. Additionally, we identified a two-base deletion in exon 4, c.286_287delGA (p.E96Gfs77*); a homozygous splice site variant in intron 14, c.1495+4A>C; and a novel missense variation in exon 15, c.1561C>T (p.P521S). All mutations segregated with the disease phenotype in the respective families and were absent in ethnically matched control chromosomes. Haplotype analysis suggested (p<10(-6)) that affected individuals inherited the causal mutation from a common ancestor. CONCLUSIONS Pathogenic mutations in TULP1 are responsible for the RP phenotype in seven familial cases with a common ancestral mutation responsible for the disease phenotype in four of the seven families.
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Affiliation(s)
- Inayat Ullah
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Muhammad Iqbal
- 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
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24
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Biswas P, Chavali VRM, Agnello G, Stone E, Chakarova C, Duncan JL, Kannabiran C, Homsher M, Bhattacharya SS, Naeem MA, Kimchi A, Sharon D, Iwata T, Riazuddin S, Reddy GB, Hejtmancik JF, Georgiou G, Riazuddin SA, Ayyagari R. A missense mutation in ASRGL1 is involved in causing autosomal recessive retinal degeneration. Hum Mol Genet 2016; 25:2483-2497. [PMID: 27106100 DOI: 10.1093/hmg/ddw113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 03/22/2016] [Accepted: 04/11/2016] [Indexed: 12/31/2022] Open
Abstract
Inherited retinal dystrophies are a group of genetically heterogeneous conditions with broad phenotypic heterogeneity. We analyzed a large five-generation pedigree with early-onset recessive retinal degeneration to identify the causative mutation. Linkage analysis and homozygosity mapping combined with exome sequencing were carried out to map the disease locus and identify the p.G178R mutation in the asparaginase like-1 gene (ASRGL1), segregating with the retinal dystrophy phenotype in the study pedigree. ASRGL1 encodes an enzyme that catalyzes the hydrolysis of L-asparagine and isoaspartyl-peptides. Studies on the ASRGL1 expressed in Escherichia coli and transiently transfected mammalian cells indicated that the p.G178R mutation impairs the autocatalytic processing of this enzyme resulting in the loss of functional ASRGL1 and leaving the inactive precursor protein as a destabilized and aggregation-prone protein. A zebrafish model overexpressing the mutant hASRGL1 developed retinal abnormalities and loss of cone photoreceptors. Our studies suggest that the p.G178R mutation in ASRGL1 leads to photoreceptor degeneration resulting in progressive vision loss.
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Affiliation(s)
- Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA
| | - Venkata Ramana Murthy Chavali
- Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA.,Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | - Giulia Agnello
- Departments of Biomedical and Chemical Engineering, Molecular Biosciences, Section of Molecular Genetics and Microbiology, and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Everett Stone
- Departments of Biomedical and Chemical Engineering, Molecular Biosciences, Section of Molecular Genetics and Microbiology, and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | | | - Jacque L Duncan
- Ophthalmology, University of California San Francisco, San Francisco, CA, USA
| | - Chitra Kannabiran
- Kallam Anji Reddy Molecular Genetics Laboratory, L V Prasad Eye Institute (LVPEI), Kallam Anji Reddy Campus, L V Prasad Marg, Hyderabad 500 034, India
| | - Melissa Homsher
- Ophthalmology, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Adva Kimchi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Shaikh Riazuddin
- Allama Iqbal Medical College, University of Health Sciences Lahore, Pakistan.,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | | | | | - George Georgiou
- Departments of Biomedical and Chemical Engineering, Molecular Biosciences, Section of Molecular Genetics and Microbiology, and Institute for Cell and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, USA
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