1
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da Palma MM, Marra M, Igelman AD, Ku CA, Burr A, Andersen K, Everett LA, Porto FBO, Sallum JMF, Yang P, Pennesi ME. Expanding the phenotypic and genotypic spectrum of patients with HGSNAT-related retinopathy. Ophthalmic Genet 2024; 45:167-174. [PMID: 37592806 DOI: 10.1080/13816810.2023.2245035] [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: 03/12/2023] [Accepted: 08/01/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Variants in HGSNAT have historically been associated with syndromic mucopolysaccharidosis type IIIC (MPSIIIC) but more recent studies demonstrate cases of HGSNAT-related non-syndromic retinitis pigmentosa. We describe and expand the genotypic and phenotypic spectrum of this disease. MATERIALS AND METHODS This is a retrospective, observational, case series of 11 patients with pericentral retinitis pigmentosa due to variants in HGSNAT gene without a syndromic diagnosis of MPSIIIC. We reviewed ophthalmologic data extracted from medical records, genetic testing, color fundus photos, fundus autofluorescence (FAF), and optical coherence tomography (OCT). RESULTS Of the 11 patients, the mean age was 52 years (range: 26-78). The mean age of ophthalmologic symptoms onset was 45 years (range: 15-72). The visual acuity varied from 20/20 to 20/80 (mean 20/30 median 20/20). We described five novel variants in HGSNAT: c.715del (p.Arg239Alafs *37), c.118 G>A (p.Asp40Asn), c.1218_1220delinsTAT, c.1297A>G (p.Asn433Asp), and c.1726 G>T (p.Gly576*). CONCLUSIONS HGSNAT has high phenotypic heterogeneity. Data from our cohort showed that all patients who had at least one variant of c.1843 G>A (p.Ala615Thr) presented with the onset of ocular symptoms after the fourth decade of life. The two patients with onset of ocular symptoms before the fourth decade did not carry this variant. This may suggest that c.1843 G>A variant is associated with a later onset of retinopathy.
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Affiliation(s)
- Mariana Matioli da Palma
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo Escola Paulista de Medicina (UNIFESP), São Paulo, Brazil
- Instituto de Genética Ocular, São Paulo, Brazil
- Department of Surgery & Hospital Clinic of Barcelona, School of Medicine, Universitat de Barcelona, Barcelona, Spain
| | - Molly Marra
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Austin D Igelman
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Cristy A Ku
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
- Department of Ophthalmology & Vision Science, University of California Davis, Sacramento, California, USA
| | - Amanda Burr
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Katherine Andersen
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Lesley A Everett
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | | | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo Escola Paulista de Medicina (UNIFESP), São Paulo, Brazil
- Instituto de Genética Ocular, São Paulo, Brazil
| | - Paul Yang
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
| | - Mark E Pennesi
- Department of Ophthalmology, Casey Eye Institute at Oregon Health & Science University (OHSU), Portland, Oregon, USA
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2
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Sangermano R, Gupta P, Price C, Han J, Navarro J, Condroyer C, Place EM, Antonio A, Mukai S, Zanlonghi X, Sahel JA, Duncan JL, Pierce EA, Zeitz C, Audo I, Huckfeldt RM, Bujakowska KM. Coding and non-coding variants in the ciliopathy gene CFAP410 cause early-onset non-syndromic retinal degeneration. RESEARCH SQUARE 2024:rs.3.rs-3871956. [PMID: 38405922 PMCID: PMC10889070 DOI: 10.21203/rs.3.rs-3871956/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Inherited retinal degenerations are blinding genetic disorders characterized by high genetic and phenotypic heterogeneity. The implementation of next-generation sequencing in routine diagnostics, together with advanced clinical phenotyping including multimodal retinal imaging, have contributed to the increase of reports describing novel genotype-phenotype associations and phenotypic expansions. In this study, we describe sixteen families with early-onset non-syndromic retinal degenerations in which affected probands carried rare bi-allelic variants in CFAP410, a ciliary gene previously associated with syndromic recessive Jeune syndrome. The most common retinal phenotypes were cone-rod and rod-cone dystrophies, but the clinical presentations were unified by their early onset as well as the severe impact on central visual function. Twelve variants were detected (three pathogenic, seven likely pathogenic, two of uncertain significance), eight of which were novel. One deep intronic change, c.373+91A>G, led to the creation of a cryptic splice acceptor site in intron four, followed by the inclusion of a 200- base pair pseudoexon and subsequent premature stop codon formation. To our knowledge this is the first likely pathogenic deep-intronic variant identified in this gene. Meta-analysis of all published and novel CFAP410 variants revealed no clear correlation between the severity of the CFAP410-associated phenotypes and the identified causal variants. This is supported by the fact that the frequently encountered missense variant p.(Arg73Pro), often found in syndromic cases, was also associated with non-syndromic retinal degeneration. This study expands the current knowledge of CFAP410-associated ciliopathy by enriching its mutational landscape and supports its association with non-syndromic retinal degeneration.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Priya Gupta
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Cherrell Price
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Jinu Han
- Institute of Vision Research, Department of Ophthalmology, Gangnam Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Julien Navarro
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | | | - Emily M. Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Aline Antonio
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Shizuo Mukai
- Retina Service, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Xavier Zanlonghi
- Centre de compétence maladies rares, Service d’Ophtalmologie, CHU Rennes, Rennes, France
| | - José-Alain Sahel
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
- Vision Institute, University of Pittsburgh Medical Center and School of Medicine, Pennsylvania, USA
| | - Jacque L. Duncan
- Department of Ophthalmology, University of California, San Francisco, California, USA
| | - Eric A. Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Christina Zeitz
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Isabelle Audo
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
- Centre Hospitalier National d’Ophtalmologie des Quinze-Vingts, Centre de Référence Maladies Rares REFERET and INSERM-DGOS CIC 1423, Paris, France
| | - Rachel M. Huckfeldt
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kinga M. Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
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3
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Sangermano R, Galdikaité-Braziené E, Bujakowska KM. Non-syndromic Retinal Degeneration Caused by Pathogenic Variants in Joubert Syndrome Genes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1415:173-182. [PMID: 37440031 DOI: 10.1007/978-3-031-27681-1_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/14/2023]
Abstract
Inherited retinal degenerations (IRDs) are a group of genetic disorders characterized by progressive dysfunction and loss of photoreceptors. IRDs are classified as non-syndromic or syndromic, depending on whether retinal degeneration manifests alone or in combination with other associated symptoms. Joubert syndrome (JBTS) is a genetically and clinically heterogeneous disorder affecting the central nervous system and other organs and tissues, including the neuroretina. To date, 39 genes have been associated with JBTS, a majority of which encode structural or functional components of the primary cilium, a specialized sensory organelle present in most post-mitotic cells, including photoreceptors. The use of whole exome and IRD panel next-generation sequencing in routine diagnostics of non-syndromic IRD cases led to the discovery of pathogenic variants in JBTS genes that cause photoreceptor loss without other syndromic features. Here, we recapitulate these findings, describing the JBTS gene defects leading to non-syndromic IRDs.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Egle Galdikaité-Braziené
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA.
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4
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Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, Arno G. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype. NPJ Genom Med 2022; 7:60. [PMID: 36266294 PMCID: PMC9581764 DOI: 10.1038/s41525-022-00330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK.
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Catherina H Z Li
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert A Heaton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - Janine Reurink
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James Bellingham
- Institute of Ophthalmology, University College London, London, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Georgia Yioti
- University of Ioannina Medical School, Ioannina, Greece
| | | | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK. .,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK.
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5
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Patel P, Jones K, Friedman DI, Birch DG, Ufret-Vincenty RL. Unexpected Etiology in a Case of Bilateral Maculopathy. Case Rep Ophthalmol 2021; 12:622-628. [PMID: 34326763 PMCID: PMC8299408 DOI: 10.1159/000514705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/24/2021] [Indexed: 11/30/2022] Open
Abstract
A 74-year-old woman with a history of rheumatoid arthritis using hydroxychloroquine presented with gradually progressive decreased vision in both eyes and was found to have a bilateral maculopathy. Initial genetic testing was negative, and after discussing the low likelihood of her severe findings being secondary to her relatively low hydroxychloroquine exposure, the possibility of an autoimmune retinopathy was entertained. Updated data on the genetic testing reclassified one of her mutations in HGSNAT as pathogenic. This case highlights the value of genetic testing and the need to keep a high index of suspicion even after initial negative results, given the fact that our knowledge of mutations leading to retinal degeneration is constantly evolving.
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Affiliation(s)
- Prem Patel
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - Kaylie Jones
- Retina Foundation of the Southwest, Dallas, Texas, USA
| | - Deborah I Friedman
- Department of Ophthalmology, UT Southwestern Medical Center, Dallas, Texas, USA.,Department of Neurology, UT Southwestern Medical Center, Dallas, Texas, USA
| | - David G Birch
- Retina Foundation of the Southwest, Dallas, Texas, USA
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6
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Broadening INPP5E phenotypic spectrum: detection of rare variants in syndromic and non-syndromic IRD. NPJ Genom Med 2021; 6:53. [PMID: 34188062 PMCID: PMC8242099 DOI: 10.1038/s41525-021-00214-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 05/21/2021] [Indexed: 02/06/2023] Open
Abstract
Pathogenic variants in INPP5E cause Joubert syndrome (JBTS), a ciliopathy with retinal involvement. However, despite sporadic cases in large cohort sequencing studies, a clear association with non-syndromic inherited retinal degenerations (IRDs) has not been made. We validate this association by reporting 16 non-syndromic IRD patients from ten families with bi-allelic mutations in INPP5E. Additional two patients showed early onset IRD with limited JBTS features. Detailed phenotypic description for all probands is presented. We report 14 rare INPP5E variants, 12 of which have not been reported in previous studies. We present tertiary protein modeling and analyze all INPP5E variants for deleteriousness and phenotypic correlation. We observe that the combined impact of INPP5E variants in JBTS and non-syndromic IRD patients does not reveal a clear genotype-phenotype correlation, suggesting the involvement of genetic modifiers. Our study cements the wide phenotypic spectrum of INPP5E disease, adding proof that sequence defects in this gene can lead to early-onset non-syndromic IRD.
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7
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Beard H, Chidlow G, Neumann D, Nazri N, Douglass M, Trim PJ, Snel MF, Casson RJ, Hemsley KM. Is the eye a window to the brain in Sanfilippo syndrome? Acta Neuropathol Commun 2020; 8:194. [PMID: 33203474 PMCID: PMC7672954 DOI: 10.1186/s40478-020-01070-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 10/28/2020] [Indexed: 11/10/2022] Open
Abstract
Sanfilippo syndrome is an untreatable form of childhood-onset dementia. Whilst several therapeutic strategies are being evaluated in human clinical trials including i.v. delivery of AAV9-based gene therapy, an urgent unmet need is the availability of non-invasive, quantitative measures of neurodegeneration. We hypothesise that as part of the central nervous system, the retina may provide a window through which to 'visualise' degenerative lesions in brain and amelioration of them following treatment. This is reliant on the age of onset and the rate of disease progression being equivalent in retina and brain. For the first time we have assessed in parallel, the nature, age of onset and rate of retinal and brain degeneration in a mouse model of Sanfilippo syndrome. Significant accumulation of heparan sulphate and expansion of the endo/lysosomal system was observed in both retina and brain pre-symptomatically (by 3 weeks of age). Robust and early activation of micro- and macroglia was also observed in both tissues. There was substantial thinning of retina and loss of rod and cone photoreceptors by ~ 12 weeks of age, a time at which cognitive symptoms are noted. Intravenous delivery of a clinically relevant AAV9-human sulphamidase vector to neonatal mice prevented disease lesion appearance in retina and most areas of brain when assessed 6 weeks later. Collectively, the findings highlight the previously unrecognised early and significant involvement of retina in the Sanfilippo disease process, lesions that are preventable by neonatal treatment with AAV9-sulphamidase. Critically, our data demonstrate for the first time that the advancement of retinal disease parallels that occurring in brain in Sanfilippo syndrome, thus retina may provide an easily accessible neural tissue via which brain disease development and its amelioration with treatment can be monitored.
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8
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Tatour Y, Ben-Yosef T. Syndromic Inherited Retinal Diseases: Genetic, Clinical and Diagnostic Aspects. Diagnostics (Basel) 2020; 10:diagnostics10100779. [PMID: 33023209 PMCID: PMC7600643 DOI: 10.3390/diagnostics10100779] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal diseases (IRDs), which are among the most common genetic diseases in humans, define a clinically and genetically heterogeneous group of disorders. Over 80 forms of syndromic IRDs have been described. Approximately 200 genes are associated with these syndromes. The majority of syndromic IRDs are recessively inherited and rare. Many, although not all, syndromic IRDs can be classified into one of two major disease groups: inborn errors of metabolism and ciliopathies. Besides the retina, the systems and organs most commonly involved in syndromic IRDs are the central nervous system, ophthalmic extra-retinal tissues, ear, skeleton, kidney and the cardiovascular system. Due to the high degree of phenotypic variability and phenotypic overlap found in syndromic IRDs, correct diagnosis based on phenotypic features alone may be challenging and sometimes misleading. Therefore, genetic testing has become the benchmark for the diagnosis and management of patients with these conditions, as it complements the clinical findings and facilitates an accurate clinical diagnosis and treatment.
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9
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Schiff ER, Daich Varela M, Robson AG, Pierpoint K, Ba-Abbad R, Nutan S, Zein WM, Ullah E, Huryn LA, Tuupanen S, Mahroo OA, Michaelides M, Burke D, Harvey K, Arno G, Hufnagel RB, Webster AR. A genetic and clinical study of individuals with nonsyndromic retinopathy consequent upon sequence variants in HGSNAT, the gene associated with Sanfilippo C mucopolysaccharidosis. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:631-643. [PMID: 32770643 PMCID: PMC8125330 DOI: 10.1002/ajmg.c.31822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/02/2020] [Accepted: 07/21/2020] [Indexed: 11/06/2022]
Abstract
Pathogenic variants in the gene HGSNAT (heparan-α-glucosaminide N-acetyltransferase) have been reported to underlie two distinct recessive conditions, depending on the specific genotype, mucopolysaccharidosis type IIIC (MPSIIIC)-a severe childhood-onset lysosomal storage disorder, and adult-onset nonsyndromic retinitis pigmentosa (RP). Here we describe the largest cohort to-date of HGSNAT-associated nonsyndromic RP patients, and describe their retinal phenotype, leukocyte enzymatic activity, and likely pathogenic genotypes. We identified biallelic HGSNAT variants in 17 individuals (15 families) as the likely cause of their RP. None showed any other symptoms of MPSIIIC. All had a mild but significant reduction of HGSNAT enzyme activity in leukocytes. The retinal condition was generally of late-onset, showing progressive degeneration of a concentric area of paramacular retina, with preservation but reduced electroretinogram responses. Symptoms, electrophysiology, and imaging suggest the rod photoreceptor to be the cell initially compromised. HGSNAT enzymatic testing was useful in resolving diagnostic dilemmas in compatible patients. We identified seven novel sequence variants [p.(Arg239Cys); p.(Ser296Leu); p.(Phe428Cys); p.(Gly248Ala); p.(Gly418Arg), c.1543-2A>C; c.1708delA], three of which were considered to be retina-disease-specific alleles. The most prevalent retina-disease-specific allele p.(Ala615Thr) was observed heterozygously or homozygously in 8 and 5 individuals respectively (7 and 4 families). Two siblings in one family, while identical for the HGSNAT locus, but discordant for retinal disease, suggest the influence of trans-acting genetic or environmental modifying factors.
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Affiliation(s)
- Elena R Schiff
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Malena Daich Varela
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Anthony G Robson
- UCL Institute of Ophthalmology, London, UK.,Department of Electrophysiology, Moorfields Eye Hospital, London, UK
| | | | - Rola Ba-Abbad
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Savita Nutan
- North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Wadih M Zein
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ehsan Ullah
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Laryssa A Huryn
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | - Omar A Mahroo
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK.,Section of Ophthalmology, King's College London, London, UK
| | - Michel Michaelides
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
| | - Derek Burke
- Enzyme Unit, Chemical Pathology, Paediatric Laboratory Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Katie Harvey
- Enzyme Unit, Chemical Pathology, Paediatric Laboratory Medicine, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Gavin Arno
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK.,North Thames Genomic Laboratory Hub, Great Ormond Street NHS Foundation Trust, London, UK
| | - Robert B Hufnagel
- Ophthalmic Genetics and Visual Function branch, National Eye Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Andrew R Webster
- Genetics Service, Moorfields Eye Hospital, London, UK.,UCL Institute of Ophthalmology, London, UK
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10
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Long Y, Li S, Dai L, Liu X, Yin X, Ren J, Guo H, Liu Y, Meng X, Li S. Nonsyndromic retinitis pigmentosa caused by two novel variants in the HGSNAT gene in a Chinese family. Ophthalmic Genet 2020; 41:390-393. [PMID: 32347150 DOI: 10.1080/13816810.2020.1755986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yanling Long
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Sha Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Limeng Dai
- Department of Medical Genetics, Third Military Medical University (Army Medical University) , Chongqing, China
| | - Xiao Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Xin Yin
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Jiayun Ren
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, Third Military Medical University (Army Medical University) , Chongqing, China
| | - Yong Liu
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Xiaohong Meng
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
| | - Shiying Li
- Southwest Hospital/Southwest Eye Hospital, Third Military Medical University (Army Medical University) , Chongqing, China.,Key Lab of Visual Damage and Regeneration & Restoration of Chongqing , Chongqing, China
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11
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Karali M, Testa F, Brunetti-Pierri R, Di Iorio V, Pizzo M, Melillo P, Barillari MR, Torella A, Musacchia F, D’Angelo L, Banfi S, Simonelli F. Clinical and Genetic Analysis of a European Cohort with Pericentral Retinitis Pigmentosa. Int J Mol Sci 2019; 21:ijms21010086. [PMID: 31877679 PMCID: PMC6982348 DOI: 10.3390/ijms21010086] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/12/2019] [Accepted: 12/19/2019] [Indexed: 12/28/2022] Open
Abstract
Retinitis pigmentosa (RP) is a clinically heterogenous disease that comprises a wide range of phenotypic and genetic subtypes. Pericentral RP is an atypical form of RP characterized by bone-spicule pigmentation and/or atrophy confined in the near mid-periphery of the retina. In contrast to classic RP, the far periphery is better preserved in pericentral RP. The aim of this study was to perform the first detailed clinical and genetic analysis of a cohort of European subjects with pericentral RP to determine the phenotypic features and the genetic bases of the disease. A total of 54 subjects from 48 independent families with pericentral RP, non-syndromic and syndromic, were evaluated through a full ophthalmological examination and underwent clinical exome or retinopathy gene panel sequencing. Disease-causative variants were identified in 22 of the 35 families (63%) in 10 different genes, four of which are also responsible for syndromic RP. Thirteen of the 34 likely pathogenic variants were novel. Intra-familiar variability was also observed. The current study confirms the mild phenotype of pericentral RP and extends the spectrum of genes associated with this condition.
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Affiliation(s)
- Marianthi Karali
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Raffaella Brunetti-Pierri
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Valentina Di Iorio
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Mariateresa Pizzo
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Paolo Melillo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Maria Rosaria Barillari
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Annalaura Torella
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
| | - Francesco Musacchia
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
| | - Luigi D’Angelo
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
| | - Sandro Banfi
- Medical Genetics, Department of Precision Medicine, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Luigi De Crecchio 7, 80138 Naples, Italy; (M.K.); (A.T.)
- Telethon Institute of Genetics and Medicine, via Campi Flegrei 34, 80078 Pozzuoli, Italy; (M.P.); (F.M.)
- Correspondence: (S.B.); (F.S.); Tel.: +39-081-19230628 (S.B.); +39-081-7704501 (F.S.)
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, Università degli Studi della Campania ‘Luigi Vanvitelli’, via Pansini 5, 80131 Naples, Italy; (F.T.); (R.B.-P.); (V.D.I.); (P.M.); (M.R.B.); (L.D.A.)
- Correspondence: (S.B.); (F.S.); Tel.: +39-081-19230628 (S.B.); +39-081-7704501 (F.S.)
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12
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Nijmeijer SCM, van den Born LI, Kievit AJA, Stepien KM, Langendonk J, Marchal JP, Roosing S, Wijburg FA, Wagenmakers MAEM. The attenuated end of the phenotypic spectrum in MPS III: from late-onset stable cognitive impairment to a non-neuronopathic phenotype. Orphanet J Rare Dis 2019; 14:249. [PMID: 31718697 PMCID: PMC6852993 DOI: 10.1186/s13023-019-1232-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 10/22/2019] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The phenotypic spectrum of many rare disorders is much wider than previously considered. Mucopolysaccharidosis type III (Sanfilippo syndrome, MPS III), is a lysosomal storage disorder traditionally considered to be characterized by childhood onset, progressive neurocognitive deterioration with a rapidly or slowly progressing phenotype. The presented MPS III case series demonstrates adult onset phenotypes with mild cognitive impairment or non-neuronopathic phenotypes. METHODS In this case series all adult MPS III patients with a mild- or non-neuronopathic phenotype, who attend the outpatient clinic of 3 expert centers for lysosomal storage disorders were included. A mild- or non-neuronopathic phenotype was defined as having completed regular secondary education and attaining a level of independency during adulthood, involving either independent living or a paid job. RESULTS Twelve patients from six families, with a median age at diagnosis of 43 years (range 3-68) were included (11 MPS IIIA, 1 MPS IIIB). In the four index patients symptoms which led to diagnostic studies (whole exome sequencing and metabolomics) resulting in the diagnosis of MPS III; two patients presented with retinal dystrophy, one with hypertrophic cardiomyopathy and one with neurocognitive decline. The other eight patients were diagnosed by family screening. At a median age of 47 years (range 19-74) 9 out of the 12 patients had normal cognitive functions. Nine patients had retinal dystrophy and 8 patients hypertrophic cardiomyopathy. CONCLUSION We show the very mild end of the phenotypic spectrum of MPS III, ranging from late-onset stable neurocognitive impairment to a fully non-neuronopathic phenotype. Awareness of this phenotype could lead to timely diagnosis and genetic counseling.
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Affiliation(s)
- Stephanie C M Nijmeijer
- Amsterdam UMC, Pediatric Metabolic Diseases, Amsterdam Lysosome Center "Sphinx", University of Amsterdam, H8-264, Meibergdreef 9, Amsterdam, The Netherlands
| | | | - Anneke J A Kievit
- Erasmus MC, Department of Clinical Genetics, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Karolina M Stepien
- Salford Royal NHS Foundation Trust, Adult Inherited Metabolic Disorders, Mark Holland Metabolic Unit, Salford, UK
| | - Janneke Langendonk
- Erasmus MC, Center for Lysosomal and Metabolic disease, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Jan Pieter Marchal
- Amsterdam UMC, Psychosocial Department, Amsterdam Public Health Research Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Susanne Roosing
- Radboud University Medical Center, Donders Institute for Brain, Cognition and Behaviour, Department of Human Genetics, Nijmegen, The Netherlands
| | - Frits A Wijburg
- Amsterdam UMC, Pediatric Metabolic Diseases, Amsterdam Lysosome Center "Sphinx", University of Amsterdam, H8-264, Meibergdreef 9, Amsterdam, The Netherlands.
| | - Margreet A E M Wagenmakers
- Erasmus MC, Center for Lysosomal and Metabolic disease, Department of Internal Medicine, University Medical Center Rotterdam, Rotterdam, The Netherlands
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13
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Blond F, Léveillard T. Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. Int J Mol Sci 2019; 20:E4922. [PMID: 31590277 PMCID: PMC6801968 DOI: 10.3390/ijms20194922] [Citation(s) in RCA: 5] [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: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022] Open
Abstract
The retina is the light sensitive part of the eye and nervous tissue that have been used extensively to characterize the function of the central nervous system. The retina has a central position both in fundamental biology and in the physiopathology of neurodegenerative diseases. We address the contribution of functional genomics to the understanding of retinal biology by reviewing key events in their historical perspective as an introduction to major findings that were obtained through the study of the retina using genomics, transcriptomics and proteomics. We illustrate our purpose by showing that most of the genes of interest for retinal development and those involved in inherited retinal degenerations have a restricted expression to the retina and most particularly to photoreceptors cells. We show that the exponential growth of data generated by functional genomics is a future challenge not only in terms of storage but also in terms of accessibility to the scientific community of retinal biologists in the future. Finally, we emphasize on novel perspectives that emerge from the development of redox-proteomics, the new frontier in retinal biology.
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Affiliation(s)
- Frédéric Blond
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
| | - Thierry Léveillard
- Department of Genetics, Sorbonne Université, INSERM, CNRS, Institut de la Vision, 17 rue Moreau, F-75012 Paris, France.
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14
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Wang J, Zhao L, Wang X, Chen Y, Xu M, Soens ZT, Ge Z, Wang PR, Wang F, Chen R. GRIPT: a novel case-control analysis method for Mendelian disease gene discovery. Genome Biol 2018; 19:203. [PMID: 30477545 PMCID: PMC6258408 DOI: 10.1186/s13059-018-1579-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 11/02/2018] [Indexed: 11/10/2022] Open
Abstract
Despite rapid progress of next-generation sequencing (NGS) technologies, the disease-causing genes underpinning about half of all Mendelian diseases remain elusive. One main challenge is the high genetic heterogeneity of Mendelian diseases in which similar phenotypes are caused by different genes and each gene only accounts for a small proportion of the patients. To overcome this gap, we developed a novel method, the Gene Ranking, Identification and Prediction Tool (GRIPT), for performing case-control analysis of NGS data. Analyses of simulated and real datasets show that GRIPT is well-powered for disease gene discovery, especially for diseases with high locus heterogeneity.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Li Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
| | - Xia Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Baylor Miraca Genetics Laboratories, Houston, TX 77030 USA
| | - Yong Chen
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zachry T. Soens
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Zhongqi Ge
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Peter Ronghan Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Fei Wang
- Shanghai Key Lab of Intelligent Information Processing, School of Computer Science and Technology, Fudan University, Shanghai, China
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030 USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, TX 77030 USA
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15
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Puvabanditsin S, Gengel N, Botti C, Jacob M, Jalil M, Cabrera K, Mehta R. 8p 11 Microduplication Is Associated with Neonatal Stridor. Mol Syndromol 2018; 9:324-327. [PMID: 30800050 DOI: 10.1159/000494796] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2018] [Indexed: 12/26/2022] Open
Abstract
We report a term male infant with congenital stridor secondary to tracheomalacia and a mild coarctation of the aorta. Developmental delay was noted upon follow-up. Whole genome SNP microarray analysis showed an ∼846-kb interstitial duplication of the short arm of chromosome 8 (8p11.21p11.1). We report novel clinical findings of this rare genetic condition.
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Affiliation(s)
| | | | - Christina Botti
- Division of Medical Genetics, Rutgers Robert Wood Johnson Medical School (RWJMS), New Brunswick, NJ, USA
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16
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Comander J, Weigel-DiFranco C, Maher M, Place E, Wan A, Harper S, Sandberg MA, Navarro-Gomez D, Pierce EA. The Genetic Basis of Pericentral Retinitis Pigmentosa-A Form of Mild Retinitis Pigmentosa. Genes (Basel) 2017; 8:genes8100256. [PMID: 28981474 PMCID: PMC5664106 DOI: 10.3390/genes8100256] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 09/06/2017] [Accepted: 09/19/2017] [Indexed: 12/25/2022] Open
Abstract
Pericentral retinitis pigmentosa (RP) is an atypical form of RP that affects the near-peripheral retina first and tends to spare the far periphery. This study was performed to further define the genetic basis of this phenotype. We identified a cohort of 43 probands with pericentral RP based on a comprehensive analysis of their retinal phenotype. Genetic analyses of DNA samples from these patients were performed using panel-based next-generation sequencing, copy number variations, and whole exome sequencing (WES). Mutations provisionally responsible for disease were found in 19 of the 43 families (44%) analyzed. These include mutations in RHO (five patients), USH2A (four patients), and PDE6B (two patients). Of 28 putatively pathogenic alleles, 15 (54%) have been previously identified in patients with more common forms of typical RP, while the remaining 13 mutations (46%) were novel. Burden testing of WES data successfully identified HGSNAT as a cause of pericentral RP in at least two patients, suggesting it is also a relatively common cause of pericentral RP. While additional sequencing might uncover new genes specifically associated with pericentral RP, the current results suggest that genetically pericentral RP is not a separate clinical entity, but rather is part of the spectrum of mild RP phenotypes.
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Affiliation(s)
- Jason Comander
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Carol Weigel-DiFranco
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Matthew Maher
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Emily Place
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Aliete Wan
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Shyana Harper
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Michael A Sandberg
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Daniel Navarro-Gomez
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
| | - Eric A Pierce
- Ocular Genomics Institute, Berman-Gund Laboratory for the Study of Retinal Degenerations, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Boston, MA 02114, USA.
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17
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Ku CA, Hull S, Arno G, Vincent A, Carss K, Kayton R, Weeks D, Anderson GW, Geraets R, Parker C, Pearce DA, Michaelides M, MacLaren RE, Robson AG, Holder GE, Heon E, Raymond FL, Moore AT, Webster AR, Pennesi ME. Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration. JAMA Ophthalmol 2017; 135:749-760. [PMID: 28542676 DOI: 10.1001/jamaophthalmol.2017.1401] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Importance Mutations in genes traditionally associated with syndromic retinal disease are increasingly found to cause nonsyndromic inherited retinal degenerations. Mutations in CLN3 are classically associated with juvenile neuronal ceroid lipofuscinosis, a rare neurodegenerative disease with early retinal degeneration and progressive neurologic deterioration, but have recently also been identified in patients with nonsyndromic inherited retinal degenerations. To our knowledge, detailed clinical characterization of such cases has yet to be reported. Objective To provide detailed clinical, electrophysiologic, structural, and molecular genetic findings in nonsyndromic inherited retinal degenerations associated with CLN3 mutations. Design, Setting, and Participants A multi-institutional case series of 10 patients who presented with isolated nonsyndromic retinal disease and mutations in CLN3. Patient ages ranged from 16 to 70 years; duration of follow-up ranged from 3 to 29 years. Main Outcomes and Measures Longitudinal clinical evaluation, including full ophthalmic examination, multimodal retinal imaging, perimetry, and electrophysiology. Molecular analyses were performed using whole-genome sequencing or whole-exome sequencing. Electron microscopy studies of peripheral lymphocytes and CLN3 transcript analysis with polymerase chain reaction amplification were performed in a subset of patients. Results There were 7 females and 3 males in this case series, with a mean (range) age at last review of 37.1 (16-70) years. Of the 10 patients, 4 had a progressive late-onset rod-cone dystrophy, with a mean (range) age at onset of 29.7 (20-40) years, and 6 had an earlier onset rod-cone dystrophy, with a mean (range) age at onset of 12.1 (7-17) years. Ophthalmoscopic examination features included macular edema, mild intraretinal pigment migration, and widespread atrophy in advanced disease. Optical coherence tomography imaging demonstrated significant photoreceptor loss except in patients with late-onset disease who had a focal preservation of the ellipsoid zone and outer nuclear layer in the fovea. Electroretinography revealed a rod-cone pattern of dysfunction in 6 patients and were completely undetectable in 2 patients. Six novel CLN3 variants were identified in molecular analyses. Conclusions and Relevance This report describes detailed clinical, imaging, and genetic features of CLN3-associated nonsyndromic retinal degeneration. The age at onset and natural progression of retinal disease differs greatly between syndromic and nonsyndromic CLN3 disease, which may be associated with genotypic differences.
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Affiliation(s)
- Cristy A Ku
- Casey Eye Institute, Oregon Health & Science University, Portland
| | - Sarah Hull
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Gavin Arno
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Ajoy Vincent
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Keren Carss
- National Health Service Blood and Transplant Centre, Department of Haematology, University of Cambridge, Cambridge, England6National Institute for Health Research BioResource: Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, England
| | - Robert Kayton
- Pathology Department, Oregon Health & Science University, Portland
| | - Douglas Weeks
- Pathology Department, Oregon Health & Science University, Portland
| | - Glenn W Anderson
- Histopathology Department, Great Ormond Street Hospital for Children, London, England
| | - Ryan Geraets
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - Camille Parker
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota
| | - David A Pearce
- Sanford Children's Health Research Center, Sanford Research, Sioux Falls, South Dakota10Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls
| | - Michel Michaelides
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Robert E MacLaren
- Moorfields Eye Hospital, London, England11Nuffield Laboratory of Ophthalmology, Department of Clinical Neurosciences, University of Oxford, Oxford, England12Oxford University Hospitals National Health Service Foundation Trust, Oxford, England
| | - Anthony G Robson
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Graham E Holder
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Elise Heon
- Department of Ophthalmology and Vision Sciences, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - F Lucy Raymond
- National Health Service Blood and Transplant Centre, Department of Haematology, University of Cambridge, Cambridge, England6National Institute for Health Research BioResource: Rare Diseases, Cambridge University Hospitals, Cambridge Biomedical Campus, Cambridge, England13Cambridge Institute for Medical Research, Department of Medical Genetics, University of Cambridge, Cambridge, England
| | - Anthony T Moore
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England14Department of Ophthalmology, University of California, San Francisco Medical School, San Francisco
| | - Andrew R Webster
- University College London Institute of Ophthalmology, London, England3Moorfields Eye Hospital, London, England
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health & Science University, Portland
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18
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Genetic characterization and disease mechanism of retinitis pigmentosa; current scenario. 3 Biotech 2017; 7:251. [PMID: 28721681 DOI: 10.1007/s13205-017-0878-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 07/10/2017] [Indexed: 12/21/2022] Open
Abstract
Retinitis pigmentosa is a group of genetically transmitted disorders affecting 1 in 3000-8000 individual people worldwide ultimately affecting the quality of life. Retinitis pigmentosa is characterized as a heterogeneous genetic disorder which leads by progressive devolution of the retina leading to a progressive visual loss. It can occur in syndromic (with Usher syndrome and Bardet-Biedl syndrome) as well as non-syndromic nature. The mode of inheritance can be X-linked, autosomal dominant or autosomal recessive manner. To date 58 genes have been reported to associate with retinitis pigmentosa most of them are either expressed in photoreceptors or the retinal pigment epithelium. This review focuses on the disease mechanisms and genetics of retinitis pigmentosa. As retinitis pigmentosa is tremendously heterogeneous disorder expressing a multiplicity of mutations; different variations in the same gene might induce different disorders. In recent years, latest technologies including whole-exome sequencing contributing effectively to uncover the hidden genesis of retinitis pigmentosa by reporting new genetic mutations. In future, these advancements will help in better understanding the genotype-phenotype correlations of disease and likely to develop new therapies.
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19
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Nguyen TMT, Hull S, Roepman R, van den Born LI, Oud MM, de Vrieze E, Hetterschijt L, Letteboer SJF, van Beersum SEC, Blokland EA, Yntema HG, Cremers FPM, van der Zwaag PA, Arno G, van Wijk E, Webster AR, Haer-Wigman L. Missense mutations in the WD40 domain of AHI1 cause non-syndromic retinitis pigmentosa. J Med Genet 2017; 54:624-632. [PMID: 28442542 PMCID: PMC5574394 DOI: 10.1136/jmedgenet-2016-104200] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 02/02/2017] [Accepted: 02/27/2017] [Indexed: 12/31/2022]
Abstract
Background Recent findings suggesting that Abelson helper integration site 1 (AHI1) is involved in non-syndromic retinal disease have been debated, as the functional significance of identified missense variants was uncertain. We assessed whether AHI1 variants cause non-syndromic retinitis pigmentosa (RP). Methods Exome sequencing was performed in three probands with RP. The effects of the identified missense variants in AHI1 were predicted by three-dimensional structure homology modelling. Ciliary parameters were evaluated in patient’s fibroblasts, and recombinant mutant proteins were expressed in ciliated retinal pigmented epithelium cells. Results In the three patients with RP, three sets of compound heterozygous variants were detected in AHI1 (c.2174G>A; p.Trp725* and c.2258A>T; p.Asp753Val, c.660delC; p.Ser221Glnfs*10 and c.2090C>T; p.Pro697Leu, c.2087A>G; p.His696Arg and c.2429C>T; p.Pro810Leu). All four missense variants were present in the conserved WD40 domain of Jouberin, the ciliary protein encoded by AHI1, with variable predicted implications for the domain structure. No significant changes in the percentage of ciliated cells, nor in cilium length or intraflagellar transport were detected. However, expression of mutant recombinant Jouberin in ciliated cells showed a significantly decreased enrichment at the ciliary base. Conclusions This report confirms that mutations in AHI1 can underlie autosomal recessive RP. Moreover, it structurally and functionally validates the effect of the RP-associated AHI1 variants on protein function, thus proposing a new genotype–phenotype correlation for AHI1 mutation associated retinal ciliopathies.
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Affiliation(s)
- Thanh-Minh T Nguyen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sarah Hull
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Ronald Roepman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Machteld M Oud
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Stef J F Letteboer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Sylvia E C van Beersum
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen A Blokland
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Helger G Yntema
- 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.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Paul A van der Zwaag
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Gavin Arno
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
| | - Andrew R Webster
- UniversityCollege London, Instituteof Ophthalmology, London, United Kingdom.,Moorfields Eye Hospital, London, United Kingdom
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University, Nijmegen, The Netherlands
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20
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Pierrache LHM, Kimchi A, Ratnapriya R, Roberts L, Astuti GDN, Obolensky A, Beryozkin A, Tjon-Fo-Sang MJH, Schuil J, Klaver CCW, Bongers EMHF, Haer-Wigman L, Schalij N, Breuning MH, Fischer GM, Banin E, Ramesar RS, Swaroop A, van den Born LI, Sharon D, Cremers FPM. Whole-Exome Sequencing Identifies Biallelic IDH3A Variants as a Cause of Retinitis Pigmentosa Accompanied by Pseudocoloboma. Ophthalmology 2017; 124:992-1003. [PMID: 28412069 DOI: 10.1016/j.ophtha.2017.03.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/28/2017] [Accepted: 03/03/2017] [Indexed: 12/25/2022] Open
Abstract
PURPOSE To identify the genetic cause of and describe the phenotype in 4 families with autosomal recessive retinitis pigmentosa (arRP) that can be associated with pseudocoloboma. DESIGN Case series. PARTICIPANTS Seven patients from 4 unrelated families with arRP, among whom 3 patients had bilateral early-onset macular pseudocoloboma. METHODS We performed homozygosity mapping and whole-exome sequencing in 5 probands and 2 unaffected family members from 4 unrelated families. Subsequently, Sanger sequencing and segregation analysis were performed in additional family members. We reviewed the medical history of individuals carrying IDH3A variants and performed additional ophthalmic examinations, including full-field electroretinography, fundus photography, fundus autofluorescence imaging, and optical coherence tomography. MAIN OUTCOME MEASURES IDH3A variants, age at diagnosis, visual acuity, fundus appearance, visual field, and full-field electroretinography, fundus autofluorescence, and optical coherence tomography findings. RESULTS We identified 7 different variants in IDH3A in 4 unrelated families, that is, 5 missense, 1 nonsense, and 1 frameshift variant. All participants showed symptoms early in life, ranging from night blindness to decreased visual acuity, and were diagnosed between the ages of 1 and 11 years. Four participants with biallelic IDH3A variants displayed a typical arRP phenotype and 3 participants were diagnosed with arRP and pseudocoloboma of the macula. CONCLUSIONS IDH3A variants were identified as a novel cause of typical arRP in some individuals associated with macular pseudocoloboma. We observed both phenotypes in 2 siblings carrying the same compound heterozygous variants, which could be explained by variable disease expression and warrants caution when making assertions about genotype-phenotype correlations.
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Affiliation(s)
- Laurence H M Pierrache
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands; Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands; Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Adva Kimchi
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rinki Ratnapriya
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - Lisa Roberts
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands; Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Alexey Obolensky
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Avigail Beryozkin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Jose Schuil
- Bartiméus Institute for the Visually Impaired, Zeist, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ernie M H F Bongers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Nicoline Schalij
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands
| | - Martijn H Breuning
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Gratia M Fischer
- Department of Ophthalmology, Dr. George Mukhari Academic Hospital, Sefako Makgatho Health Sciences University (SMU), Ga-Rankuwa, Pretoria, South Africa
| | - Eyal Banin
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Raj S Ramesar
- UCT/MRC Human Genetics Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Anand Swaroop
- Neurobiology-Neurodegeneration & Repair Laboratory, National Eye Institute, National Institutes of Health, Bethesda, Maryland
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, Rotterdam, The Netherlands; Rotterdam Ophthalmic Institute, Rotterdam, The Netherlands
| | - Dror Sharon
- Department of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, Nijmegen, The Netherlands.
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21
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Van Cauwenbergh C, Van Schil K, Cannoodt R, Bauwens M, Van Laethem T, De Jaegere S, Steyaert W, Sante T, Menten B, Leroy BP, Coppieters F, De Baere E. arrEYE: a customized platform for high-resolution copy number analysis of coding and noncoding regions of known and candidate retinal dystrophy genes and retinal noncoding RNAs. Genet Med 2016; 19:457-466. [PMID: 27608171 PMCID: PMC5392597 DOI: 10.1038/gim.2016.119] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/06/2016] [Indexed: 12/13/2022] Open
Abstract
Purpose: Our goal was to design a customized microarray, arrEYE, for high-resolution copy number variant (CNV) analysis of known and candidate genes for inherited retinal dystrophy (iRD) and retina-expressed noncoding RNAs (ncRNAs). Methods: arrEYE contains probes for the full genomic region of 106 known iRD genes, including those implicated in retinitis pigmentosa (RP) (the most frequent iRD), cone–rod dystrophies, macular dystrophies, and an additional 60 candidate iRD genes and 196 ncRNAs. Eight CNVs in iRD genes identified by other techniques were used as positive controls. The test cohort consisted of 57 patients with autosomal dominant, X-linked, or simplex RP. Results: In an RP patient, a novel heterozygous deletion of exons 7 and 8 of the HGSNAT gene was identified: c.634-408_820+338delinsAGAATATG, p.(Glu212Glyfs*2). A known variant was found on the second allele: c.1843G>A, p.(Ala615Thr). Furthermore, we expanded the allelic spectrum of USH2A and RCBTB1 with novel CNVs. Conclusion: The arrEYE platform revealed subtle single-exon to larger CNVs in iRD genes that could be characterized at the nucleotide level, facilitated by the high resolution of the platform. We report the first CNV in HGSNAT that, combined with another mutation, leads to RP, further supporting its recently identified role in nonsyndromic iRD. Genet Med19 4, 457–466.
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Affiliation(s)
- Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Kristof Van Schil
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Robrecht Cannoodt
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Data Mining and Modeling for Biomedicine group, VIB Inflammation Research Center, Ghent, Belgium.,Department of Internal Medicine, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Sarah De Jaegere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Tom Sante
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Björn Menten
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology and Center for Cellular & Molecular Therapeutics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Frauke Coppieters
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
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22
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Zhang Q, Xu M, Verriotto JD, Li Y, Wang H, Gan L, Lam BL, Chen R. Next-generation sequencing-based molecular diagnosis of 35 Hispanic retinitis pigmentosa probands. Sci Rep 2016; 6:32792. [PMID: 27596865 PMCID: PMC5011706 DOI: 10.1038/srep32792] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 07/29/2016] [Indexed: 12/13/2022] Open
Abstract
Retinitis pigmentosa (RP) is a heterogeneous group of inherited retinal diseases. The prevalence of RP and the mutation spectrum vary across populations. Hispanic people account for approximately 17% of the United States population, and the genetic etiologies of RP of this ethnic group still remain not well defined. Utilizing next-generation sequencing (NGS), we screened mutations in known retinal disease-causing genes in an RP cohort of 35 unrelated Hispanic probands from the Miami area. We achieved a solving rate of 66% and identified 15 novel putative pathogenic mutations, including a frequent founder mutation disrupting PRPF31 splicing. Our data show that the mutation spectrum of Hispanic RP receives a significant impact from disease-causing alleles of Spanish origin and may also contain population-specific alleles.
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Affiliation(s)
- Qi Zhang
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Mingchu Xu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Jennifer D. Verriotto
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Hui Wang
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Lin Gan
- College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China
- Institute of Life Sciences, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Byron L. Lam
- Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, United States
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
- Structural and Computational Biology and Molecular Biophysics Graduate Program, Baylor College of Medicine, Houston, Texas, USA
- The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas, USA
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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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Kabir F, Ullah I, Ali S, Gottsch AD, Naeem MA, Assir MZ, Khan SN, Akram J, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Loss of function mutations in RP1 are responsible for retinitis pigmentosa in consanguineous familial cases. Mol Vis 2016; 22:610-25. [PMID: 27307693 PMCID: PMC4901054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 06/08/2016] [Indexed: 10/31/2022] Open
Abstract
PURPOSE This study was undertaken to identify causal mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in consanguineous families. METHODS Large consanguineous families were ascertained from the Punjab province of Pakistan. An ophthalmic examination consisting of a fundus evaluation and electroretinography (ERG) was completed, and small aliquots of blood were collected from all participating individuals. Genomic DNA was extracted from white blood cells, and a genome-wide linkage or a locus-specific exclusion analysis was completed with polymorphic short tandem repeats (STRs). Two-point logarithm of odds (LOD) scores were calculated, and all coding exons and exon-intron boundaries of RP1 were sequenced to identify the causal mutation. RESULTS The ophthalmic examination showed that affected individuals in all families manifest cardinal symptoms of RP. Genome-wide scans localized the disease phenotype to chromosome 8q, a region harboring RP1, a gene previously implicated in the pathogenesis of RP. Sanger sequencing identified a homozygous single base deletion in exon 4: c.3697delT (p.S1233Pfs22*), a single base substitution in intron 3: c.787+1G>A (p.I263Nfs8*), a 2 bp duplication in exon 2: c.551_552dupTA (p.Q185Yfs4*) and an 11,117 bp deletion that removes all three coding exons of RP1. These variations segregated with the disease phenotype within the respective families and were not present in ethnically matched control samples. CONCLUSIONS These results strongly suggest that these mutations in RP1 are responsible for the retinal phenotype in affected individuals of all four consanguineous families.
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Affiliation(s)
- Firoz Kabir
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Inayat Ullah
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Shahbaz Ali
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | | | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Zaman Assir
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Shaheen N. Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Javed Akram
- Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan,Allama Iqbal Medical College, University of Health Sciences, Lahore, Pakistan,National Centre for Genetic Diseases, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, Pakistan
| | - Radha Ayyagari
- Shiley Eye Institute, University of California, San Diego, CA
| | - J. Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD
| | - S. Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD
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25
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Autosomal recessive retinitis pigmentosa with homozygous rhodopsin mutation E150K and non-coding cis-regulatory variants in CRX-binding regions of SAMD7. Sci Rep 2016; 6:21307. [PMID: 26887858 PMCID: PMC4758057 DOI: 10.1038/srep21307] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 01/19/2016] [Indexed: 01/17/2023] Open
Abstract
The aim of this study was to unravel the molecular pathogenesis of an unusual retinitis pigmentosa (RP) phenotype observed in a Turkish consanguineous family. Homozygosity mapping revealed two candidate genes, SAMD7 and RHO. A homozygous RHO mutation c.448G > A, p.E150K was found in two affected siblings, while no coding SAMD7 mutations were identified. Interestingly, four non-coding homozygous variants were found in two SAMD7 genomic regions relevant for binding of the retinal transcription factor CRX (CRX-bound regions, CBRs) in these affected siblings. Three variants are located in a promoter CBR termed CBR1, while the fourth is located more downstream in CBR2. Transcriptional activity of these variants was assessed by luciferase assays and electroporation of mouse retinal explants with reporter constructs of wild-type and variant SAMD7 CBRs. The combined CBR2/CBR1 variant construct showed significantly decreased SAMD7 reporter activity compared to the wild-type sequence, suggesting a cis-regulatory effect on SAMD7 expression. As Samd7 is a recently identified Crx-regulated transcriptional repressor in retina, we hypothesize that these SAMD7 variants might contribute to the retinal phenotype observed here, characterized by unusual, recognizable pigment deposits, differing from the classic spicular intraretinal pigmentation observed in other individuals homozygous for p.E150K, and typically associated with RP in general.
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26
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Xu M, Yamada T, Sun Z, Eblimit A, Lopez I, Wang F, Manya H, Xu S, Zhao L, Li Y, Kimchi A, Sharon D, Sui R, Endo T, Koenekoop RK, Chen R. Mutations in POMGNT1 cause non-syndromic retinitis pigmentosa. Hum Mol Genet 2016; 25:1479-88. [PMID: 26908613 DOI: 10.1093/hmg/ddw022] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/25/2016] [Indexed: 11/12/2022] Open
Abstract
A growing number of human diseases have been linked to defects in protein glycosylation that affects a wide range of organs. Among them, O-mannosylation is an unusual type of protein glycosylation that is largely restricted to the muscular and nerve system. Consistently, mutations in genes involved in the O-mannosylation pathway result in infantile-onset, severe developmental defects involving skeleton muscle, brain and eye, such as the muscle-eye-brain disease (MIM no. 253280). However, the functional importance of O-mannosylation in these tissues at later stages remains largely unknown. In our study, we have identified recessive mutations in POMGNT1, which encodes an essential component in O-mannosylation pathway, in three unrelated families with autosomal recessive retinitis pigmentosa (RP), but without extraocular involvement. Enzymatic assay of these mutant alleles demonstrate that they greatly reduce the POMGNT1 enzymatic activity and are likely to be hypomorphic. Immunohistochemistry shows that POMGNT1 is specifically expressed in photoreceptor basal body. Taken together, our work identifies a novel disease-causing gene for RP and indicates that proper protein O-mannosylation is not only essential for early organ development, but also important for maintaining survival and function of the highly specialized retinal cells at later stages.
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Affiliation(s)
- Mingchu Xu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Takeyuki Yamada
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Zixi Sun
- Department of Ophthalmology, Peking Union Medical College, Beijing 100730, China
| | - Aiden Eblimit
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Irma Lopez
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec H3H 1P3, Canada and
| | - Feng Wang
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Hiroshi Manya
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Shan Xu
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Li Zhao
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Structural and Computational Biology and Molecular Biophysics Graduate Program
| | - Yumei Li
- Department of Molecular and Human Genetics, Human Genome Sequencing Center
| | - Adva Kimchi
- Departments of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Dror Sharon
- Departments of Ophthalmology, Hadassah-Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Ruifang Sui
- Department of Ophthalmology, Peking Union Medical College, Beijing 100730, China
| | - Tamao Endo
- Molecular Glycobiology, Research Team for Mechanism of Aging, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, Tokyo 173-0015, Japan
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec H3H 1P3, Canada and
| | - Rui Chen
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Structural and Computational Biology and Molecular Biophysics Graduate Program, The Verna and Marrs Mclean Department of Biochemistry and Molecular Biology and Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA,
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Fedele AO. Sanfilippo syndrome: causes, consequences, and treatments. APPLICATION OF CLINICAL GENETICS 2015; 8:269-81. [PMID: 26648750 PMCID: PMC4664539 DOI: 10.2147/tacg.s57672] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Sanfilippo syndrome, or mucopolysaccharidosis (MPS) type III, refers to one of five autosomal recessive, neurodegenerative lysosomal storage disorders (MPS IIIA to MPS IIIE) whose symptoms are caused by the deficiency of enzymes involved exclusively in heparan sulfate degradation. The primary characteristic of MPS III is the degeneration of the central nervous system, resulting in mental retardation and hyperactivity, typically commencing during childhood. The significance of the order of events leading from heparan sulfate accumulation through to downstream changes in the levels of biomolecules within the cell and ultimately the (predominantly neuropathological) clinical symptoms is not well understood. The genes whose deficiencies cause the MPS III subtypes have been identified, and their gene products, as well as a selection of disease-causing mutations, have been characterized to varying degrees with respect to both frequency and direct biochemical consequences. A number of genetic and biochemical diagnostic methods have been developed and adopted by diagnostic laboratories. However, there is no effective therapy available for any form of MPS III, with treatment currently limited to clinical management of neurological symptoms. The availability of animal models for all forms of MPS III, whether spontaneous or generated via gene targeting, has contributed to improved understanding of the MPS III subtypes, and has provided and will deliver invaluable tools to appraise emerging therapies. Indeed, clinical trials to evaluate intrathecally-delivered enzyme replacement therapy in MPS IIIA patients, and gene therapy for MPS IIIA and MPS IIIB patients are planned or underway.
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Affiliation(s)
- Anthony O Fedele
- Lysosomal Diseases Research Unit, South Australian Health and Medical Research Institute, Adelaide, SA, Australia
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Expanding the clinical, allelic, and locus heterogeneity of retinal dystrophies. Genet Med 2015; 18:554-62. [PMID: 26355662 DOI: 10.1038/gim.2015.127] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 08/04/2015] [Indexed: 12/11/2022] Open
Abstract
PURPOSE Retinal dystrophies (RD) are heterogeneous hereditary disorders of the retina that are usually progressive in nature. The aim of this study was to clinically and molecularly characterize a large cohort of RD patients. METHODS We have developed a next-generation sequencing assay that allows known RD genes to be sequenced simultaneously. We also performed mapping studies and exome sequencing on familial and on syndromic RD patients who tested negative on the panel. RESULTS Our panel identified the likely causal mutation in >60% of the 292 RD families tested. Mapping studies on all 162 familial RD patients who tested negative on the panel identified two novel disease loci on Chr2:25,550,180-28,794,007 and Chr16:59,225,000-72,511,000. Whole-exome sequencing revealed the likely candidate as AGBL5 and CDH16, respectively. We also performed exome sequencing on negative syndromic RD cases and identified a novel homozygous truncating mutation in GNS in a family with the novel combination of mucopolysaccharidosis and RD. Moreover, we identified a homozygous truncating mutation in DNAJC17 in a family with an apparently novel syndrome of retinitis pigmentosa and hypogammaglobulinemia. CONCLUSION Our study expands the clinical and allelic spectrum of known RD genes, and reveals AGBL5, CDH16, and DNAJC17 as novel disease candidates.Genet Med 18 6, 554-562.
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