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Thuma TBT, Procopio RA, Jimenez HJ, Gunton KB, Pulido JS. Hypomorphic variants in inherited retinal and ocular diseases: A review of the literature with clinical cases. Surv Ophthalmol 2024; 69:337-348. [PMID: 38036193 DOI: 10.1016/j.survophthal.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 11/17/2023] [Accepted: 11/20/2023] [Indexed: 12/02/2023]
Abstract
Hypomorphic variants decrease, but do not eliminate, gene function via a reduction in the amount of mRNA or protein product produced by a gene or by production of a gene product with reduced function. Many hypomorphic variants have been implicated in inherited retinal diseases (IRDs) and other genetic ocular conditions; however, there is heterogeneity in the use of the term "hypomorphic" in the scientific literature. We searched for all hypomorphic variants reported to cause IRDs and ocular disorders. We also discuss the presence of hypomorphic variants in the patient population of our ocular genetics department over the past decade. We propose that standardized criteria should be adopted for use of the term "hypomorphic" to describe gene variants to improve genetic counseling and patient care outcomes.
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Affiliation(s)
- Tobin B T Thuma
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | | | - Hiram J Jimenez
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA
| | - Kammi B Gunton
- Department of Pediatric Ophthalmology and Strabismus, Wills Eye Hospital, Philadelphia, PA, USA
| | - Jose S Pulido
- Vickie and Jack Farber Vision Research Center, Wills Eye Hospital, Philadelphia, PA, USA; Retina Service, Wills Eye Hospital, Philadelphia, PA, USA.
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2
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Hitti-Malin RJ, Panneman DM, Corradi Z, Boonen EGM, Astuti G, Dhaenens CM, Stöhr H, Weber BHF, Sharon D, Banin E, Karali M, Banfi S, Ben-Yosef T, Glavač D, Farrar GJ, Ayuso C, Liskova P, Dudakova L, Vajter M, Ołdak M, Szaflik JP, Matynia A, Gorin MB, Kämpjärvi K, Bauwens M, De Baere E, Hoyng CB, Li CHZ, Klaver CCW, Inglehearn CF, Fujinami K, Rivolta C, Allikmets R, Zernant J, Lee W, Podhajcer OL, Fakin A, Sajovic J, AlTalbishi A, Valeina S, Taurina G, Vincent AL, Roberts L, Ramesar R, Sartor G, Luppi E, Downes SM, van den Born LI, McLaren TL, De Roach JN, Lamey TM, Thompson JA, Chen FK, Tracewska AM, Kamakari S, Sallum JMF, Bolz HJ, Kayserili H, Roosing S, Cremers FPM. Towards Uncovering the Role of Incomplete Penetrance in Maculopathies through Sequencing of 105 Disease-Associated Genes. Biomolecules 2024; 14:367. [PMID: 38540785 PMCID: PMC10967834 DOI: 10.3390/biom14030367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024] Open
Abstract
Inherited macular dystrophies (iMDs) are a group of genetic disorders, which affect the central region of the retina. To investigate the genetic basis of iMDs, we used single-molecule Molecular Inversion Probes to sequence 105 maculopathy-associated genes in 1352 patients diagnosed with iMDs. Within this cohort, 39.8% of patients were considered genetically explained by 460 different variants in 49 distinct genes of which 73 were novel variants, with some affecting splicing. The top five most frequent causative genes were ABCA4 (37.2%), PRPH2 (6.7%), CDHR1 (6.1%), PROM1 (4.3%) and RP1L1 (3.1%). Interestingly, variants with incomplete penetrance were revealed in almost one-third of patients considered solved (28.1%), and therefore, a proportion of patients may not be explained solely by the variants reported. This includes eight previously reported variants with incomplete penetrance in addition to CDHR1:c.783G>A and CNGB3:c.1208G>A. Notably, segregation analysis was not routinely performed for variant phasing-a limitation, which may also impact the overall diagnostic yield. The relatively high proportion of probands without any putative causal variant (60.2%) highlights the need to explore variants with incomplete penetrance, the potential modifiers of disease and the genetic overlap between iMDs and age-related macular degeneration. Our results provide valuable insights into the genetic landscape of iMDs and warrant future exploration to determine the involvement of other maculopathy genes.
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Affiliation(s)
- Rebekkah J. Hitti-Malin
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Daan M. Panneman
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Zelia Corradi
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Erica G. M. Boonen
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Galuh Astuti
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Claire-Marie Dhaenens
- Univ. Lille, Inserm, CHU Lille, U1172-LilNCog-Lille Neuroscience & Cognition, F-59000 Lille, France
| | - Heidi Stöhr
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
| | - Bernhard H. F. Weber
- Institute of Human Genetics, University of Regensburg, 93053 Regensburg, Germany
- Institute of Clinical Human Genetics, University Hospital Regensburg, 93053 Regensburg, Germany
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Marianthi Karali
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania ‘Luigi Vanvitelli’, 80131 Naples, Italy
| | - Sandro Banfi
- Department of Precision Medicine, University of Campania ‘Luigi Vanvitelli’, 80138 Naples, Italy
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania ‘Luigi Vanvitelli’, 80131 Naples, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy
| | - Tamar Ben-Yosef
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Damjan Glavač
- Department of Molecular Genetics, Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
- Center for Human Genetics and Pharmacogenomics, Faculty of Medicine, University of Maribor, 2000 Maribor, Slovenia
| | - G. Jane Farrar
- The School of Genetics and Microbiology, The University of Dublin Trinity College, D02 VF25 Dublin, Ireland
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28049 Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Petra Liskova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Lubica Dudakova
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Marie Vajter
- Department of Paediatrics and Inherited Metabolic Disorders, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
- Department of Ophthalmology, First Faculty of Medicine, Charles University and General University Hospital in Prague, 128 08 Prague, Czech Republic
| | - Monika Ołdak
- Department of Histology and Embryology, Medical University of Warsaw, 02-004 Warsaw, Poland
| | - Jacek P. Szaflik
- Department of Ophthalmology, Medical University of Warsaw, SPKSO Ophthalmic University Hospital, 03-709 Warsaw, Poland
| | - Anna Matynia
- College of Optometry, University of Houston, Houston, TX 77004, USA
- Jules Stein Eye Institute, Los Angeles, CA 90095, USA
- Ophthalmology, University of California Los Angeles David Geffen School of Medicine, Los Angeles, CA 90095, USA
| | | | | | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Catherina H. Z. Li
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Caroline C. W. Klaver
- Department of Ophthalmology, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Chris F. Inglehearn
- Division of Molecular Medicine, Leeds Institute of Medical Research, St. James’s University Hospital, University of Leeds, Leeds LS9 7TF, UK
| | - Kaoru Fujinami
- Department of Ophthalmology, The Jikei University School of Medicine, Tokyo 105-8461, Japan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland
| | - Rando Allikmets
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY 10027, USA
| | - Jana Zernant
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
| | - Winston Lee
- Department of Ophthalmology, Columbia University, New York, NY 10027, USA
| | - Osvaldo L. Podhajcer
- Laboratorio de Terapia Molecular y Celular (Genocan), Fundación Instituto Leloir, CONICET, Buenos Aires 1405, Argentina
| | - Ana Fakin
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Jana Sajovic
- Eye Hospital, University Medical Centre Ljubljana, 1000 Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Alaa AlTalbishi
- St John of Jerusalem Eye Hospital Group, East Jerusalem 91198, Palestine
| | - Sandra Valeina
- Department of Ophthalmology, Riga Stradins University, LV-1007 Riga, Latvia
- Children’s Clinical University Hospital, LV-1004 Riga, Latvia
| | - Gita Taurina
- Children’s Clinical University Hospital, LV-1004 Riga, Latvia
| | - Andrea L. Vincent
- Department of Ophthalmology, New Zealand National Eye Centre, Faculty of Medical and Health Sciences, The University of Auckland, Grafton, Auckland 1023, New Zealand
- Eye Department, Greenlane Clinical Centre, Auckland District Health Board, Auckland 1142, New Zealand
| | - Lisa Roberts
- University of Cape Town/MRC Precision and Genomic Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Raj Ramesar
- University of Cape Town/MRC Precision and Genomic Medicine Research Unit, Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Giovanna Sartor
- Department of Pharmacy and Biotechnology, University of Bologna, 40127 Bologna, Italy
| | - Elena Luppi
- Department of Medical and Surgical Sciences, University of Bologna, 40127 Bologna, Italy
- Unit of Medical Genetics, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Susan M. Downes
- Nuffield Laboratory of Ophthalmology, Nuffield Department of Clinical Neurosciences, Oxford University, Oxford OX3 9DU, UK
- Oxford Eye Hospital, Oxford University NHS Foundation Trust, Oxford OX3 9DU, UK
| | | | - Terri L. McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - John N. De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Tina M. Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | - Jennifer A. Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Fred K. Chen
- Centre for Ophthalmology and Visual Science, The University of Western Australia, Nedlands, WA 6009, Australia
| | | | - Smaragda Kamakari
- Ophthalmic Genetics Unit, OMMA Ophthalmological Institute of Athens, 115 25 Athens, Greece
| | - Juliana Maria Ferraz Sallum
- Department of Ophthalmology and Visual Sciences, Universidade Federal de São Paulo, São Paulo 04023-062, SP, Brazil
- Instituto de Genética Ocular, São Paulo 04552-050, SP, Brazil
| | - Hanno J. Bolz
- Institute of Human Genetics, University Hospital of Cologne, 50937 Cologne, Germany
| | - Hülya Kayserili
- Department of Medical Genetics, Koc University School of Medicine (KUSOM), 34450 Istanbul, Turkey
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB Nijmegen, The Netherlands
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3
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Sadr Z, Ghasemi A, Rohani M, Alavi A. NMNAT1 and hereditary spastic paraplegia (HSP): expanding the phenotypic spectrum of NMNAT1 variants. Neuromuscul Disord 2023; 33:295-301. [PMID: 36871412 DOI: 10.1016/j.nmd.2023.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 02/05/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
In the NAD biosynthetic network, the nicotinamide mononucleotide adenylyltransferase (NMNAT) enzyme fuels NAD as a co-substrate for a group of enzymes. Mutations in the nuclear-specific isoform, NMNAT1, have been extensively reported as the cause of Leber congenital amaurosis-type 9 (LCA9). However, there are no reports of NMNAT1 mutations causing neurological disorders by disrupting the maintenance of physiological NAD homeostasis in other types of neurons. In this study, for the first time, the potential association between a NMNAT1 variant and hereditary spastic paraplegia (HSP) is described. Whole-exome sequencing was performed for two affected siblings diagnosed with HSP. Runs of homozygosity (ROH) were detected. The shared variants of the siblings located in the homozygosity blocks were selected. The candidate variant was amplified and Sanger sequenced in the proband and other family members. Homozygous variant c.769G>A:p.(Glu257Lys) in NMNAT1, the most common variant of NMNAT1 in LCA9 patients, located in the ROH of chromosome 1, was detected as a probable disease-causing variant. After detection of the variant in NMNAT1, as a LCA9-causative gene, ophthalmological and neurological re-evaluations were performed. No ophthalmological abnormality was detected and the clinical manifestations of these patients were completely consistent with pure HSP. No NMNAT1 variant had ever been previously reported in HSP patients. However, NMNAT1 variants have been reported in a syndromic form of LCA which is associated with ataxia. In conclusion, our patients expand the clinical spectrum of NMNAT1 variants and represent the first evidence of the probable correlation between NMNAT1 variants and HSP.
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Affiliation(s)
- Zahra Sadr
- Genetics research center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Aida Ghasemi
- Genetics research center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Mohammad Rohani
- Department of Neurology, Iran University of Medical Sciences, Hazrat Rasool Hospital, Tehran, Iran.
| | - Afagh Alavi
- Genetics research center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
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4
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Yi Z, Li S, Wang S, Xiao X, Sun W, Zhang Q. Clinical features and genetic spectrum of NMNAT1-associated retinal degeneration. Eye (Lond) 2022; 36:2279-2285. [PMID: 34837036 PMCID: PMC9674661 DOI: 10.1038/s41433-021-01853-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/14/2021] [Accepted: 11/10/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES To systematically analyse the NMNAT1 variant spectrum and frequency, the associated phenotypic characteristics, and potential genotype-phenotype correlations based on our data and literature review. METHODS Biallelic potential pathogenic variants (PPV) in NMNAT1 were collected from our in-house exome sequencing data. Whole-genome sequencing was conducted subsequently for patients with only one heterozygous PPV detected in NMNAT1. The clinical data were reviewed and evaluated in detail. Furthermore, the literature was reviewed for reports of NMNAT1 variants and their associated phenotypes. RESULTS Eleven NMNAT1 variants, including two novel variants, were detected in 8 families from our cohort. All of the 9 available patients showed generalized tapetoretinal dystrophy at an early age (88.9% in the first decade), and disciform macular atrophy was identified in six patients from five unrelated families. Among a total of 125 patients from 8 families of our cohort and 91 families reported by the available literature, 92.9% patients showed onset of disease in the first year after birth, and 89.0% patients showed visual acuity of 0.05 or lower. All of the 39 patients with fundus photos available presented disciform macular atrophy with generalized tapetoretinal dystrophy. Most (54/80, 67.5%) of causative NMNAT1 variants were missense. The most frequent variants in Caucasian and Asian population are p.E257K and p.R237C, respectively. CONCLUSIONS Early-onset age, disciform macular atrophy with generalized tapetoretinal dystrophy, and poor visual acuity are the typical features of NMNAT1-associated retinal degeneration. Different variant hot spots of NMNAT1 were observed in different populations.
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Affiliation(s)
- Zhen Yi
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Shiqiang Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Siyu Wang
- Department of Ophthalmology, Li Chuan People's Hospital, Enshi, HuBei, 445400, China
| | - Xueshan Xiao
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Wenmin Sun
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China
| | - Qingjiong Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, 54 Xianlie Road, Guangzhou, 510060, China.
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5
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Kayazawa T, Kuniyoshi K, Hatsukawa Y, Fujinami K, Yoshitake K, Tsunoda K, Shimojo H, Iwata T, Kusaka S. Clinical course of a Japanese girl with Leber congenital amaurosis associated with a novel nonsense pathogenic variant in NMNAT1: a case report and mini review. Ophthalmic Genet 2022; 43:400-408. [PMID: 35026968 DOI: 10.1080/13816810.2021.2023195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Leber congenital amaurosis (LCA), although rare, is one of the most severe forms of early-onset inherited retinal dystrophy (IRD). Here, we review the molecular genetics and phenotypic characteristics of patients with NMNAT1-associated IRD. The longitudinal clinical and molecular findings of a Japanese girl diagnosed with LCA associated with pathogenic variants in NMNAT1 c.648delG, (p.Trp216Ter*) and c.709C>T (p.Arg237Cys) have been described to highlight the salient clinical features of NMNAT1-associated IRD.
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Affiliation(s)
- Tomoyasu Kayazawa
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Kazuki Kuniyoshi
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka, Japan
| | - Yoshikazu Hatsukawa
- Department of Ophthalmology, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kaoru Fujinami
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Genetics, UCL Institute of Ophthalmology Associated with Moorfields Eye Hospital, London, UK.,Department of Ophthalmology, Keio University School of Medicine, Tokyo, Japan
| | - Kazutoshi Yoshitake
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan.,Graduate School of Agricultural and Life Science, Faculty of Agriculture, The University of Tokyo, Tokyo, Japan
| | - Kazushige Tsunoda
- Laboratory of Visual Physiology, Division of Vision Research, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Hiroshi Shimojo
- Department of Ophthalmology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Takeshi Iwata
- Division of Molecular and Cellular Biology, National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, Tokyo, Japan
| | - Shunji Kusaka
- Department of Ophthalmology, Kindai University Faculty of Medicine, Osaka, Japan
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Bedoni N, Quinodoz M, Pinelli M, Cappuccio G, Torella A, Nigro V, Testa F, Simonelli F, Corton M, Lualdi S, Lanza F, Morana G, Ayuso C, Di Rocco M, Filocamo M, Banfi S, Brunetti-Pierri N, Superti-Furga A, Rivolta C. An Alu-mediated duplication in NMNAT1, involved in NAD biosynthesis, causes a novel syndrome, SHILCA, affecting multiple tissues and organs. Hum Mol Genet 2021; 29:2250-2260. [PMID: 32533184 DOI: 10.1093/hmg/ddaa112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/30/2020] [Accepted: 06/01/2020] [Indexed: 12/22/2022] Open
Abstract
We investigated the genetic origin of the phenotype displayed by three children from two unrelated Italian families, presenting with a previously unrecognized autosomal recessive disorder that included a severe form of spondylo-epiphyseal dysplasia, sensorineural hearing loss, intellectual disability and Leber congenital amaurosis (SHILCA), as well as some brain anomalies that were visible at the MRI. Autozygome-based analysis showed that these children shared a 4.76 Mb region of homozygosity on chromosome 1, with an identical haplotype. Nonetheless, whole-exome sequencing failed to identify any shared rare coding variants, in this region or elsewhere. We then determined the transcriptome of patients' fibroblasts by RNA sequencing, followed by additional whole-genome sequencing experiments. Gene expression analysis revealed a 4-fold downregulation of the gene NMNAT1, residing indeed in the shared autozygous interval. Short- and long-read whole-genome sequencing highlighted a duplication involving 2 out of the 5 exons of NMNAT1 main isoform (NM_022787.3), leading to the production of aberrant mRNAs. Pathogenic variants in NMNAT1 have been previously shown to cause non-syndromic Leber congenital amaurosis (LCA). However, no patient with null biallelic mutations has ever been described, and murine Nmnat1 knockouts show embryonic lethality, indicating that complete absence of NMNAT1 activity is probably not compatible with life. The rearrangement found in our cases, presumably causing a strong but not complete reduction of enzymatic activity, may therefore result in an intermediate syndromic phenotype with respect to LCA and lethality.
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Affiliation(s)
- Nicola Bedoni
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, University of Lausanne, 1011 Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Michele Pinelli
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Gerarda Cappuccio
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Annalaura Torella
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Francesco Testa
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | - Francesca Simonelli
- Eye Clinic, Multidisciplinary Department of Medical, Surgical and Dental Sciences, University of Campania "Luigi Vanvitelli", 80131 Naples, Italy
| | | | - Marta Corton
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Susanna Lualdi
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Federica Lanza
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Giovanni Morana
- Neuroradiology Unit, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Carmen Ayuso
- Department of Genetics, Instituto de Investigación Sanitaria - Fundación Jiménez Díaz, University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), 28040 Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), ISCIII, 28029 Madrid, Spain
| | - Maja Di Rocco
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Mirella Filocamo
- Laboratorio di Genetica Molecolare e Biobanche, Istituto G. Gaslini, 16147 Genoa, Italy
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Medical Genetics, Department of Precision Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), 80078 Pozzuoli, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, 80131 Naples, Italy
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of LE1 7RH Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland.,Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
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7
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A hypomorphic variant in EYS detected by genome-wide association study contributes toward retinitis pigmentosa. Commun Biol 2021; 4:140. [PMID: 33514863 PMCID: PMC7846782 DOI: 10.1038/s42003-021-01662-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 01/06/2021] [Indexed: 12/26/2022] Open
Abstract
The genetic basis of Japanese autosomal recessive retinitis pigmentosa (ARRP) remains largely unknown. Herein, we applied a 2-step genome-wide association study (GWAS) in 640 Japanese patients. Meta-GWAS identified three independent peaks at P < 5.0 × 10−8, all within the major ARRP gene EYS. Two of the three were each in linkage disequilibrium with a different low frequency variant (allele frequency < 0.05); a known founder Mendelian mutation (c.4957dupA, p.S1653Kfs*2) and a non-synonymous variant (c.2528 G > A, p.G843E) of unknown significance. mRNA harboring c.2528 G > A failed to restore rhodopsin mislocalization induced by morpholino-mediated knockdown of eys in zebrafish, consistent with the variant being pathogenic. c.2528 G > A solved an additional 7.0% of Japanese ARRP cases. The third peak was in linkage disequilibrium with a common non-synonymous variant (c.7666 A > T, p.S2556C), possibly representing an unreported disease-susceptibility signal. GWAS successfully unraveled genetic causes of a rare monogenic disorder and identified a high frequency variant potentially linked to development of local genome therapeutics. Koji Nishiguchi et al. identify three genetic variants within the EYS gene that are associated with retinitis pigmentosa using a genome-wide association study. They demonstrate that one of these variants (G843E) causes retinal dysfunction in zebrafish, suggesting a causal role for EYS in retinitis pigmentosa.
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8
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Skorczyk-Werner A, Niedziela Z, Stopa M, Krawczyński MR. Novel gene variants in Polish patients with Leber congenital amaurosis (LCA). Orphanet J Rare Dis 2020; 15:345. [PMID: 33308271 PMCID: PMC7731562 DOI: 10.1186/s13023-020-01634-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
Background Leber congenital amaurosis (LCA) is a rare retinal disease that is the most frequent cause of congenital blindness in children and the most severe form of inherited retinal dystrophies. To date, 25 genes have been implicated in the pathogenesis of LCA. As gene therapy is becoming available, the identification of potential treatment candidates is crucial. The aim of the study was to report the molecular basis of Leber congenital amaurosis in 22 Polish families.
Methods Single Nucleotide Polymorphism-microarray for LCA genes or Next Generation Sequencing diagnostic panel for LCA genes (or both tests) were performed to identify potentially pathogenic variants. Bidirectional Sanger sequencing was carried out for validation and segregation analysis of the variants identified within the families. Results The molecular background was established in 22 families. From a total of 24 identified variants, 23 were predicted to affect protein-coding or splicing, including 10 novel variants. The variants were identified in 7 genes: CEP290, GUCY2D, RPE65, NMNAT1, CRB1, RPGRIP1, and CRX. More than one-third of the patients, with clinical LCA diagnosis confirmed by the results of molecular analysis, appeared to be affected with a severe form of the disease: LCA10 caused by the CEP290 gene variants. Intronic mutation c.2991+1655A>G in the CEP290 gene was the most frequent variant identified in the studied group. Conclusions This study provides the first molecular genetic characteristics of patients with Leber congenital amaurosis from the previously unexplored Polish population. Our study expands the mutational spectrum as we report 10 novel variants identified in LCA genes. The fact that the most frequent causes of the disease in the studied group of Polish patients are mutations in one out of three genes that are currently the targets for gene therapy (CEP290, GUCY2D, and RPE65) strongly emphasizes the importance of the molecular background analyses of LCA in Polish patients.
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Affiliation(s)
- Anna Skorczyk-Werner
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.
| | - Zuzanna Niedziela
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.,Department of Ophthalmology, Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Marcin Stopa
- Department of Ophthalmology, Chair of Ophthalmology and Optometry, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Robert Krawczyński
- Department of Medical Genetics, Poznan University of Medical Sciences, 8, Rokietnicka St, 60-806, Poznan, Poland.,Centers for Medical Genetics GENESIS, Poznan, Poland
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9
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Sasaki Y, Kakita H, Kubota S, Sene A, Lee TJ, Ban N, Dong Z, Lin JB, Boye SL, DiAntonio A, Boye SE, Apte RS, Milbrandt J. SARM1 depletion rescues NMNAT1-dependent photoreceptor cell death and retinal degeneration. eLife 2020; 9:e62027. [PMID: 33107823 PMCID: PMC7591247 DOI: 10.7554/elife.62027] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 10/13/2020] [Indexed: 01/02/2023] Open
Abstract
Leber congenital amaurosis type nine is an autosomal recessive retinopathy caused by mutations of the NAD+ synthesis enzyme NMNAT1. Despite the ubiquitous expression of NMNAT1, patients do not manifest pathologies other than retinal degeneration. Here we demonstrate that widespread NMNAT1 depletion in adult mice mirrors the human pathology, with selective loss of photoreceptors highlighting the exquisite vulnerability of these cells to NMNAT1 loss. Conditional deletion demonstrates that NMNAT1 is required within the photoreceptor. Mechanistically, loss of NMNAT1 activates the NADase SARM1, the central executioner of axon degeneration, to trigger photoreceptor death and vision loss. Hence, the essential function of NMNAT1 in photoreceptors is to inhibit SARM1, highlighting an unexpected shared mechanism between axonal degeneration and photoreceptor neurodegeneration. These results define a novel SARM1-dependent photoreceptor cell death pathway and identifies SARM1 as a therapeutic candidate for retinopathies.
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Affiliation(s)
- Yo Sasaki
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
| | - Hiroki Kakita
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
- Department of Perinatal and Neonatal Medicine, Aichi Medical UniversityAichiJapan
| | - Shunsuke Kubota
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Abdoulaye Sene
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Tae Jun Lee
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Norimitsu Ban
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Zhenyu Dong
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Joseph B Lin
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
| | - Sanford L Boye
- Department of Pediatrics, Powell Gene Therapy CenterGainesvilleUnited States
| | - Aaron DiAntonio
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Needleman Center for Neurometabolism and Axonal TherapeuticsSt. LouisUnited States
| | - Shannon E Boye
- Department of Pediatrics, Division of Cellular and Molecular TherapyGainesvilleUnited States
| | - Rajendra S Apte
- Department of Ophthalmology and Visual Sciences, Washington University School of MedicineSt. LouisUnited States
- Department of Developmental Biology, Washington University School of MedicineSt. LouisUnited States
- Department of Medicine, Washington University School of MedicineSt. LouisUnited States
| | - Jeffrey Milbrandt
- Department of Genetics, Washington University School of MedicineSt. LouisUnited States
- Needleman Center for Neurometabolism and Axonal TherapeuticsSt. LouisUnited States
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10
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NMNAT1-ASSOCIATED CONE-ROD DYSTROPHY: EVIDENCE FOR A SPECTRUM OF FOVEAL MALDEVELOPMENT. Retin Cases Brief Rep 2020; 16:385-392. [PMID: 32150116 DOI: 10.1097/icb.0000000000000992] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE To describe in detail the phenotype of two siblings with biallelic NMNAT1 mutations. METHODS A 4-year-old male patient (P1) and his 7-year-old sister (P2), product of a nonconsanguineous union of Egyptian ancestry, underwent a comprehensive ophthalmic examination, retinal imaging with spectral domain optical coherence tomography and near infrared (NIR) fundus autofluorescence (FAF), and full-field electroretinograms (ERG). RESULTS Patients had blurred vision and nystagmus at ∼3 years of age. P2 was hyperopic (+6D). Visual acuity in P1 was 20/100 at age 3 and remained at ∼20/125 at age 4; P2 visual acuity was 20/70 at age 4 and declined to ∼20/200 at age 7. ERGs recorded in P1 showed relatively large rod-mediated responses but nearly undetectable cone signals. There was foveal/parafoveal depigmentation. Spectral domain optical coherence tomography showed hypoplastic foveas, a thin outer nuclear layer centrally but normal thickness beyond the vascular arcades. At the foveal center, cone outer segments were absent and the outer nuclear layer was further hyporreflective. The inner retina was mostly within normal limits. There was central depigmentation on near infrared fundus autofluorescence. Biallelic mutations were identified in NMNAT1: One was previously reported (c.769 G>A; pGlu257Lys), and the other one (c.245T>C; pVal82Ala) was novel. CONCLUSION NMNAT1 mutations cause a consistent phenotype characterized by early-onset, progressive, cone>rod retinawide dysfunction and predominantly central abnormalities ranging from a hypoplastic to an atrophic fovea, supporting a critical role for NMNAT1 in central retinal development and maintenance. Relatively preserved inner retina and detectable photoreceptors may become therapeutic targets.
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11
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Runhart EH, Valkenburg D, Cornelis SS, Khan M, Sangermano R, Albert S, Bax NM, Astuti GDN, Gilissen C, Pott JWR, Verheij JBGM, Blokland EAW, Cremers FPM, van den Born LI, Hoyng CB. Late-Onset Stargardt Disease Due to Mild, Deep-Intronic ABCA4 Alleles. Invest Ophthalmol Vis Sci 2020; 60:4249-4256. [PMID: 31618761 DOI: 10.1167/iovs.19-27524] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To investigate the role of two deep-intronic ABCA4 variants, that showed a mild splice defect in vitro and can occur on the same allele as the low penetrant c.5603A>T, in Stargardt disease (STGD1). Methods Ophthalmic data were assessed of 18 STGD1 patients who harbored c.769-784C>T or c.4253+43G>A in combination with a severe ABCA4 variant. Subjects carrying c.[769-784C>T; 5603A>T] were clinically compared with a STGD1 cohort previously published carrying c.5603A>T noncomplex. We calculated the penetrances of the intronic variants using ABCA4 allele frequency data of the general population and investigated the effect of c.769-784C>T on splicing in photoreceptor progenitor cells (PPCs). Results Mostly, late-onset, foveal-sparing STGD1 was observed among subjects harboring c.769-784C>T or c.4253+43G>A (median age of onset, 54.5 and 52.0 years, respectively). However, ages of onset, phenotypes in fundo, and visual acuity courses varied widely. No significant clinical differences were observed between the c.[769-784C>T; 5603A>T] cohort and the c.4253+43G>A or the c.5603A>T cohort. The penetrances of c.769-784C>T (20.5%-39.6%) and c.4253+43G>A (35.8%-43.1%) were reduced, when not considering the effect of yet unidentified or known factors in cis, such as c.5603A>T (identified in 7/7 probands with c.769-784C>T; 1/8 probands with c.4253+43G>A). Variant c.769-784C>T resulted in a pseudo-exon insertion in 15% of the total mRNA (i.e., ∼30% of the c.769-784C>T allele alone). Conclusions Two mild intronic ABCA4 variants could further explain missing heritability in late-onset STGD1, distinguishing it from AMD. The observed clinical variability and calculated reduced penetrance urge research into modifiers within and outside of the ABCA4 gene.
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Affiliation(s)
- Esmee H Runhart
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Dyon Valkenburg
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Stéphanie S Cornelis
- 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
| | - Mubeen Khan
- 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
| | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, United States
| | - Silvia Albert
- 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
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Galuh D N Astuti
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Division of Human Genetics, Center for Biomedical Research, Faculty of Medicine, Diponegoro University, Semarang, Indonesia
| | - Christian Gilissen
- 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
| | - Jan-Willem R Pott
- Department of Ophthalmology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Joke B G M Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Ellen A W Blokland
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- 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
| | | | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
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12
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NMNAT1 E257K variant, associated with Leber Congenital Amaurosis (LCA9), causes a mild retinal degeneration phenotype. Exp Eye Res 2018; 173:32-43. [PMID: 29674119 DOI: 10.1016/j.exer.2018.04.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 03/18/2018] [Accepted: 04/13/2018] [Indexed: 01/25/2023]
Abstract
NMNAT1 (nicotinamide mononucleotide adenylyltransferase 1) encodes a rate-limiting enzyme that catalyzes the biosynthesis of NAD+ and plays a role in neuroprotection. Mutations in NMNAT1 have been identified to cause a recessive, non-syndromic early form of blindness genetically defined as Leber Congenital Amaurosis 9 (LCA9). One of the most common alleles reported so far in NMNAT1 is the c.769G > A (E257K) missense mutation, which occurs in 70% of all LCA9 cases. However, given its relatively high population frequency and the observation of individuals with homozygous E257K variant without phenotype, the pathogenicity of this allele has been questioned. To address this issue, we have studied the pathogenic effects of this allele by generating a knock-in mouse model. Interestingly, no obvious morphological or functional defects are observed in Nmnat1 E257K homozygous mice up to one year old, even after light-damage. Together with the previous clinical reports, we propose that the E257K allele is a weak hypomorphic allele that has significantly reduced penetrance in the homozygous state. In contrast, compound heterozygous Nmnat1E257K/- mice exhibit photoreceptor defects which are exacerbated upon exposure to light. Furthermore, retina tissue- specific Nmnat1 conditional knockout mice exhibit photoreceptor degeneration before the retina has terminally differentiated. These findings suggest that NMNAT1 plays an important role in photoreceptors and is likely involved in both retinal development and maintenance of photoreceptor integrity.
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13
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Special Issue Introduction: Inherited Retinal Disease: Novel Candidate Genes, Genotype-Phenotype Correlations, and Inheritance Models. Genes (Basel) 2018; 9:genes9040215. [PMID: 29659558 PMCID: PMC5924557 DOI: 10.3390/genes9040215] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Inherited retinal diseases (IRDs) are genetically and clinically heterogeneous disorders.[...].
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14
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Nash BM, Symes R, Goel H, Dinger ME, Bennetts B, Grigg JR, Jamieson RV. NMNAT1 variants cause cone and cone-rod dystrophy. Eur J Hum Genet 2017; 26:428-433. [PMID: 29184169 DOI: 10.1038/s41431-017-0029-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 09/13/2017] [Accepted: 10/10/2017] [Indexed: 11/09/2022] Open
Abstract
Cone and cone-rod dystrophies (CD and CRD, respectively) are degenerative retinal diseases that predominantly affect the cone photoreceptors. The underlying disease gene is not known in approximately 75% of autosomal recessive cases. Variants in NMNAT1 cause a severe, early-onset retinal dystrophy called Leber congenital amaurosis (LCA). We report two patients where clinical phenotyping indicated diagnoses of CD and CRD, respectively. NMNAT1 variants were identified, with Case 1 showing an extremely rare homozygous variant c.[271G > A] p.(Glu91Lys) and Case 2 compound heterozygous variants c.[53 A > G];[769G > A] p.(Asn18Ser);(Glu257Lys). The detailed variant analysis, in combination with the observation of an associated macular atrophy phenotype, indicated that these variants were disease-causing. This report demonstrates that the variants in NMNAT1 may cause CD or CRD associated with macular atrophy. Genetic investigations of the patients with CD or CRD should include NMNAT1 in the genes examined.
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Affiliation(s)
- Benjamin M Nash
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.,Disciplines of Genetic Medicine, and Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia.,Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Richard Symes
- Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | - Marcel E Dinger
- Kinghorn Centre for Clinical Genomics, Garvan Institute for Medical Research, Sydney, NSW, Australia.,St Vincent's Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Bruce Bennetts
- Sydney Genome Diagnostics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia
| | - John R Grigg
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia.,Discipline of Ophthalmology, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Robyn V Jamieson
- Eye Genetics Research, The Children's Hospital at Westmead, Save Sight Institute, Children's Medical Research Institute, University of Sydney, Sydney, NSW, Australia. .,Disciplines of Genetic Medicine, and Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia. .,Department of Clinical Genetics, Western Sydney Genetics Program, The Children's Hospital at Westmead, Sydney, NSW, Australia.
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15
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Thompson JA, De Roach JN, McLaren TL, Montgomery HE, Hoffmann LH, Campbell IR, Chen FK, Mackey DA, Lamey TM. The genetic profile of Leber congenital amaurosis in an Australian cohort. Mol Genet Genomic Med 2017; 5:652-667. [PMID: 29178642 PMCID: PMC5702575 DOI: 10.1002/mgg3.321] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/27/2017] [Accepted: 06/29/2017] [Indexed: 12/21/2022] Open
Abstract
Background Leber congenital amaurosis (LCA) is a severe visual impairment responsible for infantile blindness, representing ~5% of all inherited retinal dystrophies. LCA encompasses a group of heterogeneous disorders, with 24 genes currently implicated in pathogenesis. Such clinical and genetic heterogeneity poses great challenges for treatment, with personalized therapies anticipated to be the best treatment candidates. Unraveling the individual genetic etiology of disease is a prerequisite for personalized therapies, and could identify potential treatment candidates, inform patient management, and discriminate syndromic forms of disease. Methods We have genetically analyzed 45 affected and 82 unaffected individuals from 34 unrelated LCA pedigrees using predominantly next‐generation sequencing and Array CGH technology. Results We present the molecular findings for an Australian LCA cohort, sourced from the Australian Inherited Retinal Disease Registry & DNA Bank. CEP290 and GUCY2D mutations, each represent 19% of unrelated LCA cases, followed by NMNAT1 (12%). Genetic subtypes were consistent with other reports, and were resolved in 90% of this cohort. Conclusion The high resolution rate achieved, equivalent to recent findings using whole exome/genome sequencing, reflects the progression from hypothesis (LCA Panel) to non‐hypothesis (RD Panel) testing and, coupled with Array CGH analysis, is a highly effective first‐tier test for LCA.
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Affiliation(s)
- Jennifer A Thompson
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - John N De Roach
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
| | - Terri L McLaren
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Hannah E Montgomery
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Ling H Hoffmann
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Isabella R Campbell
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia
| | - Fred K Chen
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia.,Lions Eye Institute, Nedlands, Western Australia, Australia.,Department of Ophthalmology, Royal Perth Hospital, Perth, Western Australia, Australia
| | - David A Mackey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia.,Lions Eye Institute, Nedlands, Western Australia, Australia
| | - Tina M Lamey
- Australian Inherited Retinal Disease Registry and DNA Bank, Department of Medical Technology and Physics, Sir Charles Gairdner Hospital, Perth, Western Australia, Australia.,Centre for Ophthalmology and Visual Science, The University of Western Australia, Crawley, Western Australia, Australia
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16
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Fujikura K. Global Carrier Rates of Rare Inherited Disorders Using Population Exome Sequences. PLoS One 2016; 11:e0155552. [PMID: 27219052 PMCID: PMC4878778 DOI: 10.1371/journal.pone.0155552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2016] [Accepted: 04/29/2016] [Indexed: 12/22/2022] Open
Abstract
Exome sequencing has revealed the causative mutations behind numerous rare, inherited disorders, but it is challenging to find reliable epidemiological values for rare disorders. Here, I provide a genetic epidemiology method to identify the causative mutations behind rare, inherited disorders using two population exome sequences (1000 Genomes and NHLBI). I created global maps of carrier rate distribution for 18 recessive disorders in 16 diverse ethnic populations. Out of a total of 161 mutations associated with 18 recessive disorders, I detected 24 mutations in either or both exome studies. The genetic mapping revealed strong international spatial heterogeneities in the carrier patterns of the inherited disorders. I next validated this methodology by statistically evaluating the carrier rate of one well-understood disorder, sickle cell anemia (SCA). The population exome-based epidemiology of SCA [African (allele frequency (AF) = 0.0454, N = 2447), Asian (AF = 0, N = 286), European (AF = 0.000214, N = 4677), and Hispanic (AF = 0.0111, N = 362)] was not significantly different from that obtained from a clinical prevalence survey. A pair-wise proportion test revealed no significant differences between the two exome projects in terms of AF (46/48 cases; P > 0.05). I conclude that population exome-based carrier rates can form the foundation for a prospectively maintained database of use to clinical geneticists. Similar modeling methods can be applied to many inherited disorders.
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Affiliation(s)
- Kohei Fujikura
- Kobe University School of Medicine, 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
- * E-mail:
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17
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Greenwald SH, Charette JR, Staniszewska M, Shi LY, Brown SDM, Stone L, Liu Q, Hicks WL, Collin GB, Bowl MR, Krebs MP, Nishina PM, Pierce EA. Mouse Models of NMNAT1-Leber Congenital Amaurosis (LCA9) Recapitulate Key Features of the Human Disease. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:1925-1938. [PMID: 27207593 DOI: 10.1016/j.ajpath.2016.03.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 03/08/2016] [Accepted: 03/16/2016] [Indexed: 12/20/2022]
Abstract
The nicotinamide nucleotide adenylyltransferase 1 (NMNAT1) enzyme is essential for regenerating the nuclear pool of NAD(+) in all nucleated cells in the body, and mounting evidence also suggests that it has a separate role in neuroprotection. Recently, mutations in the NMNAT1 gene were associated with Leber congenital amaurosis, a severe retinal degenerative disease that causes blindness during infancy. Availability of a reliable mammalian model of NMNAT1-Leber congenital amaurosis would assist in determining the mechanisms through which disruptions in NMNAT1 lead to retinal cell degeneration and would provide a resource for testing treatment options. To this end, we identified two separate N-ethyl-N-nitrosourea-generated mouse lines that harbor either a p.V9M or a p.D243G mutation. Both mouse models recapitulate key aspects of the human disease and confirm the pathogenicity of mutant NMNAT1. Homozygous Nmnat1 mutant mice develop a rapidly progressing chorioretinal disease that begins with photoreceptor degeneration and includes attenuation of the retinal vasculature, optic atrophy, and retinal pigment epithelium loss. Retinal function deteriorates in both mouse lines, and, in the more rapidly progressing homozygous Nmnat1(V9M) mutant mice, the electroretinogram becomes undetectable and the pupillary light response weakens. These mouse models offer an opportunity for investigating the cellular mechanisms underlying disease pathogenesis, evaluating potential therapies for NMNAT1-Leber congenital amaurosis, and conducting in situ studies on NMNAT1 function and NAD(+) metabolism.
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Affiliation(s)
- Scott H Greenwald
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | | | - Magdalena Staniszewska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | | | - Steve D M Brown
- Mammalian Genetics Unit, Medical Research Council (MRC), Harwell Campus, Oxfordshire, United Kingdom
| | - Lisa Stone
- The Jackson Laboratory, Bar Harbor, Maine
| | - Qin Liu
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, Massachusetts
| | | | | | - Michael R Bowl
- Mammalian Genetics Unit, Medical Research Council (MRC), Harwell Campus, Oxfordshire, United Kingdom
| | | | | | - Eric A Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye & Ear Infirmary, Harvard Medical School, Boston, Massachusetts.
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18
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Improving the management of Inherited Retinal Dystrophies by targeted sequencing of a population-specific gene panel. Sci Rep 2016; 6:23910. [PMID: 27032803 PMCID: PMC4817143 DOI: 10.1038/srep23910] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/10/2016] [Indexed: 11/08/2022] Open
Abstract
Next-generation sequencing (NGS) has overcome important limitations to the molecular diagnosis of Inherited Retinal Dystrophies (IRD) such as the high clinical and genetic heterogeneity and the overlapping phenotypes. The purpose of this study was the identification of the genetic defect in 32 Spanish families with different forms of IRD. With that aim, we implemented a custom NGS panel comprising 64 IRD-associated genes in our population, and three disease-associated intronic regions. A total of 37 pathogenic mutations (14 novels) were found in 73% of IRD patients ranging from 50% for autosomal dominant cases, 75% for syndromic cases, 83% for autosomal recessive cases, and 100% for X-linked cases. Additionally, unexpected phenotype-genotype correlations were found in 6 probands, which led to the refinement of their clinical diagnoses. Furthermore, intra- and interfamilial phenotypic variability was observed in two cases. Moreover, two cases unsuccessfully analysed by exome sequencing were resolved by applying this panel. Our results demonstrate that this hypothesis-free approach based on frequently mutated, population-specific loci is highly cost-efficient for the routine diagnosis of this heterogeneous condition and allows the unbiased analysis of a miscellaneous cohort. The molecular information found here has aid clinical diagnosis and has improved genetic counselling and patient management.
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19
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Hedergott A, Volk AE, Herkenrath P, Thiele H, Fricke J, Altmüller J, Nürnberg P, Kubisch C, Neugebauer A. Clinical and genetic findings in a family with NMNAT1-associated Leber congenital amaurosis: case report and review of the literature. Graefes Arch Clin Exp Ophthalmol 2015; 253:2239-46. [PMID: 26464178 DOI: 10.1007/s00417-015-3174-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 08/31/2015] [Accepted: 09/02/2015] [Indexed: 10/23/2022] Open
Abstract
BACKGROUND Leber congenital amaurosis (LCA) is a severe retinal dystrophy, typically manifesting in the first year of life. Mutations in more than 18 genes have been reported to date. In recent studies, biallelic mutations in NMNAT1 encoding nicotinamide mononucleotide adenylyltransferase 1 have been found to cause LCA. PURPOSE To broaden the knowledge regarding the phenotype of NMNAT1-associated LCA. METHODS Clinical ophthalmologic examinations were performed in two sisters with LCA. Whole exome sequencing was performed in one of the affected girls, with subsequent segregation analysis in the affected sister and unaffected parents. The literature was reviewed for reports of NMNAT1-associated LCA. RESULTS Exome sequencing revealed the known NMNAT1 mutation c.25G>A (p.Val9Met) in a homozygous state. Segregation analysis showed the same homozygous mutation in the affected younger sister. Both parents were found to be heterozygous carriers of the mutation. The two girls both presented with severe visual impairment, nystagmus, central atrophy of the pigment epithelium, and pigment clumping in the periphery before the age of 6 months. Retinal vessels were attenuated. Both children were hyperopic. In the older sister, differential diagnosis included an inflammatory origin, but electrophysiology in her as well as her sister confirmed a diagnosis of LCA. Pallor of the optic nerve head was not present at birth but developed progressively. CONCLUSIONS We confirmed a diagnosis of NMNAT1-associated LCA in two siblings through identification of the mutation (c.25G>A [p. Val9Met]) in a homozygous state. In infants with non-detectable electroretinogram (ERG), along with severe congenital visual dysfunction or blindness and central pigment epithelium atrophy with pigment clumping resembling scarring due to chorioretinitis, LCA due to NMNAT1 mutations should be considered.
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Affiliation(s)
- A Hedergott
- Department of Ophthalmology, University Hospital Cologne, Joseph Stelzmann Str.9, D-50931, Cologne, Germany.
| | - A E Volk
- Institute of Human Genetics, Ulm University, 89081, Ulm, Germany.,Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - P Herkenrath
- Department of Paediatrics, University Hospital Cologne, 50931, Cologne, Germany
| | - H Thiele
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany
| | - J Fricke
- Department of Ophthalmology, University Hospital Cologne, Joseph Stelzmann Str.9, D-50931, Cologne, Germany
| | - J Altmüller
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany.,Institute of Human Genetics, University Hospital Cologne, 50931, Cologne, Germany
| | - P Nürnberg
- Cologne Center for Genomics, University of Cologne, 50931, Cologne, Germany.,University of Cologne, Center for Molecular Medicine Cologne (CMMC), 50931, Cologne, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, 50931, Cologne, Germany
| | - C Kubisch
- Institute of Human Genetics, Ulm University, 89081, Ulm, Germany.,Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, 20246, Hamburg, Germany
| | - A Neugebauer
- Department of Ophthalmology, University Hospital Cologne, Joseph Stelzmann Str.9, D-50931, Cologne, Germany
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20
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Coppieters F, Todeschini AL, Fujimaki T, Baert A, De Bruyne M, Van Cauwenbergh C, Verdin H, Bauwens M, Ongenaert M, Kondo M, Meire F, Murakami A, Veitia RA, Leroy BP, De Baere E. Hidden Genetic Variation in LCA9-Associated Congenital Blindness Explained by 5'UTR Mutations and Copy-Number Variations of NMNAT1. Hum Mutat 2015; 36:1188-96. [PMID: 26316326 PMCID: PMC5054839 DOI: 10.1002/humu.22899] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/19/2015] [Indexed: 11/28/2022]
Abstract
Leber congenital amaurosis (LCA) is a severe autosomal‐recessive retinal dystrophy leading to congenital blindness. A recently identified LCA gene is NMNAT1, located in the LCA9 locus. Although most mutations in blindness genes are coding variations, there is accumulating evidence for hidden noncoding defects or structural variations (SVs). The starting point of this study was an LCA9‐associated consanguineous family in which no coding mutations were found in the LCA9 region. Exploring the untranslated regions of NMNAT1 revealed a novel homozygous 5′UTR variant, c.‐70A>T. Moreover, an adjacent 5′UTR variant, c.‐69C>T, was identified in a second consanguineous family displaying a similar phenotype. Both 5′UTR variants resulted in decreased NMNAT1 mRNA abundance in patients’ lymphocytes, and caused decreased luciferase activity in human retinal pigment epithelial RPE‐1 cells. Second, we unraveled pseudohomozygosity of a coding NMNAT1 mutation in two unrelated LCA patients by the identification of two distinct heterozygous partial NMNAT1 deletions. Molecular characterization of the breakpoint junctions revealed a complex Alu‐rich genomic architecture. Our study uncovered hidden genetic variation in NMNAT1‐associated LCA and emphasized a shift from coding to noncoding regulatory mutations and repeat‐mediated SVs in the molecular pathogenesis of heterogeneous recessive disorders such as hereditary blindness.
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Affiliation(s)
| | | | - Takuro Fujimaki
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Annelot Baert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | | | | | - Hannah Verdin
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Maté Ongenaert
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
| | - Mineo Kondo
- Department of Ophthalmology, Mie University Graduate School of Medicine, Mie, Japan
| | - Françoise Meire
- Department of Ophthalmology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Reiner A Veitia
- Institut Jacques Monod, UMR 7592 CNRS-Université Paris Diderot, Paris, France
| | - Bart P Leroy
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium.,Department of Ophthalmology, Ghent University Hospital, Ghent, Belgium.,Division of Ophthalmology, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University, Ghent, Belgium
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21
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Boulanger-Scemama E, El Shamieh S, Démontant V, Condroyer C, Antonio A, Michiels C, Boyard F, Saraiva JP, Letexier M, Souied E, Mohand-Saïd S, Sahel JA, Zeitz C, Audo I. Next-generation sequencing applied to a large French cone and cone-rod dystrophy cohort: mutation spectrum and new genotype-phenotype correlation. Orphanet J Rare Dis 2015; 10:85. [PMID: 26103963 PMCID: PMC4566196 DOI: 10.1186/s13023-015-0300-3] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Accepted: 06/15/2015] [Indexed: 12/21/2022] Open
Abstract
Background Cone and cone-rod dystrophies are clinically and genetically heterogeneous inherited retinal disorders with predominant cone impairment. They should be distinguished from the more common group of rod-cone dystrophies (retinitis pigmentosa) due to their more severe visual prognosis with early central vision loss. The purpose of our study was to document mutation spectrum of a large French cohort of cone and cone-rod dystrophies. Methods We applied Next-Generation Sequencing targeting a panel of 123 genes implicated in retinal diseases to 96 patients. A systematic filtering approach was used to identify likely disease causing variants, subsequently confirmed by Sanger sequencing and co-segregation analysis when possible. Results Overall, the likely causative mutations were detected in 62.1 % of cases, revealing 33 known and 35 novel mutations. This rate was higher for autosomal dominant (100 %) than autosomal recessive cases (53.8 %). Mutations in ABCA4 and GUCY2D were responsible for 19.2 % and 29.4 % of resolved cases with recessive and dominant inheritance, respectively. Furthermore, unexpected genotype-phenotype correlations were identified, confirming the complexity of inherited retinal disorders with phenotypic overlap between cone-rod dystrophies and other retinal diseases. Conclusions In summary, this time-efficient approach allowed mutation detection in the most important cohort of cone-rod dystrophies investigated so far covering the largest number of genes. Association of known gene defects with novel phenotypes and mode of inheritance were established. Electronic supplementary material The online version of this article (doi:10.1186/s13023-015-0300-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elise Boulanger-Scemama
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Said El Shamieh
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Vanessa Démontant
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Christel Condroyer
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Aline Antonio
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - Christelle Michiels
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Fiona Boyard
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France
| | - Jean-Paul Saraiva
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Mélanie Letexier
- IntegraGen SA, Genopole CAMPUS 1 bat G8 FR-91030 EVRY, Paris, France
| | - Eric Souied
- Centre Hospitalier Intercommunal de Créteil, Department of Ophthalmology, Université Paris-Est Créteil, 94000, Créteil, France
| | - Saddek Mohand-Saïd
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France
| | - José-Alain Sahel
- INSERM, U968, Paris, F-75012, France.,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France.,CNRS, UMR_7210, Paris, F-75012, France.,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France.,Fondation Ophtalmologique Adolphe de Rothschild, 75019, Paris, France.,Académie des Sciences-Institut de France, 75006, Paris, France.,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK
| | - Christina Zeitz
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France.
| | - Isabelle Audo
- INSERM, U968, Paris, F-75012, France. .,Institut de la Vision, Sorbonne Universités, UPMC Univ Paris 06, UMR_S 968, 17, rue Moreau, Paris, F-75012, France. .,CNRS, UMR_7210, Paris, F-75012, France. .,Centre Hospitalier National d'Ophtalmologie des Quinze-Vingts, DHU ViewMaintain, INSERM-DHOS CIC 1423, Paris, F-75012, France. .,University College London Institute of Ophthalmology, 11-43 Bath Street, London, EC1V 9EL, UK.
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22
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Sasaki Y, Margolin Z, Borgo B, Havranek JJ, Milbrandt J. Characterization of Leber Congenital Amaurosis-associated NMNAT1 Mutants. J Biol Chem 2015; 290:17228-38. [PMID: 26018082 DOI: 10.1074/jbc.m115.637850] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Indexed: 01/27/2023] Open
Abstract
Leber congenital amaurosis 9 (LCA9) is an autosomal recessive retinal degeneration condition caused by mutations in the NAD(+) biosynthetic enzyme NMNAT1. This condition leads to early blindness but no other consistent deficits have been reported in patients with NMNAT1 mutations despite its central role in metabolism and ubiquitous expression. To study how these mutations affect NMNAT1 function and ultimately lead to the retinal degeneration phenotype, we performed detailed analysis of LCA-associated NMNAT1 mutants, including the expression, nuclear localization, enzymatic activity, secondary structure, oligomerization, and promotion of axonal and cellular integrity in response to injury. In many assays, most mutants produced results similar to wild type NMNAT1. Indeed, NAD(+) synthetic activity is unlikely to be a primary mechanism underlying retinal degeneration as most LCA-associated NMNAT1 mutants had normal enzymatic activity. In contrast, the secondary structure of many NMNAT1 mutants was relatively less stable as they lost enzymatic activity after heat shock, whereas wild type NMNAT1 retains significant activity after this stress. These results suggest that LCA-associated NMNAT1 mutants are more vulnerable to stressful conditions that lead to protein unfolding, a potential contributor to the retinal degeneration observed in this syndrome.
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Affiliation(s)
- Yo Sasaki
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Zachary Margolin
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Benjamin Borgo
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - James J Havranek
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Jeffrey Milbrandt
- From the Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63110
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23
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Fujikura K. Global epidemiology of Familial Mediterranean fever mutations using population exome sequences. Mol Genet Genomic Med 2015; 3:272-82. [PMID: 26247045 PMCID: PMC4521964 DOI: 10.1002/mgg3.140] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Revised: 02/25/2015] [Accepted: 02/26/2015] [Indexed: 11/12/2022] Open
Abstract
Familial Mediterranean fever (FMF) is an inherited disorder characterized by recurrent episodes of fever accompanied by sterile peritonitis, arthritis, and pleuritis. Many mutations in the MEFV gene have been identified as causing FMF. However, accompanying epidemiological information remains quite scarce except in some Mediterranean countries, and the degree of penetrance has been a subject of controversy. Here, I established a genetic epidemiology of full FMF mutations using two population exome studies. Of 57 mutations associated with FMF, 22 were detected in a total of 9007 individuals from two exome sequences. Exome-based epidemiology revealed the carrier rates of FMF in 28 populations in 19 countries by individual mutation and showed strong population specificity for the MEFV mutations. Unexpectedly high carrier rates suggested that some mutations are benign variants with no pathological significance and highlighted the need for caution in analyzing MEFV mutations. Similar approach could be used to uncover the incomplete or no penetrance of mutations in most inherited disorders.
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Affiliation(s)
- Kohei Fujikura
- Kobe University School of Medicine 7-5-1, Kusunoki-cho, Chuo-ku, Kobe, 650-0017, Japan
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24
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Gaston D, Hansford S, Oliveira C, Nightingale M, Pinheiro H, Macgillivray C, Kaurah P, Rideout AL, Steele P, Soares G, Huang WY, Whitehouse S, Blowers S, LeBlanc MA, Jiang H, Greer W, Samuels ME, Orr A, Fernandez CV, Majewski J, Ludman M, Dyack S, Penney LS, McMaster CR, Huntsman D, Bedard K. Germline mutations in MAP3K6 are associated with familial gastric cancer. PLoS Genet 2014; 10:e1004669. [PMID: 25340522 PMCID: PMC4207611 DOI: 10.1371/journal.pgen.1004669] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 08/14/2014] [Indexed: 12/13/2022] Open
Abstract
Gastric cancer is among the leading causes of cancer-related deaths worldwide. While heritable forms of gastric cancer are relatively rare, identifying the genes responsible for such cases can inform diagnosis and treatment for both hereditary and sporadic cases of gastric cancer. Mutations in the E-cadherin gene, CDH1, account for 40% of the most common form of familial gastric cancer (FGC), hereditary diffuse gastric cancer (HDGC). The genes responsible for the remaining forms of FGC are currently unknown. Here we examined a large family from Maritime Canada with FGC without CDH1 mutations, and identified a germline coding variant (p.P946L) in mitogen-activated protein kinase kinase kinase 6 (MAP3K6). Based on conservation, predicted pathogenicity and a known role of the gene in cancer predisposition, MAP3K6 was considered a strong candidate and was investigated further. Screening of an additional 115 unrelated individuals with non-CDH1 FGC identified the p.P946L MAP3K6 variant, as well as four additional coding variants in MAP3K6 (p.F849Sfs*142, p.P958T, p.D200Y and p.V207G). A somatic second-hit variant (p.H506Y) was present in DNA obtained from one of the tumor specimens, and evidence of DNA hypermethylation within the MAP3K6 gene was observed in DNA from the tumor of another affected individual. These findings, together with previous evidence from mouse models that MAP3K6 acts as a tumor suppressor, and studies showing the presence of somatic mutations in MAP3K6 in non-hereditary gastric cancers and gastric cancer cell lines, point towards MAP3K6 variants as a predisposing factor for FGC. The underlying genetic mutations involved in 60% of inherited gastric cancer cases remain unknown. Here we present a large, extended pedigree with familial gastric cancer and an association in part of the family with a mutation in MAP3K6. The conservation, predicted pathogenicity of the variant, tissue distribution, and known function of MAP3K6 made this a strong candidate that warranted further investigation. Examination of an additional 115 unrelated probands identified additional mutations in MAP3K6, including a truncating mutation.
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Affiliation(s)
- Daniel Gaston
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Samantha Hansford
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carla Oliveira
- Expression Regulation in Cancer Group, IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto & Medical Faculty of the University of Porto, Porto, Portugal
| | - Mathew Nightingale
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Hugo Pinheiro
- Expression Regulation in Cancer Group, IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto & Medical Faculty of the University of Porto, Porto, Portugal
| | - Christine Macgillivray
- Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Pardeep Kaurah
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Patricia Steele
- Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
| | - Gabriela Soares
- Center of Medical Genetics Jacinto de Magalhães, Porto Hospital Center, Porto, Portugal
| | - Weei-Yuarn Huang
- Division of Anatomical Pathology, Department of Pathology, Queen Elizabeth II Health Science Center and Dalhousie University, Halifax, Nova Scotia, Canada
| | - Scott Whitehouse
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sarah Blowers
- Queen's Family Health Team, Kingston, Ontario, Canada
| | - Marissa A. LeBlanc
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Haiyan Jiang
- Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Wenda Greer
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Mark E. Samuels
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre de Recherche du CHU Ste-Justine and Department of Medicine, University of Montreal, Montreal, Quebec, Canada
| | - Andrew Orr
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- Department of Ophthalmology and Visual Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Conrad V. Fernandez
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Mark Ludman
- Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Oncogenetics Service, Institute of Medical Genetics, Meir Medical Center, Kfar Saba, Israel
| | - Sarah Dyack
- Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lynette S. Penney
- Medical Genetics, IWK Health Centre, Halifax, Nova Scotia, Canada
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | | | - David Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Karen Bedard
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada
- * E-mail:
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