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Calame DG, Wong JH, Panda P, Nguyen DT, Leong NC, Sangermano R, Patankar SG, Abdel-Hamid M, AlAbdi L, Safwat S, Flannery KP, Dardas Z, Fatih JM, Murali C, Kannan V, Lotze TE, Herman I, Ammouri F, Rezich B, Efthymiou S, Alavi S, Murphy D, Firoozfar Z, Nasab ME, Bahreini A, Ghasemi M, Haridy NA, Goldouzi HR, Eghbal F, Karimiani EG, Srinivasan VM, Gowda VK, Du H, Jhangiani SN, Coban-Akdemir Z, Marafi D, Rodan L, Isikay S, Rosenfeld JA, Ramanathan S, Staton M, Kerby C. Oberg, Clark RD, Wenman C, Loughlin S, Saad R, Ashraf T, Male A, Tadros S, Boostani R, Abdel-Salam GM, Zaki M, Abdalla E, Manzini MC, Pehlivan D, Posey JE, Gibbs RA, Houlden H, Alkuraya FS, Bujakowska K, Maroofian R, Lupski JR, Nguyen LN. Biallelic variation in the choline and ethanolamine transporter FLVCR1 underlies a pleiotropic disease spectrum from adult neurodegeneration to severe developmental disorders. medRxiv 2024:2024.02.09.24302464. [PMID: 38405817 PMCID: PMC10888986 DOI: 10.1101/2024.02.09.24302464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
FLVCR1 encodes Feline leukemia virus subgroup C receptor 1 (FLVCR1), a solute carrier (SLC) transporter within the Major Facilitator Superfamily. FLVCR1 is a widely expressed transmembrane protein with plasma membrane and mitochondrial isoforms implicated in heme, choline, and ethanolamine transport. While Flvcr1 knockout mice die in utero with skeletal malformations and defective erythropoiesis reminiscent of Diamond-Blackfan anemia, rare biallelic pathogenic FLVCR1 variants are linked to childhood or adult-onset neurodegeneration of the retina, spinal cord, and peripheral nervous system. We ascertained from research and clinical exome sequencing 27 individuals from 20 unrelated families with biallelic ultra-rare missense and predicted loss-of-function (pLoF) FLVCR1 variant alleles. We characterize an expansive FLVCR1 phenotypic spectrum ranging from adult-onset retinitis pigmentosa to severe developmental disorders with microcephaly, reduced brain volume, epilepsy, spasticity, and premature death. The most severely affected individuals, including three individuals with homozygous pLoF variants, share traits with Flvcr1 knockout mice and Diamond-Blackfan anemia including macrocytic anemia and congenital skeletal malformations. Pathogenic FLVCR1 missense variants primarily lie within transmembrane domains and reduce choline and ethanolamine transport activity compared with wild-type FLVCR1 with minimal impact on FLVCR1 stability or subcellular localization. Several variants disrupt splicing in a mini-gene assay which may contribute to genotype-phenotype correlations. Taken together, these data support an allele-specific gene dosage model in which phenotypic severity reflects residual FLVCR1 activity. This study expands our understanding of Mendelian disorders of choline and ethanolamine transport and demonstrates the importance of choline and ethanolamine in neurodevelopment and neuronal homeostasis.
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Affiliation(s)
- Daniel G. Calame
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jovi Huixin Wong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Puravi Panda
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Dat Tuan Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Nancy C.P. Leong
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
| | - Riccardo Sangermano
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Sohil G. Patankar
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Mohamed Abdel-Hamid
- Medical Molecular Genetics Department, Human Genetics and Genome Research Institute, National Research Centre, Cairo, Egypt
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sylvia Safwat
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - Kyle P. Flannery
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jawid M. Fatih
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Chaya Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Varun Kannan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Timothy E. Lotze
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Isabella Herman
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Boys Town National Research Hospital, Boys Town, NE, USA
| | - Farah Ammouri
- Boys Town National Research Hospital, Boys Town, NE, USA
- The University of Kansas Health System, Westwood, KS, USA
| | - Brianna Rezich
- Munroe-Meyer Institute for Genetics and Rehabilitation, University of Nebraska Medical Center, Omaha, NE, USA
| | - Stephanie Efthymiou
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Shahryar Alavi
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - David Murphy
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, University College London, United Kingdom
| | | | | | - Amir Bahreini
- KaryoGen, Isfahan, Iran
- Department of Human Genetics, University of Pittsburgh, PA, USA
| | - Majid Ghasemi
- Department of Neurology, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Hamid Reza Goldouzi
- Department of Pediatrics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Eghbal
- Department of Medical Genetics, Next Generation Genetic Polyclinic, Mashhad, Iran
| | - Ehsan Ghayoor Karimiani
- Molecular and Clinical Sciences Institute, St George’s, University of London, Cranmer Terrace London, London, UK
| | | | - Vykuntaraju K. Gowda
- Department of Pediatric Neurology, Indira Gandhi Institute of Child Health, Bangalore, India
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Dana Marafi
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Faculty of Medicine, Kuwait University, Kuwait
| | - Lance Rodan
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Sedat Isikay
- Gaziantep Islam Science and Technology University, Medical Faculty, Department of Pediatric Neurology, Gaziantep, Turkey
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics Laboratories, Houston, TX, USA
| | - Subhadra Ramanathan
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Michael Staton
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Kerby C. Oberg
- Department of Pathology and Human Anatomy, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Robin D. Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | - Catharina Wenman
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Sam Loughlin
- Rare & Inherited Disease Laboratory, NHS North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, WC1N 3BH, UK
| | - Ramy Saad
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Tazeen Ashraf
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Alison Male
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Shereen Tadros
- North East Thames Regional Genetic Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Reza Boostani
- Department of Neurology, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ghada M.H. Abdel-Salam
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Maha Zaki
- Department of Clinical Genetics, Human Genetics and Genome Research Division, National Research Centre, Cairo, Egypt
| | - Ebtesam Abdalla
- Department of Genetics, Medical Research Institute, Alexandria University, Alexandria, Egypt
| | - M. Chiara Manzini
- Department of Neuroscience and Cell Biology, Rutgers-Robert Wood Johnson Medical School, Child Health Institute of New Jersey, NY, USA
| | - Davut Pehlivan
- Section of Pediatric Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Jennifer E. Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Henry Houlden
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - Fowzan S. Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Kinga Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA
| | - Reza Maroofian
- Department of Neuromuscular diseases, UCL Institute of Neurology, WC1N 3BG, London, UK
| | - James R. Lupski
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Long Nam Nguyen
- Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119228
- Immunology Program, Life Sciences Institute, National University of Singapore, Singapore 117456
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore 117456
- Cardiovascular Disease Research (CVD) Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545
- Immunology Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117456
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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. Res Sq 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] [What about the content of this article? (0)] [Affiliation(s)] [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. Adv Exp Med Biol 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sangermano R, Biswas P, Sullivan LS, Place EM, Borooah S, Straubhaar J, Pierce EA, Daiger SP, Bujakowska KM, Ayaggari R. Identification of a novel large multigene deletion and a frameshift indel in PDE6B as the underlying cause of early-onset recessive rod-cone degeneration. Cold Spring Harb Mol Case Stud 2022; 8:a006247. [PMID: 36376065 PMCID: PMC9808551 DOI: 10.1101/mcs.a006247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/02/2022] [Indexed: 11/15/2022] Open
Abstract
A family, with two affected identical twins with early-onset recessive inherited retinal degeneration, was analyzed to determine the underlying genetic cause of pathology. Exome sequencing revealed a rare and previously reported causative variant (c.1923_1969delinsTCTGGG; p.Asn643Glyfs*29) in the PDE6B gene in the affected twins and their unaffected father. Further investigation, using genome sequencing, identified a novel ∼7.5-kb deletion (Chr 4:670,405-677,862del) encompassing the ATP5ME gene, part of the 5' UTR of MYL5, and a 378-bp (Chr 4:670,405-670,782) region from the 3' UTR of PDE6B in the affected twins and their unaffected mother. Both variants segregated with disease in the family. Analysis of the relative expression of PDE6B, in peripheral blood cells, also revealed a significantly lower level of PDE6B transcript in affected siblings compared to a normal control. PDE6B is associated with recessive rod-cone degeneration and autosomal dominant congenital stationary night blindness. Ophthalmic evaluation of these patients showed night blindness, fundus abnormalities, and peripheral vision loss, which are consistent with PDE6B-associated recessive retinal degeneration. These findings suggest that the loss of PDE6B transcript resulting from the compound heterozygous pathogenic variants is the underlying cause of recessive rod-cone degeneration in the study family.
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Affiliation(s)
- Riccardo Sangermano
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, USA
| | - Lori S Sullivan
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Emily M Place
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Shyamanga Borooah
- Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, USA
| | - Juerg Straubhaar
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Eric A Pierce
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Stephen P Daiger
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas 77030, USA
| | - Kinga M Bujakowska
- Ocular Genomics Institute, Massachusetts Eye and Ear Infirmary, Department of Ophthalmology, Harvard Medical School, Boston, Massachusetts 02114, USA
| | - Radha Ayaggari
- Shiley Eye Institute, University of California San Diego, La Jolla, California 92093, USA
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5
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Catomeris AJ, Ballios BG, Sangermano R, Wagner NE, Comander JI, Pierce EA, Place EM, Bujakowska KM, Huckfeldt RM. Novel RCBTB1 variants causing later-onset non-syndromic retinal dystrophy with macular chorioretinal atrophy. Ophthalmic Genet 2022; 43:332-339. [DOI: 10.1080/13816810.2021.2023196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Andrew J. Catomeris
- Georgetown School of Medicine, Washington, District of Columbia, USA
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Brian G. Ballios
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
- Department of Ophthalmology and Vision Sciences, Temerty Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Riccardo Sangermano
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Naomi E. Wagner
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Jason I. Comander
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Eric A. Pierce
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Emily M. Place
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Kinga M. Bujakowska
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
| | - Rachel M. Huckfeldt
- Ocular Genomics Institute, Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, Massachusetts, USA
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Bronstein R, Capowski EE, Mehrotra S, Jansen AD, Navarro-Gomez D, Maher M, Place E, Sangermano R, Bujakowska KM, Gamm DM, Pierce EA. A combined RNA-seq and whole genome sequencing approach for identification of non-coding pathogenic variants in single families. Hum Mol Genet 2020; 29:967-979. [PMID: 32011687 PMCID: PMC7158377 DOI: 10.1093/hmg/ddaa016] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Revised: 11/23/2019] [Accepted: 01/21/2020] [Indexed: 12/13/2022] Open
Abstract
Inherited retinal degenerations (IRDs) are at the focus of current genetic therapeutic advancements. For a genetic treatment such as gene therapy to be successful, an accurate genetic diagnostic is required. Genetic diagnostics relies on the assessment of the probability that a given DNA variant is pathogenic. Non-coding variants present a unique challenge for such assessments as compared to coding variants. For one, non-coding variants are present at much higher number in the genome than coding variants. In addition, our understanding of the rules that govern the non-coding regions of the genome is less complete than our understanding of the coding regions. Methods that allow for both the identification of candidate non-coding pathogenic variants and their functional validation may help overcome these caveats allowing for a greater number of patients to benefit from advancements in genetic therapeutics. We present here an unbiased approach combining whole genome sequencing (WGS) with patient-induced pluripotent stem cell (iPSC)-derived retinal organoids (ROs) transcriptome analysis. With this approach, we identified and functionally validated a novel pathogenic non-coding variant in a small family with a previously unresolved genetic diagnosis.
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Affiliation(s)
- Revital Bronstein
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Elizabeth E Capowski
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Sudeep Mehrotra
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Alex D Jansen
- Waisman Center Stem Cell Research Program, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Daniel Navarro-Gomez
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Mathew Maher
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Emily Place
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Riccardo Sangermano
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - Kinga M Bujakowska
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
| | - David M Gamm
- Department of Ophthalmology and Visual Sciences, Waisman Center Stem Cell Research Program, McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Eric A Pierce
- Massachusetts Eye and Ear Infirmary, Harvard Medical School, Ocular Genomics Institute, Boston, MA 02114, USA
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7
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Rosa L, Lepanto MS, Cutone A, Ianiro G, Pernarella S, Sangermano R, Musci G, Ottolenghi L, Valenti P. Lactoferrin and oral pathologies: a therapeutic treatment. Biochem Cell Biol 2020; 99:81-90. [PMID: 32213143 DOI: 10.1139/bcb-2020-0052] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The oral cavity is a non-uniform, extraordinary environment characterized by mucosal, epithelial, abiotic surfaces and secretions as saliva. Aerobic and anaerobic commensal and pathogenic microorganisms colonize the tongue, teeth, jowl, gingiva, and periodontium. Commensals exert an important role in host defenses, while pathogenic microorganisms can nullify this protective function causing oral and systemic diseases. Every day, 750-1000 mL of saliva, containing several host defense constituents including lactoferrin (Lf), are secreted and swallowed. Lf is a multifunctional iron-chelating cationic glycoprotein of innate immunity. Depending on, or regardless of its iron-binding ability, Lf exerts bacteriostatic, bactericidal, antibiofilm, antioxidant, antiadhesive, anti-invasive, and anti-inflammatory activities. Here, we report the protective role of Lf in different oral pathologies, such as xerostomia, halitosis, alveolar or maxillary bone damage, gingivitis, periodontitis, and black stain. Unlike antibiotic therapy, which is ineffective against bacteria that are within a biofilm, adherent, or intracellular, the topical administration of Lf, through its simultaneous activity against microbial replication, biofilms, adhesion, and invasiveness, as well as inflammation, has been proven to be efficient in the treatment of all known oral pathologies without any adverse effects.
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Affiliation(s)
- Luigi Rosa
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
| | | | - Antimo Cutone
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Giusi Ianiro
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Stefania Pernarella
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Italy
| | - Riccardo Sangermano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
| | - Giovanni Musci
- Department of Biosciences and Territory, University of Molise, Pesche, Italy
| | - Livia Ottolenghi
- Department of Oral and Maxillofacial Sciences, Sapienza University of Rome, Italy
| | - Piera Valenti
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Italy
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8
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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: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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9
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Sangermano R, Pernarella S, Straker M, Lepanto MS, Rosa L, Cutone A, Valenti P, Ottolenghi L. The treatment of black stain associated with of iron metabolism disorders with lactoferrin: a litterature search and two case studies. Clin Ter 2019; 170:e373-e381. [PMID: 31612196 DOI: 10.7417/ct.2019.2163] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Among the various pathologies of the oral cavity, the formation of "unsightly black spots" on the surface of the tooth, universally known as Black Stain (BS) has recently been acquiring more interest. Usually BS is typically found in individuals in prepubertal age, even though it has been identified in adults associated with microbial exchange and / or with iron metabolism disorders. Microbial exchange concerns the possible exchange of bacteria between family members which can take place directly, through effusions, or indirectly, through brushes, cutlery or glasses. For this reason, it is recommended that toothbrushes of family members not be left damp and in contact with each other. The bathroom, being a warm-humid environment, is in fact an optimal habitat for microbial proliferation. Of specific importance in BS is the accumulation of iron in tissues and secretions which, together with chromogenic bacteria, are the primary cause of this pathology. In fact, among the metabolic products synthesized by bacteria in the oral cavity, hydrogen sulfide is of considerable interest, since upon reacting with iron available in saliva, in pathological conditions (iron metabolism disorders), it forms black precipitates consisting of ferric sulfide. These precipitates bind to the surface of the teeth, tending to form a stria that usually follows the contour of the gingiva, with an unsightly and variable chromatic intensity. In physiological situations, iron homeostasis is defined as the state of equilibrium between iron present in tissues and in secretions and that which is present in the circulation. Instead, in pathological conditions, defined as iron metabolism disorders, there is an accumulation of iron in tissues and secretions and a lack of it in the circulation. It is also important to remember that subjects affected by BS are more protected from carious processes than healthy subjects, probably due to a significant predominance of chromogenic bacteria compared to those responsible for caries. It should also be remembered that in young subjects BS tends to regress with pubertal development and the transition to adult life. In any case, using common professional hygiene procedures, it is possible to remove BS as well as plaque and tartar deposits. In particular, with ultrasonic scalers, polishing pastes and powders carried by air and water jets, the surfaces of the teeth can be restored to their natural healthy state. All the techniques for removing the precipitates, are not enough however, to fix and permanently eradicate their appearance, as these precipitates last only for short periods and recur very frequently. Due to the frequent recurrences, new oral microbiota control therapies are emerging; among these the use of lactoferrin (Lf) in the dental field and particularly in the treatment of BS appears to be very promising. Taken togheter, here the effect of Lf in subjects affected by BS has been investigated.
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Affiliation(s)
- R Sangermano
- Department of Public Health and Infectious Diseases
| | - S Pernarella
- Department of Oral and Maxillofacial Sciences, 'Sapienza' University of Rome, Italia
| | - M Straker
- Department of Oral and Maxillofacial Sciences, 'Sapienza' University of Rome, Italia
| | - M S Lepanto
- Department of Public Health and Infectious Diseases
| | - L Rosa
- Department of Public Health and Infectious Diseases
| | - A Cutone
- Department of Public Health and Infectious Diseases
| | - P Valenti
- Department of Public Health and Infectious Diseases
| | - L Ottolenghi
- Department of Oral and Maxillofacial Sciences, 'Sapienza' University of Rome, Italia
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10
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Runhart EH, Sangermano R, Cornelis SS, Verheij JBGM, Plomp AS, Boon CJF, Lugtenberg D, Roosing S, Bax NM, Blokland EAW, Jacobs-Camps MHM, van der Velde-Visser SD, Pott JWR, Rohrschneider K, Thiadens AAHJ, Klaver CCW, van den Born LI, Hoyng CB, Cremers FPM. The Common ABCA4 Variant p.Asn1868Ile Shows Nonpenetrance and Variable Expression of Stargardt Disease When Present in trans With Severe Variants. Invest Ophthalmol Vis Sci 2019; 59:3220-3231. [PMID: 29971439 DOI: 10.1167/iovs.18-23881] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose To assess the occurrence and the disease expression of the common p.Asn1868Ile variant in patients with Stargardt disease (STGD1) harboring known, monoallelic causal ABCA4 variants. Methods The coding and noncoding regions of ABCA4 were sequenced in 67 and 63 STGD1 probands respectively, harboring monoallelic ABCA4 variants. In case p.Asn1868Ile was detected, segregation analysis was performed whenever possible. Probands and affected siblings harboring p.Asn1868Ile without additional variants in cis were clinically evaluated retrospectively. Two asymptomatic siblings carrying the same ABCA4 variants as their probands were clinically examined. The penetrance of p.Asn1868Ile was calculated using allele frequency data of ABCA4 variants in non-Finnish European individuals. Results The p.Asn1868Ile variant was found in cis with known variants in 14/67 probands. In 27/67 probands, we identified p.Asn1868Ile without additional variants in cis, in combination with known, mainly severe ABCA4 variants. In 23/27 probands, the trans configuration was established. Among 27 probands and 6/7 STGD1 siblings carrying p.Asn1868Ile, 42% manifested late-onset disease (>44 years). We additionally identified four asymptomatic relatives carrying a combination of a severe variant and p.Asn1868Ile; ophthalmologic examination in two persons did not reveal STGD1. Based on ABCA4 allele frequency data, we conservatively estimated the penetrance of p.Asn1868Ile, when present in trans with a severe variant, to be below 5%. Conclusions A significant fraction of genetically unexplained STGD1 cases carries p.Asn1868Ile as a second variant. Our findings suggest exceptional differences in disease expression or even nonpenetrance of this ABCA4 variant, pointing toward an important role for genetic or environmental modifiers in STGD1.
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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
| | - Riccardo Sangermano
- 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.,Radboud Institute of Molecular Life Sciences, 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
| | - Joke B G M Verheij
- Department of Medical Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Astrid S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, The Netherlands
| | - Camiel J F Boon
- Department of Ophthalmology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Ophthalmology, Academic Medical Center, Amsterdam, The Netherlands
| | - Dorien Lugtenberg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - 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
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ellen A W Blokland
- 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
| | - Klaus Rohrschneider
- Universitätsaugenklinik, Ruprecht-Karls-Universität, Heidelberg, Heidelberg, Germany
| | - Alberta A H J Thiadens
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Caroline C W Klaver
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.,Department of Ophthalmology, Erasmus Medical Center, Rotterdam, The Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Carel B Hoyng
- Department of Ophthalmology, 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
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11
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Bauwens M, Garanto A, Sangermano R, Naessens S, Weisschuh N, De Zaeytijd J, Khan M, Sadler F, Balikova I, Van Cauwenbergh C, Rosseel T, Bauwens J, De Leeneer K, De Jaegere S, Van Laethem T, De Vries M, Carss K, Arno G, Fakin A, Webster AR, de Ravel de l'Argentière TJL, Sznajer Y, Vuylsteke M, Kohl S, Wissinger B, Cherry T, Collin RWJ, Cremers FPM, Leroy BP, De Baere E. ABCA4-associated disease as a model for missing heritability in autosomal recessive disorders: novel noncoding splice, cis-regulatory, structural, and recurrent hypomorphic variants. Genet Med 2019; 21:1761-1771. [PMID: 30670881 PMCID: PMC6752479 DOI: 10.1038/s41436-018-0420-y] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 12/17/2018] [Indexed: 12/30/2022] Open
Abstract
Purpose ABCA4-associated disease, a recessive retinal dystrophy, is hallmarked by a large proportion of patients with only one pathogenic ABCA4 variant, suggestive for missing heritability. Methods By locus-specific analysis of ABCA4, combined with extensive functional studies, we aimed to unravel the missing alleles in a cohort of 67 patients (p), with one (p = 64) or no (p = 3) identified coding pathogenic variants of ABCA4. Results We identified eight pathogenic (deep-)intronic ABCA4 splice variants, of which five are novel and six structural variants, four of which are novel, including two duplications. Together, these variants account for the missing alleles in 40.3% of patients. Furthermore, two novel variants with a putative cis-regulatory effect were identified. The common hypomorphic variant c.5603A>T p.(Asn1868Ile) was found as a candidate second allele in 43.3% of patients. Overall, we have elucidated the missing heritability in 83.6% of our cohort. In addition, we successfully rescued three deep-intronic variants using antisense oligonucleotide (AON)-mediated treatment in HEK 293-T cells and in patient-derived fibroblast cells. Conclusion Noncoding pathogenic variants, novel structural variants, and a common hypomorphic allele of the ABCA4 gene explain the majority of unsolved cases with ABCA4-associated disease, rendering this retinopathy a model for missing heritability in autosomal recessive disorders.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riccardo Sangermano
- 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 Naessens
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Nicole Weisschuh
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Julie De Zaeytijd
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Mubeen Khan
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Françoise Sadler
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Irina Balikova
- Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Caroline Van Cauwenbergh
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.,Department of Ophthalmology, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Toon Rosseel
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Jim Bauwens
- Department of Computer Science, Free University of Brussels, Brussels, Belgium
| | - Kim De Leeneer
- 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
| | - Thalia Van Laethem
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Meindert De Vries
- Department of Ophthalmology, Hôpital des Enfants Reine Fabiola, Brussels, Belgium
| | - Keren Carss
- Department of Haematology, University of Cambridge, NHS Blood and Transplant Centre, Cambridge, UK.,UK NIHR BioResource, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK
| | - Gavin Arno
- UCL Institute of Ophthalmology, London, UK
| | - Ana Fakin
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London, UK.,Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | | | - Yves Sznajer
- Centre de Génétique Humaine, Cliniques Universitaires St. Luc, Université Catholique de Louvain, Brussels, Belgium
| | | | - Susanne Kohl
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Bernd Wissinger
- Molecular Genetics Laboratory, Institute for Ophthalmic Research, University of Tuebingen, Tuebingen, Germany
| | - Timothy Cherry
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA.,Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, 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 Medical Center, Nijmegen, The Netherlands
| | - 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, PA, USA
| | - Elfride De Baere
- Center for Medical Genetics Ghent, Ghent University and Ghent University Hospital, Ghent, Belgium.
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12
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Albert S, Garanto A, Sangermano R, Khan M, Bax NM, Hoyng CB, Zernant J, Lee W, Allikmets R, Collin RW, Cremers FP. Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease. Am J Hum Genet 2018. [PMID: 29526278 DOI: 10.1016/j.ajhg.2018.02.008] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Sequence analysis of the coding regions and splice site sequences in inherited retinal diseases is not able to uncover ∼40% of the causal variants. Whole-genome sequencing can identify most of the non-coding variants, but their interpretation is still very challenging, in particular when the relevant gene is expressed in a tissue-specific manner. Deep-intronic variants in ABCA4 have been associated with autosomal-recessive Stargardt disease (STGD1), but the exact pathogenic mechanism is unknown. By generating photoreceptor precursor cells (PPCs) from fibroblasts obtained from individuals with STGD1, we demonstrated that two neighboring deep-intronic ABCA4 variants (c.4539+2001G>A and c.4539+2028C>T) result in a retina-specific 345-nt pseudoexon insertion (predicted protein change: p.Arg1514Leufs∗36), likely due to the creation of exonic enhancers. Administration of antisense oligonucleotides (AONs) targeting the 345-nt pseudoexon can significantly rescue the splicing defect observed in PPCs of two individuals with these mutations. Intriguingly, an AON that is complementary to c.4539+2001G>A rescued the splicing defect only in PPCs derived from an individual with STGD1 with this but not the other mutation, demonstrating the high specificity of AONs. In addition, a single AON molecule rescued splicing defects associated with different neighboring mutations, thereby providing new strategies for the treatment of persons with STGD1. As many genes associated with human genetic conditions are expressed in specific tissues and pre-mRNA splicing may also rely on organ-specific factors, our approach to investigate and treat splicing variants using differentiated cells derived from individuals with STGD1 can be applied to any tissue of interest.
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13
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Sangermano R, Khan M, Cornelis SS, Richelle V, Albert S, Garanto A, Elmelik D, Qamar R, Lugtenberg D, van den Born LI, Collin RWJ, Cremers FPM. ABCA4 midigenes reveal the full splice spectrum of all reported noncanonical splice site variants in Stargardt disease. Genome Res 2018. [PMID: 29162642 DOI: 10.1101/gr.226621.117/-/dc1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Stargardt disease is caused by variants in the ABCA4 gene, a significant part of which are noncanonical splice site (NCSS) variants. In case a gene of interest is not expressed in available somatic cells, small genomic fragments carrying potential disease-associated variants are tested for splice abnormalities using in vitro splice assays. We recently discovered that when using small minigenes lacking the proper genomic context, in vitro results do not correlate with splice defects observed in patient cells. We therefore devised a novel strategy in which a bacterial artificial chromosome was employed to generate midigenes, splice vectors of varying lengths (up to 11.7 kb) covering almost the entire ABCA4 gene. These midigenes were used to analyze the effect of all 44 reported and three novel NCSS variants on ABCA4 pre-mRNA splicing. Intriguingly, multi-exon skipping events were observed, as well as exon elongation and intron retention. The analysis of all reported NCSS variants in ABCA4 allowed us to reveal the nature of aberrant splicing events and to classify the severity of these mutations based on the residual fraction of wild-type mRNA. Our strategy to generate large overlapping splice vectors carrying multiple exons, creating a toolbox for robust and high-throughput analysis of splice variants, can be applied to all human genes.
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Affiliation(s)
- Riccardo Sangermano
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Mubeen Khan
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands.,Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Stéphanie S Cornelis
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Valerie Richelle
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Silvia Albert
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Alejandro Garanto
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Duaa Elmelik
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Raheel Qamar
- Department of Biosciences, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan
| | - Dorien Lugtenberg
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - L Ingeborgh van den Born
- The Rotterdam Eye Hospital, 3011 BH Rotterdam, The Netherlands.,The Rotterdam Ophthalmic Institute, 3011 BH Rotterdam, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics and Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
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14
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Piccolo P, Attanasio S, Secco I, Sangermano R, Strisciuglio C, Limongelli G, Miele E, Mutarelli M, Banfi S, Nigro V, Pons T, Valencia A, Zentilin L, Campione S, Nardone G, Lynnes TC, Celestino-Soper PBS, Spoonamore KG, D'Armiento FP, Giacca M, Staiano A, Vatta M, Collesi C, Brunetti-Pierri N. MIB2 variants altering NOTCH signalling result in left ventricle hypertrabeculation/non-compaction and are associated with Ménétrier-like gastropathy. Hum Mol Genet 2017; 26:33-43. [PMID: 28013292 DOI: 10.1093/hmg/ddw365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 10/19/2016] [Indexed: 12/30/2022] Open
Abstract
We performed whole exome sequencing in individuals from a family with autosomal dominant gastropathy resembling Ménétrier disease, a premalignant gastric disorder with epithelial hyperplasia and enhanced EGFR signalling. Ménétrier disease is believed to be an acquired disorder, but its aetiology is unknown. In affected members, we found a missense p.V742G variant in MIB2, a gene regulating NOTCH signalling that has not been previously linked to human diseases. The variant segregated with the disease in the pedigree, affected a highly conserved amino acid residue, and was predicted to be deleterious although it was found with a low frequency in control individuals. The purified protein carrying the p.V742G variant showed reduced ubiquitination activity in vitro and white blood cells from affected individuals exhibited significant reductions of HES1 and NOTCH3 expression reflecting alteration of NOTCH signalling. Because mutations of MIB1, the homolog of MIB2, have been found in patients with left ventricle non-compaction (LVNC), we investigated members of our family with Ménétrier-like disease for this cardiac abnormality. Asymptomatic left ventricular hypertrabeculation, the mildest end of the LVNC spectrum, was detected in two members carrying the MIB2 variant. Finally, we identified an additional MIB2 variant (p.V984L) affecting protein stability in an unrelated isolated case with LVNC. Expression of both MIB2 variants affected NOTCH signalling, proliferation and apoptosis in primary rat cardiomyocytes.In conclusion, we report the first example of left ventricular hypertrabeculation/LVNC with germline MIB2 variants resulting in altered NOTCH signalling that might be associated with a gastropathy clinically overlapping with Ménétrier disease.
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Affiliation(s)
- Pasquale Piccolo
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Sergio Attanasio
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Ilaria Secco
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Riccardo Sangermano
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy
| | - Caterina Strisciuglio
- Department of Woman, Child and General and Specialized Surgery, Second University of Naples, Naples, Italy
| | - Giuseppe Limongelli
- Department of Cardiothoracic Sciences, Monaldi Hospital, Second University of Naples, Naples, Italy
| | - Erasmo Miele
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples, Italy
| | | | - Sandro Banfi
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Vincenzo Nigro
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Department of Biochemistry, Biophysics and General Pathology, Second University of Naples, Naples, Italy
| | - Tirso Pons
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Alfonso Valencia
- Structural Biology and BioComputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Lorena Zentilin
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
| | - Severo Campione
- Department of Advanced Biomedical Sciences, Federico II University, Naples, Italy
| | - Gerardo Nardone
- Department of Clinical Medicine and Surgery, Gastroenterology Unit, Federico II University, Naples, Italy
| | - Ty C Lynnes
- Department of Medical and Molecular Genetics
| | | | - Katherine G Spoonamore
- Krannert Institute of Cardiology, Division of Cardiology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Mauro Giacca
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Annamaria Staiano
- Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples, Italy
| | - Matteo Vatta
- Department of Medical and Molecular Genetics.,Krannert Institute of Cardiology, Division of Cardiology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chiara Collesi
- Molecular Medicine Laboratory, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy.,Department of Medical, Surgical and Health Sciences, University of Trieste, Trieste, Italy
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Naples, Italy.,Department of Translational Medicine, Section of Pediatrics, Federico II University, Naples, Italy
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15
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Sangermano R, Bax NM, Bauwens M, van den Born LI, De Baere E, Garanto A, Collin RWJ, Goercharn-Ramlal ASA, den Engelsman-van Dijk AHA, Rohrschneider K, Hoyng CB, Cremers FPM, Albert S. Photoreceptor Progenitor mRNA Analysis Reveals Exon Skipping Resulting from the ABCA4 c.5461-10T→C Mutation in Stargardt Disease. Ophthalmology 2016; 123:1375-85. [PMID: 26976702 DOI: 10.1016/j.ophtha.2016.01.053] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 02/06/2023] Open
Abstract
PURPOSE To elucidate the functional effect of the ABCA4 variant c.5461-10T→C, one of the most frequent variants associated with Stargardt disease (STGD1). DESIGN Case series. PARTICIPANTS Seventeen persons with STGD1 carrying ABCA4 variants and 1 control participant. METHODS Haplotype analysis of 4 homozygotes and 11 heterozygotes for c.5461-10T→C and sequence analysis of the ABCA4 gene for a homozygous proband. Fibroblasts were reprogrammed from 3 persons with STGD1 into induced pluripotent stem cells, which were differentiated into photoreceptor progenitor cells (PPCs). The effect of the c.5461-10T→C variant on RNA splicing by reverse-transcription polymerase chain reaction was analyzed using PPC mRNA. In vitro assays were performed with minigene constructs containing ABCA4 exon 39. We analyzed the natural history and ophthalmologic characteristics of 4 persons homozygous for c.5461-10T→C. MAIN OUTCOME MEASURES Haplotype and rare variant data for ABCA4, RNA splice defects, age at diagnosis, visual acuity, fundus appearance, visual field, electroretinography (ERG) results, fluorescein angiography results, and fundus autofluorescence findings. RESULTS The frequent ABCA4 variant c.5461-10T→C has a subtle effect on splicing based on prediction programs. A founder haplotype containing c.5461-10T→C was found to span approximately 96 kb of ABCA4 and did not contain other rare sequence variants. Patient-derived PPCs showed skipping of exon 39 or exons 39 and 40 in the mRNA. HEK293T cell transduction with minigenes carrying exon 39 showed that the splice defects were the result of the c.5461-10T→C variant. All 4 subjects carrying the c.5461-10T→C variant in a homozygous state showed a young age of STGD1 onset, with low visual acuity at presentation and abnormal cone ERG results. All 4 demonstrated severe cone-rod dystrophy before 20 years of age and were legally blind by 25 years of age. CONCLUSIONS The ABCA4 variant c.5461-10T→C is located on a founder haplotype lacking other disease-causing rare sequence variants. In vitro studies revealed that it leads to mRNA exon skipping and ABCA4 protein truncation. Given the severe phenotype in persons homozygous for this variant, we conclude that this variant results in the absence of ABCA4 activity.
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Affiliation(s)
- Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Miriam Bauwens
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | | | - Elfride De Baere
- Center for Medical Genetics, Ghent University and Ghent University Hospital, Ghent, Belgium
| | - Alejandro Garanto
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | - Rob W J Collin
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands
| | | | | | - Klaus Rohrschneider
- Universitätsaugenklinik, Ruprecht-Karls-Universität, Heidelberg, Heidelberg, Germany
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands.
| | - Silvia Albert
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute of Molecular Life Sciences, Nijmegen, The Netherlands.
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16
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Bax NM, Sangermano R, Roosing S, Thiadens AAHJ, Hoefsloot LH, van den Born LI, Phan M, Klevering BJ, Westeneng-van Haaften C, Braun TA, Zonneveld-Vrieling MN, de Wijs I, Mutlu M, Stone EM, den Hollander AI, Klaver CCW, Hoyng CB, Cremers FPM. Heterozygous deep-intronic variants and deletions in ABCA4 in persons with retinal dystrophies and one exonic ABCA4 variant. Hum Mutat 2015; 36:43-7. [PMID: 25363634 DOI: 10.1002/humu.22717] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 10/18/2014] [Indexed: 11/05/2022]
Abstract
Variants in ABCA4 are responsible for autosomal-recessive Stargardt disease and cone-rod dystrophy. Sequence analysis of ABCA4 exons previously revealed one causative variant in each of 45 probands. To identify the "missing" variants in these cases, we performed multiplex ligation-dependent probe amplification-based deletion scanning of ABCA4. In addition, we sequenced the promoter region, fragments containing five deep-intronic splice variants, and 15 deep-intronic regions containing weak splice sites. Heterozygous deletions spanning ABCA4 exon 5 or exons 20-22 were found in two probands, heterozygous deep-intronic variants were identified in six probands, and a deep-intronic variant was found together with an exon 20-22 deletion in one proband. Based on ophthalmologic findings and characteristics of the identified exonic variants present in trans, the deep-intronic variants V1 and V4 were predicted to be relatively mild and severe, respectively. These findings are important for proper genetic counseling and for the development of variant-specific therapies.
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Affiliation(s)
- Nathalie M Bax
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
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17
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Roosing S, van den Born LI, Sangermano R, Banfi S, Koenekoop RK, Zonneveld-Vrieling MN, Klaver CCW, van Lith-Verhoeven JJC, Cremers FPM, den Hollander AI, Hoyng CB. Mutations in MFSD8, encoding a lysosomal membrane protein, are associated with nonsyndromic autosomal recessive macular dystrophy. Ophthalmology 2015; 122:170-9. [PMID: 25227500 DOI: 10.1016/j.ophtha.2014.07.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2014] [Revised: 05/21/2014] [Accepted: 07/21/2014] [Indexed: 01/09/2023] Open
Abstract
PURPOSE This study aimed to identify the genetic defects in 2 families with autosomal recessive macular dystrophy with central cone involvement. DESIGN Case series. PARTICIPANTS Two families and a cohort of 244 individuals with various inherited maculopathies and cone disorders. METHODS Genome-wide linkage analysis and exome sequencing were performed in 1 large family with 5 affected individuals. In addition, exome sequencing was performed in the proband of a second family. Subsequent analysis of the identified mutations in 244 patients was performed by Sanger sequencing or restriction enzyme digestion. The medical history of individuals carrying the MFSD8 variants was reviewed and additional ophthalmic examinations were performed, including electroretinography (ERG), multifocal ERG (mfERG), perimetry, optical coherence tomography (OCT), fundus autofluorescence, and fundus photography. MAIN OUTCOME MEASURES MFSD8 variants, age at diagnosis, visual acuity, fundus appearance, color vision defects, visual field, ERG, mfERG, fundus autofluorescence, and OCT findings. RESULTS Compound heterozygous variants in MFSD8, a gene encoding a lysosomal transmembrane protein, were identified in 2 families with macular dystrophy with a normal or subnormal ERG, but reduced mfERG. In both families, a heterozygous missense variant p.Glu336Gln was identified, which was predicted to have a mild effect on the protein. In the first family, a protein-truncating variant (p.Glu381*) was identified on the other allele, and in the second family, a variant (c.1102G>C) was identified that results in a splicing defect leading to skipping of exon 11 (p.Lys333Lysfs*3). The p.Glu336Gln allele was found to be significantly enriched in patients with maculopathies and cone disorders (6/488) compared with ethnically matched controls (35/18 682; P < 0.0001), suggesting that it may act as a genetic modifier. CONCLUSIONS In this study, we identified variants in MFSD8 as a novel cause of nonsyndromic autosomal recessive macular dystrophy with central cone involvement. Affected individuals showed no neurologic features typical for variant late-infantile neuronal ceroid lipofuscinosis (vLINCL), a severe and devastating multisystem lysosomal storage disease previously associated with mutations in MFSD8. We propose a genotype-phenotype model in which a combination of a severe and a mild variant cause nonsyndromic macular dystrophy with central cone involvement, and 2 severe mutations cause vLINCL.
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Affiliation(s)
- Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands; Current affiliation: Howard Hughes Medical Institute, The Rockefeller University, Department for Pediatric Brain Diseases, New York, New York
| | | | - Riccardo Sangermano
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Sandro Banfi
- Telethon Institute of Genetics and Medicine, Naples, Italy; Medical Genetics, Department of Biochemistry, Biophysics, and General Pathology, Second University of Naples, Naples, Italy
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Centre, Rotterdam, The Netherlands; Department of Epidemiology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Anneke I den Hollander
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands; Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands.
| | - Carel B Hoyng
- Department of Ophthalmology, Radboud University Medical Center, Nijmegen, The Netherlands
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