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Quinodoz M, Kaminska K, Cancellieri F, Han JH, Peter VG, Celik E, Janeschitz-Kriegl L, Schärer N, Hauenstein D, György B, Calzetti G, Hahaut V, Custódio S, Sousa AC, Wada Y, Murakami Y, Fernández AA, Hernández CR, Minguez P, Ayuso C, Nishiguchi KM, Santos C, Santos LC, Tran VH, Vaclavik V, Scholl HPN, Rivolta C. Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads. Am J Hum Genet 2024; 111:701-713. [PMID: 38531366 PMCID: PMC11023916 DOI: 10.1016/j.ajhg.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 10/23/2023] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/28/2024] Open
Abstract
Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Ophthalmology, Inselspital, Bern University Hospital, Bern, Switzerland
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Nils Schärer
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Daniela Hauenstein
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Bence György
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Vincent Hahaut
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | - Ana Cristina Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon, Portugal
| | | | - Yusuke Murakami
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Almudena Avila Fernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Cristina Rodilla Hernández
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Pablo Minguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Centre for Biomedical Network Research On Rare Diseases (CIBERER), Madrid, Spain
| | - Koji M Nishiguchi
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Cristina Santos
- NOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon, Portugal; Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon, Portugal
| | | | - Viet H Tran
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Veronika Vaclavik
- Unité d'oculogénétique, Jules Gonin Eye Hospital, University of Lausanne, Lausanne, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University of Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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2
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Han JH, Rodenburg K, Hayman T, Calzetti G, Kaminska K, Quinodoz M, Marra M, Wallerich S, Allon G, Nagy ZZ, Knézy K, Li Y, Chen R, Barboni MTS, Yang P, Pennesi ME, van den Born LI, Varsányi B, Szabó V, Sharon D, Banin E, Ben-Yosef T, Roosing S, Koenekoop RK, Rivolta C. Loss-of-function variants in UBAP1L cause autosomal recessive retinal degeneration. Genet Med 2024:101106. [PMID: 38420906 DOI: 10.1016/j.gim.2024.101106] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 02/23/2024] [Accepted: 02/23/2024] [Indexed: 03/02/2024] Open
Abstract
PURPOSE Inherited retinal diseases (IRDs) are a group of monogenic conditions that can lead to progressive blindness. Their missing heritability is still considerable, due in part to the presence of disease genes that await molecular identification. The purpose of this work was to identify novel genetic associations with IRDs. METHODS Patients underwent a comprehensive ophthalmological evaluation using standard-of-care tests, such as detailed retinal imaging (macular optical coherence tomography and short-wavelength fundus autofluorescence) and electrophysiological testing. Exome and genome sequencing, as well as computer-assisted data analysis were used for genotyping and detection of DNA variants. A minigene-driven splicing assay was performed to validate the deleterious effects of 1 of such variants. RESULTS We identified 8 unrelated families from Hungary, the United States, Israel, and The Netherlands with members presenting with a form of autosomal recessive and nonsyndromic retinal degeneration, predominantly described as rod-cone dystrophy but also including cases of cone/cone-rod dystrophy. Age of disease onset was very variable, with some patients experiencing first symptoms during their fourth decade of life or later. Myopia greater than 5 diopters was present in 5 of 7 cases with available refractive data, and retinal detachment was reported in 2 cases. All ascertained patients carried biallelic loss-of-function variants in UBAP1L (HGNC: 40028), a gene with unknown function and with homologies to UBAP1, encoding a protein involved in ubiquitin metabolism. One of these pathogenic variants, the intronic NM_001163692.2:c.910-7G>A substitution, was identified in 5 unrelated families. Minigene-driven splicing assays in HEK293T cells confirmed that this DNA change is responsible for the creation of a new acceptor splice site, resulting in aberrant splicing. CONCLUSION We identified UBAP1L as a novel IRD gene. Although its function is currently unknown, UBAP1L is almost exclusively expressed in photoreceptors and the retinal pigment epithelium, hence possibly explaining the link between pathogenic variants in this gene and an ocular phenotype.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kim Rodenburg
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tamar Hayman
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Molly Marra
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | - Sandrine Wallerich
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Gilad Allon
- Department of Ophthalmology, Meir Medical Center, Kfar Saba, Israel
| | - Zoltán Z Nagy
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Krisztina Knézy
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Yumei Li
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | - Rui Chen
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX
| | | | - Paul Yang
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | - Mark E Pennesi
- Casey Eye Institute, Oregon Health and Science University, Portland, OR
| | | | - Balázs Varsányi
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Viktória Szabó
- Department of Ophthalmology, Semmelweis University, Budapest, Hungary
| | - Dror Sharon
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Eyal Banin
- Department of Ophthalmology, Hadassah Medical Center, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Tamar Ben-Yosef
- Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert K Koenekoop
- Departments of Pediatric Surgery, Human Genetics and Ophthalmology, Montreal Children's Hospital, McGill University and McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom.
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3
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Bauwens M, Celik E, Zur D, Lin S, Quinodoz M, Michaelides M, Webster AR, Van Den Broeck F, Leroy BP, Rizel L, Moye AR, Meunier A, Tran HV, Moulin AP, Mahieu Q, Van Heetvelde M, Arno G, Rivolta C, De Baere E, Ben-Yosef T. Mutations in SAMD7 cause autosomal-recessive macular dystrophy with or without cone dysfunction. Am J Hum Genet 2024; 111:393-402. [PMID: 38272031 PMCID: PMC10870129 DOI: 10.1016/j.ajhg.2024.01.001] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 01/27/2024] Open
Abstract
Sterile alpha motif domain containing 7 (SAMD7) is a component of the Polycomb repressive complex 1, which inhibits transcription of many genes, including those activated by the transcription factor Cone-Rod Homeobox (CRX). Here we report bi-allelic mutations in SAMD7 as a cause of autosomal-recessive macular dystrophy with or without cone dysfunction. Four of these mutations affect splicing, while another mutation is a missense variant that alters the repressive effect of SAMD7 on CRX-dependent promoter activity, as shown by in vitro assays. Immunostaining of human retinal sections revealed that SAMD7 is localized in the nuclei of both rods and cones, as well as in those of cells belonging to the inner nuclear layer. These results place SAMD7 as a gene crucial for human retinal function and demonstrate a significant difference in the role of SAMD7 between the human and the mouse retina.
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Affiliation(s)
- Miriam Bauwens
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Dinah Zur
- Ophthalmology Division, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Siying Lin
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Michel Michaelides
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Andrew R Webster
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK
| | - Filip Van Den Broeck
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium
| | - Bart P Leroy
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Head & Skin, Ghent University, 9000 Ghent, Belgium; Department of Ophthalmology, Ghent University Hospital, 9000 Ghent, Belgium; The Division of Ophthalmology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leah Rizel
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
| | - Abigail R Moye
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland
| | - Audrey Meunier
- Department of Ophthalmology, Centre Hospitalier Universitaire Saint-Pierre, 1000 Brussels, Belgium
| | - Hoai Viet Tran
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland; Centre for Gene Therapy and Regenerative Medicine, King's College London, London, UK
| | - Alexandre P Moulin
- Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland
| | - Quinten Mahieu
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Mattias Van Heetvelde
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Gavin Arno
- National Institute of Health Research Biomedical Research Centre at Moorfields Eye Hospital and the Institute of Ophthalmology, London, UK; Institute of Ophthalmology, University College London, London EC1V 9EL, UK; North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3BH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University Hospital Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Elfride De Baere
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tamar Ben-Yosef
- The Ruth & Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel.
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Conti GM, Cancellieri F, Quinodoz M, Kaminska K, Vaclavik V, Rivolta C, Tran HV. GNB1-Related Rod-Cone Dystrophy: A Case Report. Case Rep Ophthalmol 2024; 15:230-237. [PMID: 38500542 PMCID: PMC10948171 DOI: 10.1159/000537997] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Introduction The GNB1 (guanine nucleotide-binding protein, β1) gene encodes for the ubiquitous β1 subunit of heterotrimeric G proteins, which are associated with G-protein-coupled receptors (GPCRs). GNB1 mutations cause a neurodevelopmental disorder characterized by a broad clinical spectrum. A novel variant has recently been confirmed in a case of rod-cone dystrophy. Case Presentation We describe the second confirmed case of a classical rod-cone dystrophy associated with a mutation located in exon 6 of GNB1 [NM_002074.5:c.217G>C, p.(Ala73Pro)] in a 56-year-old patient also presenting mild intellectual disability, attention deficit/hyperactivity disorder, and truncal obesity. Conclusion This paper confirms the role of GNB1 in the pathogenesis of a classic rod-cone dystrophy and highlights the importance of including this gene in the genetic analysis panel for inherited retinal diseases.
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Affiliation(s)
- Giovanni Marco Conti
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
- Institut D’Ophtalmologie de Vevey (INOV), Vevey, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Veronika Vaclavik
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Hoai Viet Tran
- Genetic Ophthalmic Department, Hôpital Ophtalmique Jules-Gonin, University of Lausanne and Faculty of Life Sciences, Lausanne, Switzerland
- Institut D’Ophtalmologie de Vevey (INOV), Vevey, Switzerland
- Centre for Gene Therapy and Regenerative Medicine, King’s College London, London, UK
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5
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Han JH, Cancellieri F, Perea-Romero I, Ayuso C, Quinodoz M, Rivolta C. The p.C759F Variant in USH2A Is a Pathogenic Mutation: Systematic Literature Review and Meta-Analysis of 667 Genotypes. Ophthalmic Res 2023; 67:107-114. [PMID: 38016437 DOI: 10.1159/000535545] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 11/14/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND Although the p.C759F (c.2276G>T, p.Cys759Phe) variant in the USH2A gene has been identified in association with retinal degeneration by several authors, its pathogenicity has been questioned once by the publication of two unaffected homozygotes from a single family. OBJECTIVES The objective of the study was to ascertain the role of p.C759F in hereditary retinal disease. METHODS We examined 87 research articles reporting on patients carrying this variant and then used this information as primary data for a series of meta-analytical tests. RESULTS Independent statistical analyses showed that p.C759F (i) is highly enriched in patients with respect to healthy individuals, (ii) represents a clear-cut recessive allele causing disease when it is in trans with other mutations, (iii) is pathogenic in homozygotes. CONCLUSIONS Our results confirm that p.C759F is a bona fide mutation, leading to retinal blindness according to a recessive pattern of inheritance.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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6
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Bocquet B, Borday C, Erkilic N, Mamaeva D, Donval A, Masson C, Parain K, Kaminska K, Quinodoz M, Perea-Romero I, Garcia-Garcia G, Jimenez-Medina C, Boukhaddaoui H, Coget A, Leboucq N, Calzetti G, Gandolfi S, Percesepe A, Barili V, Uliana V, Delsante M, Bozzetti F, Scholl HP, Corton M, Ayuso C, Millan JM, Rivolta C, Meunier I, Perron M, Kalatzis V. TBC1D32 variants disrupt retinal ciliogenesis and cause retinitis pigmentosa. JCI Insight 2023; 8:e169426. [PMID: 37768732 PMCID: PMC10721274 DOI: 10.1172/jci.insight.169426] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/21/2023] [Indexed: 09/29/2023] Open
Abstract
Retinitis pigmentosa (RP) is the most common inherited retinal disease (IRD) and is characterized by photoreceptor degeneration and progressive vision loss. We report 4 patients presenting with RP from 3 unrelated families with variants in TBC1D32, which to date has never been associated with an IRD. To validate TBC1D32 as a putative RP causative gene, we combined Xenopus in vivo approaches and human induced pluripotent stem cell-derived (iPSC-derived) retinal models. Our data showed that TBC1D32 was expressed during retinal development and that it played an important role in retinal pigment epithelium (RPE) differentiation. Furthermore, we identified a role for TBC1D32 in ciliogenesis of the RPE. We demonstrated elongated ciliary defects that resulted in disrupted apical tight junctions, loss of functionality (delayed retinoid cycling and altered secretion balance), and the onset of an epithelial-mesenchymal transition-like phenotype. Last, our results suggested photoreceptor differentiation defects, including connecting cilium anomalies, that resulted in impaired trafficking to the outer segment in cones and rods in TBC1D32 iPSC-derived retinal organoids. Overall, our data highlight a critical role for TBC1D32 in the retina and demonstrate that TBC1D32 mutations lead to RP. We thus identify TBC1D32 as an IRD-causative gene.
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Affiliation(s)
- Béatrice Bocquet
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Caroline Borday
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Nejla Erkilic
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Daria Mamaeva
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Alicia Donval
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Christel Masson
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karine Parain
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Irene Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Gema Garcia-Garcia
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carla Jimenez-Medina
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Hassan Boukhaddaoui
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
| | - Arthur Coget
- Department of Neuroradiology and
- Institute for Human Functional Imaging (I2FH), University of Montpellier, CHU, Montpellier, France
| | | | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Medicine and Surgery
| | | | | | | | | | | | - Francesca Bozzetti
- Neuroradiology Unit, Diagnostic Department, University Hospital of Parma, Parma, Italy
| | - Hendrik P.N. Scholl
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Marta Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Jose M. Millan
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Molecular, Cellular and Genomics Biomedicine Research Group, Instituto de Investigación Sanitaria La Fe (IIS La Fe), Valencia, Spain
- Joint Unit of Rare Diseases, IIS La Fe-Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Isabelle Meunier
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
- National Reference Centre for Inherited Sensory Diseases, University of Montpellier, CHU, Montpellier, France
| | - Muriel Perron
- Université Paris-Saclay, CNRS, Institut des Neurosciences Paris-Saclay, Saclay, France
| | - Vasiliki Kalatzis
- Institute for Neurosciences of Montpellier (INM), University of Montpellier, Inserm, Montpellier, France
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Grosso A, Yannuzzi LA, Tsang SH, Ceruti P, Sarraf D, Zamir E, Kaminska K, Quinodoz M, Amoroso A, Deaglio S, Francis JH, Fioretto M, Rivolta C, Calzetti G. A Unique Presentation of Bilateral Chorioretinal Atrophy. Asia Pac J Ophthalmol (Phila) 2023; 12:500-501. [PMID: 36650090 DOI: 10.1097/apo.0000000000000563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Andrea Grosso
- Santo Spirito Hospital, Casale Monferrato, Italy
- Centre for Macular Research, San Mauro Torinese, Italy
| | | | - Stephen H Tsang
- Jonas Children's Vision Care, and Bernard and Shirlee Brown Glaucoma Laboratory, Department of Ophthalmology, Columbia Stem Cell Initiative, Columbia University, New York, NY
| | - Piero Ceruti
- Ophthalmic Unit, Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona, Italy
| | - David Sarraf
- Jules Stein Eye Institute, University of California Los Angeles School of Medicine, Los Angeles, CA
| | - Ehud Zamir
- Centre for Eye Research Australia, Melbourne, Australia
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Antonio Amoroso
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Silvia Deaglio
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jasmine H Francis
- Ophthalmic Oncology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
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8
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Ullah M, Rehman AU, Folcher M, Ullah A, Usman F, Rashid A, Khan B, Quinodoz M, Ansar M, Rivolta C. A Novel Intronic Deletion in PDE6B Causes Autosomal Recessive Retinitis Pigmentosa by Interfering with RNA Splicing. Ophthalmic Res 2023; 66:878-884. [PMID: 37094557 DOI: 10.1159/000530800] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023]
Abstract
INTRODUCTION Retinitis pigmentosa (RP) is a rare degenerative retinal disease caused by mutations in approximately seventy genes. Currently, despite the availability of large-scale DNA sequencing technologies, ∼30-40% of patients still cannot be diagnosed at the molecular level. In this study, we investigated a novel intronic deletion of PDE6B, encoding the beta subunit of phosphodiesterase 6 in association with recessive RP. METHODS Three unrelated consanguineous families were recruited from the northwestern part of Pakistan. Whole exome sequencing was performed for the proband of each family, and the data were analyzed according to an in-house computer pipeline. Relevant DNA variants in all available members of these families were assessed through Sanger sequencing. A minigene-based splicing assay was also performed. RESULTS The clinical phenotype for all patients was compatible with rod cone degeneration, with the onset during childhood. Whole exome sequencing revealed a homozygous 18 bp intronic deletion (NM_000283.3:c.1921-20_1921-3del) in PDE6B, which co-segregated with disease in 10 affected individuals. In vitro splicing tests showed that this deletion causes aberrant RNA splicing of the gene, leading to the in-frame deletion of 6 codons and, likely, to disease. CONCLUSION Our findings further expand the mutational spectrum of the PDE6B gene.
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Affiliation(s)
- Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Department of Zoology, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Adnan Ullah
- Department of Zoology, Islamia College Peshawar, Peshawar, Pakistan
| | - Faisal Usman
- Department of Biotechnology and Genetic Engineering, Faculty of Biological and Health Sciences, Hazara University Mansehra, Mansehra, Pakistan
| | - Abdur Rashid
- Department of Higher Education, Archives and Libraries Peshawar, Peshawar, Pakistan
| | - Bilal Khan
- Medical Teaching Institution Khyber Teaching Hospital Peshawar, Peshawar, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Muhammad Ansar
- Department of Ophthalmology, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, University of Lausanne, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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9
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Koval A, Larasati YA, Savitsky M, Solis GP, Good JM, Quinodoz M, Rivolta C, Superti-Furga A, Katanaev VL. In-depth molecular profiling of an intronic GNAO1 mutant as the basis for personalized high-throughput drug screening. Med 2023; 4:311-325.e7. [PMID: 37001522 DOI: 10.1016/j.medj.2023.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/02/2022] [Revised: 03/01/2023] [Accepted: 03/07/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The GNAO1 gene, encoding the major neuronal G protein Gαo, is mutated in a subset of pediatric encephalopathies. Most such mutations consist of missense variants. METHODS In this study, we present a precision medicine workflow combining next-generation sequencing (NGS) diagnostics, molecular etiology analysis, and personalized drug discovery. FINDINGS We describe a patient carrying a de novo intronic mutation (NM_020988.3:c.724-8G>A), leading to epilepsy-negative encephalopathy with motor dysfunction from the second decade. Our data show that this mutation creates a novel splice acceptor site that in turn causes an in-frame insertion of two amino acid residues, Pro-Gln, within the regulatory switch III region of Gαo. This insertion misconfigures the switch III loop and creates novel interactions with the catalytic switch II region, resulting in increased GTP uptake, defective GTP hydrolysis, and aberrant interactions with effector proteins. In contrast, intracellular localization, Gβγ interactions, and G protein-coupled receptor (GPCR) coupling of the Gαo[insPQ] mutant protein remain unchanged. CONCLUSIONS This in-depth analysis characterizes the heterozygous c.724-8G>A mutation as partially dominant negative, providing clues to the molecular etiology of this specific pathology. Further, this analysis allows us to establish and validate a high-throughput screening platform aiming at identifying molecules that could correct the aberrant biochemical functions of the mutant Gαo. FUNDING This work was supported by the Joint Seed Money Funding scheme between the University of Geneva and the Hebrew University of Jerusalem.
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Affiliation(s)
- Alexey Koval
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Yonika A Larasati
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Mikhail Savitsky
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Gonzalo P Solis
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland
| | - Jean-Marc Good
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland; Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital (CHUV), 1011 Lausanne, Switzerland
| | - Vladimir L Katanaev
- Translational Research Center in Oncohaematology, Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1211 Geneva, Switzerland; Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690090 Vladivostok, Russia.
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10
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Peter VG, Kaminska K, Santos C, Quinodoz M, Cancellieri F, Cisarova K, Pescini Gobert R, Rodrigues R, Custódio S, Paris LP, Sousa AB, Coutinho Santos L, Rivolta C. The first genetic landscape of inherited retinal dystrophies in Portuguese patients identifies recurrent homozygous mutations as a frequent cause of pathogenesis. PNAS Nexus 2023; 2:pgad043. [PMID: 36909829 PMCID: PMC10003751 DOI: 10.1093/pnasnexus/pgad043] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/15/2023]
Abstract
Inherited retinal diseases (IRDs) are a group of ocular conditions characterized by an elevated genetic and clinical heterogeneity. They are transmitted almost invariantly as monogenic traits. However, with more than 280 disease genes identified so far, association of clinical phenotypes with genotypes can be very challenging, and molecular diagnosis is essential for genetic counseling and correct management of the disease. In addition, the prevalence and the assortment of IRD mutations are often population-specific. In this work, we examined 230 families from Portugal, with individuals suffering from a variety of IRD diagnostic classes (270 subjects in total). Overall, we identified 157 unique mutations (34 previously unreported) in 57 distinct genes, with a diagnostic rate of 76%. The IRD mutational landscape was, to some extent, different from those reported in other European populations, including Spanish cohorts. For instance, the EYS gene appeared to be the most frequently mutated, with a prevalence of 10% among all IRD cases. This was, in part, due to the presence of a recurrent and seemingly founder mutation involving the deletion of exons 13 and 14 of this gene. Moreover, our analysis highlighted that as many as 51% of our cases had mutations in a homozygous state. To our knowledge, this is the first study assessing a cross-sectional genotype-phenotype landscape of IRDs in Portugal. Our data reveal a rather unique distribution of mutations, possibly shaped by a small number of rare ancestral events that have now become prevalent alleles in patients.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Ophthalmology, Inselspital, Bern University Hospital, Bern 3010, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Cristina Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal.,iNOVA4Health, NOVA Medical School, Faculdade de Ciências Médicas, NMS, FCM, Universidade NOVA de Lisboa, Lisbon 1169-056, Portugal
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Katarina Cisarova
- Department of Computational Biology, University of Lausanne, Lausanne 1015, Switzerland
| | | | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Sónia Custódio
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal
| | - Liliana P Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon 1649-035, Portugal.,Laboratory of Basic Immunology, Faculty of Medicine, University of Lisbon, Lisbon 1649-028, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto (IOGP), Lisbon 1169-019, Portugal
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel 4031, Switzerland.,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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11
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Peter VG, Quinodoz M, Sadio S, Held S, Rodrigues M, Soares M, Sousa AB, Santos LC, Damme M, Rivolta C. New clinical and molecular evidence linking mutations in ARSG to Usher syndrome type IV. Hum Mutat 2022; 43:2326-2327. [PMID: 36317447 DOI: 10.1002/humu.24496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Butler-Laporte G, Povysil G, Kosmicki JA, Cirulli ET, Drivas T, Furini S, Saad C, Schmidt A, Olszewski P, Korotko U, Quinodoz M, Çelik E, Kundu K, Walter K, Jung J, Stockwell AD, Sloofman LG, Jordan DM, Thompson RC, Del Valle D, Simons N, Cheng E, Sebra R, Schadt EE, Kim-Schulze S, Gnjatic S, Merad M, Buxbaum JD, Beckmann ND, Charney AW, Przychodzen B, Chang T, Pottinger TD, Shang N, Brand F, Fava F, Mari F, Chwialkowska K, Niemira M, Pula S, Baillie JK, Stuckey A, Salas A, Bello X, Pardo-Seco J, Gómez-Carballa A, Rivero-Calle I, Martinón-Torres F, Ganna A, Karczewski KJ, Veerapen K, Bourgey M, Bourque G, Eveleigh RJM, Forgetta V, Morrison D, Langlais D, Lathrop M, Mooser V, Nakanishi T, Frithiof R, Hultström M, Lipcsey M, Marincevic-Zuniga Y, Nordlund J, Schiabor Barrett KM, Lee W, Bolze A, White S, Riffle S, Tanudjaja F, Sandoval E, Neveux I, Dabe S, Casadei N, Motameny S, Alaamery M, Massadeh S, Aljawini N, Almutairi MS, Arabi YM, Alqahtani SA, Al Harthi FS, Almutairi A, Alqubaishi F, Alotaibi S, Binowayn A, Alsolm EA, El Bardisy H, Fawzy M, Cai F, Soranzo N, Butterworth A, Geschwind DH, Arteaga S, Stephens A, Butte MJ, Boutros PC, Yamaguchi TN, Tao S, Eng S, Sanders T, Tung PJ, Broudy ME, Pan Y, Gonzalez A, Chavan N, Johnson R, Pasaniuc B, Yaspan B, Smieszek S, Rivolta C, Bibert S, Bochud PY, Dabrowski M, Zawadzki P, Sypniewski M, Kaja E, Chariyavilaskul P, Nilaratanakul V, Hirankarn N, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Tokunaga K, Sugiyama M, Kawai Y, Hasegawa T, Naito T, Namkoong H, Edahiro R, Kimura A, Ogawa S, Kanai T, Fukunaga K, Okada Y, Imoto S, Miyano S, Mangul S, Abedalthagafi MS, Zeberg H, Grzymski JJ, Washington NL, Ossowski S, Ludwig KU, Schulte EC, Riess O, Moniuszko M, Kwasniewski M, Mbarek H, Ismail SI, Verma A, Goldstein DB, Kiryluk K, Renieri A, Ferreira MAR, Richards JB. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet 2022; 18:e1010367. [PMID: 36327219 PMCID: PMC9632827 DOI: 10.1371/journal.pgen.1010367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/05/2022] Open
Abstract
Host genetics is a key determinant of COVID-19 outcomes. Previously, the COVID-19 Host Genetics Initiative genome-wide association study used common variants to identify multiple loci associated with COVID-19 outcomes. However, variants with the largest impact on COVID-19 outcomes are expected to be rare in the population. Hence, studying rare variants may provide additional insights into disease susceptibility and pathogenesis, thereby informing therapeutics development. Here, we combined whole-exome and whole-genome sequencing from 21 cohorts across 12 countries and performed rare variant exome-wide burden analyses for COVID-19 outcomes. In an analysis of 5,085 severe disease cases and 571,737 controls, we observed that carrying a rare deleterious variant in the SARS-CoV-2 sensor toll-like receptor TLR7 (on chromosome X) was associated with a 5.3-fold increase in severe disease (95% CI: 2.75-10.05, p = 5.41x10-7). This association was consistent across sexes. These results further support TLR7 as a genetic determinant of severe disease and suggest that larger studies on rare variants influencing COVID-19 outcomes could provide additional insights.
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Grants
- 409511 CIHR
- RG/13/13/30194 British Heart Foundation
- C18281/A29019 Cancer Research UK
- 100558 CIHR
- MC_PC_20004 Medical Research Council
- 365825 CIHR
- UL1 TR001873 NCATS NIH HHS
- RG/18/13/33946 British Heart Foundation
- CH/12/2/29428 British Heart Foundation
- CanCOGeN HostSeq
- Fonds de Recherche Québec Santé (FRQS)
- Génome Québec
- Public Health Agency of Canada
- Canadian Institutes of Health Research (CIHR)
- Lady Davis Institute of the Jewish General Hospital
- Canadian Foundation for Innovation
- NIH Foundation
- McGill Interdisciplinary Initiative in Infection and Immunity (MI4)
- Jewish General Hospital Foundation
- McGill University
- Calcul Québec and Compute Canada
- Compute Canada
- Vagelos College of Physicians & Surgeons Office for Research
- Biomedical Informatics Resource of the Columbia University Irving Institute for Clinical and Translational Research (CTSA)
- National Center for Advancing Translational Sciences, National Institutes of Health
- German Research Foundation
- NGS Competence Center Tübingen
- West German Genome Center
- Stiftung Universitätsmedizin Essen
- Technical University of Munich
- BONFOR program of the Medical Faculty, University of Bonn
- Emmy-Noether programm of the German Research Foundation
- State of Saarland
- Dr. Rolf M. Schwiete Foundation
- Munich Clinician Scientist Programm
- Netzwerk-Universitaetsmedizin-COVIM
- Federal Ministry of Education and Research
- Swiss National Science Foundation
- Leenaards Foundation
- Santos-Suarez Foundation
- Carigest
- MIUR project “Dipartimenti di Eccellenza 2018-2020”
- Bando Ricerca COVID-19 Toscana
- charity fund 2020 from Intesa San Paolo
- Italian Ministry of University and Research
- Istituto Buddista Italiano Soka Gakkai
- Instituto de Salud Carlos III
- GePEM
- DIAVIR
- Resvi-Omics
- ReSVinext
- Enterogen
- Agencia Gallega para la Gestión del Conocimiento en Salud
- BI-BACVIR
- CovidPhy
- Agencia Gallega de Innovación (GAIN):
- GEN-COVID
- Framework Partnership Agreement between the Consellería de Sanidad de la XUNTA de Galicia
- GENVIP-IDIS
- consorcio Centro de Investigación Biomédica en Red de Enfermedades Respiratorias
- F. Hoffmann-La Roche Ltd
- U.S. Department of Health and Human Services, Office of the Assistant Secretary for Preparedness and Response, and Biomedical Advanced Research and Development Authority
- Nevada Governor's Office of Economic Development
- Renown Health and the Renown Health Foundation
- Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research)
- Grant for Development of New Faculty Staff, Ratchadaphiseksomphot Endowment Fund
- e-ASIA Joint Research Program (National Science and Technology Development Agency)
- Health Systems Research Institute, TSRI Fund
- Thailand Research Fund
- Ratchadapiseksompotch Fund
- Ratchadapiseksompotch Fund, Faculty of Medicine,Chulalongkorn University, Bangkok, Thailand
- Health Systems Research Institute
- Ratchadapisek Sompoch Endowment Fund, Chulalongkorn University
- NHS Blood and Transplant
- National Institute for Health Research
- UK Medical Research Council
- Japan Agency for Medical Research and Development
- Japan Science and Technology Agency
- National Center for Global Health and Medicine
- Agency for Medical Research and Development
- Polish National Science Centre
- Medical Research Agency
- Perelman School of Medicine at University of Pennsylvania
- Smilow family
- National Center for Advancing Translational Sciences of the National Institutes of Health
- Polish Medical Research Agency
- Qatar Foundation for Education, Science and Community Development
- Saudi Ministry of Health
- King Abdulaziz City for Science and Technology
- European Union’s Horizon 2020 research and innovation program
- Science for Life Laboratory
- Swedish Research Council
- Knut and Alice Wallenberg Foundation
- OCRC
- Microsoft COVID Compute Funding
- Illumina
- UCLA David Geffen School of Medicine - Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research Award Program
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Affiliation(s)
- Guillaume Butler-Laporte
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - Gundula Povysil
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Jack A. Kosmicki
- Regeneron Genetics Center, Tarrytown, New York, United States of America
| | | | - Theodore Drivas
- Division of Human Genetics, Department of Pediatrics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Simone Furini
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
| | - Chadi Saad
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Axel Schmidt
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | | | - Urszula Korotko
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Elifnaz Çelik
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Kousik Kundu
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Klaudia Walter
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Junghyun Jung
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Amy D. Stockwell
- Genentech Inc, South San Francisco, California, United States of America
| | - Laura G. Sloofman
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Daniel M. Jordan
- Mount Sinai Clnical Intelligence Center, Charles Bronfman Institute for Personalized Medicine, Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Ryan C. Thompson
- Icahn Institute of Data Science and Genomics Technology, New York city, New York, United States of America
| | - Diane Del Valle
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Nicole Simons
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Esther Cheng
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city,New York, United States of America
| | - Seunghee Kim-Schulze
- Department of Oncological Science, Human Immune Monitoring Center, Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Sacha Gnjatic
- Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Miriam Merad
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Noam D. Beckmann
- Precision Immunology Institute, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | - Alexander W. Charney
- Mount Sinai Clinical Intelligence Center; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York city, New York, United States of America
| | | | - Timothy Chang
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Tess D. Pottinger
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
| | - Ning Shang
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Fabian Brand
- Institute of Genomic Statistics and Bioinformatics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
| | - Francesca Fava
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Francesca Mari
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | - Karolina Chwialkowska
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Magdalena Niemira
- Centre for Clinical Research, Medical University of Bialystok, Bialystok, Poland
| | | | - J Kenneth Baillie
- Roslin Institute, University of Edinburgh, Edinburgh, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
- Centre for Inflammation Research, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh, United Kingdom
- Intensive Care Unit, Royal Infirmary of Edinburgh, Edinburgh, United Kingdom
| | | | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Xabier Bello
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Jacobo Pardo-Seco
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias, Hospital Clínico Universitario de Santiago (SERGAS), Santiago de Compostela, Galicia, Spain
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
| | - Irene Rivero-Calle
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Federico Martinón-Torres
- Genetics, Vaccines and Infections Research Group (GENVIP), Instituto de Investigación Sanitaria de Santiago, Santiago de Compostela, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBER-ES), Madrid, Spain
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain
| | - Andrea Ganna
- Institute for Molecular Medicine Finland, Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
- Massachusetts General Hospital, Harvard Medical School, Boston, Massachussets, United States of America
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kumar Veerapen
- Stanley Center for Psychiatric Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Mathieu Bourgey
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Robert JM Eveleigh
- Canadian Centre for Computational Genomics, McGill University, Montréal, Québec, Canada
- McGill Genome Center, McGill University, Montréal, Québec, Canada
| | - Vincenzo Forgetta
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Morrison
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
| | - David Langlais
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Mark Lathrop
- McGill Genome Center, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Vincent Mooser
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Tomoko Nakanishi
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Kyoto-McGill International Collaborative School in Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Research Fellow, Japan Society for the Promotion of Science, Tokyo, Japan
| | - Robert Frithiof
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Michael Hultström
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Miklos Lipcsey
- Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
- Hedenstierna Laboratory, CIRRUS, Anaesthesiology and Intensive Care Medicine, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Yanara Marincevic-Zuniga
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | | | - William Lee
- Helix, San Mateo, California, United States of America
| | | | - Simon White
- Helix, San Mateo, California, United States of America
| | | | | | | | - Iva Neveux
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | - Shaun Dabe
- Renown Health, Reno, Nevada, United States of America
| | - Nicolas Casadei
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Susanne Motameny
- West German Genome Center, site Cologne, University of Cologne, Cologne, Germany
- Cologne Center for Genomics, University of Cologne, Cologne, Germany
| | - Manal Alaamery
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Salam Massadeh
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Nora Aljawini
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mansour S. Almutairi
- Developmental Medicine Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
- Saudi Human Genome Project at King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Yaseen M. Arabi
- Ministry of the National Guard Health Affairs, King Abdullah International Medical Research Center and King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Saleh A. Alqahtani
- Liver Transplant Unit, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
- Division of Gastroenterology and Hepatology, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Fawz S. Al Harthi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Amal Almutairi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fatima Alqubaishi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Sarah Alotaibi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Albandari Binowayn
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Ebtehal A. Alsolm
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hadeel El Bardisy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Mohammad Fawzy
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Fang Cai
- Genentech Inc, South San Francisco, California, United States of America
| | - Nicole Soranzo
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Adam Butterworth
- Department of Human Genetics, Wellcome Sanger Institute, Hinxton, United Kingdom
| | | | | | | | | | | | | | | | | | - Daniel H. Geschwind
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stephanie Arteaga
- Department of Neurology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alexis Stephens
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Manish J. Butte
- Department of Pediatrics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Microbiology, Immunology, and Molecular Genetics (MIMG), David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul C. Boutros
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Takafumi N. Yamaguchi
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Shu Tao
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Stefan Eng
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Timothy Sanders
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Paul J. Tung
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Michael E. Broudy
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Yu Pan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Alfredo Gonzalez
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Nikhil Chavan
- Office of Health Informatics and Analytics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Ruth Johnson
- Department of Computer Science, McGill University, Montréal, Québec, Canada
| | - Bogdan Pasaniuc
- Department of Human Genetics, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Computational Medicine, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
- Department of Pathology, David Geffen School of Medicine, University of California—Los Angeles, Los Angeles, California, United States of America
| | - Brian Yaspan
- Genentech Inc, South San Francisco, California, United States of America
| | - Sandra Smieszek
- Vanda Pharmaceuticals, Washington, District of Columbia, United States of America
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
| | - Stephanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Maciej Dabrowski
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
| | - Pawel Zawadzki
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Faculty of Physics, Adam Mickiewicz University, Poznan, Poland
| | | | - Elżbieta Kaja
- MNM Bioscience Inc., Cambridge, Massachusetts, United States of America
- Department of Medical Chemistry and Laboratory Medicine, Poznań University of Medical Sciences, Poznań, Poland
| | - Pajaree Chariyavilaskul
- Clinical Pharmacokinetics and Pharmacogenomics Research Unit, Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Voraphoj Nilaratanakul
- Healthcare-associated Infection Research Group STAR (Special Task Force for Activating Research) and Division of Infectious Diseases, Department of Medicine,Chulalongkorn University, Bangkok, Thailand
| | - Nattiya Hirankarn
- Center of Excellence in Immunology and Immune-mediated Diseases, Department of Microbiology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorasuk Shotelersuk
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, and Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Monnat Pongpanich
- Department of Mathematics and Computer Science, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Chureerat Phokaew
- Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Wanna Chetruengchai
- Center of Excellence for Medical Genomics, Medical Genomics Cluster, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Katsushi Tokunaga
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Masaya Sugiyama
- Genome Medical Science Project, Research Institute, National Center for Global Health and Medicine, Shinjuku-ku, Tokyo, Japan
| | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine (NCGM), Tokyo, Japan
| | - Takanori Hasegawa
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tatsuhiko Naito
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Ho Namkoong
- Department of Infectious Diseases, Keio University School of Medicine, Tokyo, Japan
| | - Ryuya Edahiro
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Akinori Kimura
- Institute of Research, Tokyo Medical and Dental University, Tokyo, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, Stockholm, Sweden
| | - Takanori Kanai
- Division of Gastroenterology and Hepatology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Koichi Fukunaga
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, the Institute of Medical Science, the University of Tokyo, Tokyo, Japan
| | - Satoru Miyano
- M&D Data Science Center, Tokyo Medical and Dental University, Tokyo, Japan
| | - Serghei Mangul
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, California, United States of America
| | - Malak S. Abedalthagafi
- Genomics Research Department, Saudi Human Genome Project, King Fahad Medical City and King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Hugo Zeberg
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Joseph J. Grzymski
- Center for Genomic Medicine, Desert Research Institute, Reno, Nevada United States of America
| | | | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Kerstin U. Ludwig
- Institute of Human Genetics, School of Medicine and University Hospital Bonn, University of Bonn, Bonn, Germany
- West German Genome Center, site Bonn, University of Bonn, Bonn, Germany
| | - Eva C. Schulte
- Institute of Psychiatric Phenomics and Genomics (IPPG), University Hospital, LMU Munich, Munich, Germany
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich, Germany
- Institute of Virology, Technical University Munich/Helmholtz Zentrum München, Munich, Germany
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
- NGS Competence Center Tuebingen, Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Marcin Moniuszko
- Department of Regenerative Medicine and Immune Regulation, Medical University of Bialystok, Bialystok, Poland
- Department of Allergology and Internal Medicine, Medical University of Bialystok, Bialystok, Poland
| | - Miroslaw Kwasniewski
- IMAGENE.ME SA, Bialystok, Poland
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Hamdi Mbarek
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Said I. Ismail
- Qatar Genome Program, Qatar Foundation Research, Development and Innovation, Qatar Foundation, Doha, Qatar
| | - Anurag Verma
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Corporal Michael Crescenz VA Medical Center, Philadelphia, Pennsylvania, United States of America
| | - David B. Goldstein
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Department of Genetics & Development, Columbia University, New York city, New York, United States of America
| | - Krzysztof Kiryluk
- Institute for Genomic Medicine, Columbia University, New York city, New York, United States of America
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians & Surgeons, Columbia University, New York city, New York, United States of America
| | - Alessandra Renieri
- Department of Medical Biotechnologies, Med Biotech Hub and Competence Center, University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliero-Universitaria Senese, Siena, Italy
- Medical Genetics, University of Siena, Siena, Italy
| | | | - J Brent Richards
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montréal, Québec, Canada
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec, Canada
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Twin Research, King’s College London, London, United Kingdom
- 5 Prime Sciences Inc, Montreal, Quebec, Canada
- * E-mail:
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13
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Jurkute N, Cancellieri F, Pohl L, Li CHZ, Heaton RA, Reurink J, Bellingham J, Quinodoz M, Yioti G, Stefaniotou M, Weener M, Zuleger T, Haack TB, Stingl K, Hoyng CB, Mahroo OA, Hargreaves I, Raymond FL, Michaelides M, Rivolta C, Kohl S, Roosing S, Webster AR, Arno G. Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype. NPJ Genom Med 2022; 7:60. [PMID: 36266294 PMCID: PMC9581764 DOI: 10.1038/s41525-022-00330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 09/29/2022] [Indexed: 11/21/2022] Open
Abstract
The aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
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Affiliation(s)
- Neringa Jurkute
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK.
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Lisa Pohl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany
| | - Catherina H Z Li
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Robert A Heaton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - Janine Reurink
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - James Bellingham
- Institute of Ophthalmology, University College London, London, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Georgia Yioti
- University of Ioannina Medical School, Ioannina, Greece
| | | | | | - Theresia Zuleger
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | - Katarina Stingl
- University Eye Hospital, Centre for Ophthalmology, University Hospital Tübingen, Tübingen, Germany.,Centre for Rare Diseases, University of Tübingen, Tübingen, Germany
| | | | - Carel B Hoyng
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Omar A Mahroo
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Iain Hargreaves
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores, Liverpool, UK
| | - F Lucy Raymond
- NIHR BioResource-Rare Diseases, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Michel Michaelides
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Susanne Kohl
- Institute for Ophthalmic Research, Centre for Ophthalmology, University of Tübingen, Tübingen, Germany
| | - Susanne Roosing
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands.,Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Andrew R Webster
- Moorfields Eye Hospital NHS Foundation Trust, London, UK.,Institute of Ophthalmology, University College London, London, UK
| | - Gavin Arno
- Moorfields Eye Hospital NHS Foundation Trust, London, UK. .,Institute of Ophthalmology, University College London, London, UK. .,North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children, London, UK.
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Daich Varela M, Bellingham J, Motta F, Jurkute N, Ellingford JM, Quinodoz M, Oprych K, Niblock M, Janeschitz-Kriegl L, Kaminska K, Cancellieri F, Scholl HPN, Lenassi E, Schiff E, Knight H, Black G, Rivolta C, Cheetham ME, Michaelides M, Mahroo OA, Moore AT, Webster AR, Arno G. Multidisciplinary team directed analysis of whole genome sequencing reveals pathogenic non-coding variants in molecularly undiagnosed inherited retinal dystrophies. Hum Mol Genet 2022; 32:595-607. [PMID: 36084042 PMCID: PMC9896476 DOI: 10.1093/hmg/ddac227] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/23/2022] [Accepted: 09/04/2022] [Indexed: 02/07/2023] Open
Abstract
The purpose of this paper is to identify likely pathogenic non-coding variants in inherited retinal dystrophy (IRD) genes, using genome sequencing (GS). Patients with IRD were recruited to the study and underwent comprehensive ophthalmological evaluation and GS. The results of GS were investigated through virtual gene panel analysis, and plausible pathogenic variants and clinical phenotype evaluated by the multidisciplinary team (MDT) discussion. For unsolved patients in whom a specific gene was suspected to harbor a missed pathogenic variant, targeted re-analysis of non-coding regions was performed on GS data. Candidate variants were functionally tested by messenger RNA analysis, minigene or luciferase reporter assays. Previously unreported, likely pathogenic, non-coding variants in 7 genes (PRPF31, NDP, IFT140, CRB1, USH2A, BBS10 and GUCY2D), were identified in 11 patients. These were shown to lead to mis-splicing (PRPF31, IFT140, CRB1 and USH2A) or altered transcription levels (BBS10 and GUCY2D). MDT-led, phenotype-driven, non-coding variant re-analysis of GS is effective in identifying the missing causative alleles.
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Affiliation(s)
- Malena Daich Varela
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | | | - Fabiana Motta
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Department of Ophthalmology, Universidade Federal de Sao Paulo, Sao Paulo 04021001, Brazil
| | - Neringa Jurkute
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Jamie M Ellingford
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | | | - Lucas Janeschitz-Kriegl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Karolina Kaminska
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Hendrik P N Scholl
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland
| | - Eva Lenassi
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | | | | | - Graeme Black
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, St Mary’s Hospital, Manchester M13 9WL, UK,Division of Evolution and Genomic Sciences, Neuroscience and Mental Health Domain, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester M13 9PL, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, Basel 4031, Switzerland,Department of Ophthalmology, University of Basel, Basel 4031, Switzerland,Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | | | - Michel Michaelides
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Omar A Mahroo
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Anthony T Moore
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK,University of California, San Francisco, CA 94607, USA
| | - Andrew R Webster
- UCL Institute of Ophthalmology, London EC1V 9EL, UK,Moorfields Eye Hospital, London EC1V 2PD, UK
| | - Gavin Arno
- To whom correspondence should be addressed at: UCL Institute of Ophthalmology, 11-43 Bath Street, London EC1 9EL, UK. Tel: +44 2076086971;
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15
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Ansar M, Javed S, Baig HMA, Quinodoz M, Ullah M, Han JH, Rahim MU, Kausar H, Calzetti G, Rivolta C. A new nonsense mutation in HMX1 in two siblings with oculoauricular syndrome. Ophthalmic Genet 2022; 43:720-723. [PMID: 35946463 DOI: 10.1080/13816810.2022.2096242] [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: 10/15/2022]
Affiliation(s)
- Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Samra Javed
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Hafiz Muhammad Azhar Baig
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Mukhtar Ullah
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | | | - Humera Kausar
- Department of Biotechnology, Kinnaird College for Women, Lahore, Pakistan
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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16
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Pathak GA, Karjalainen J, Stevens C, Neale BM, Daly M, Ganna A, Andrews SJ, Kanai M, Cordioli M, Polimanti R, Harerimana N, Pirinen M, Liao RG, Chwialkowska K, Trankiem A, Balaconis MK, Nguyen H, Solomonson M, Veerapen K, Wolford B, Roberts G, Park D, Ball CA, Coignet M, McCurdy S, Knight S, Partha R, Rhead B, Zhang M, Berkowitz N, Gaddis M, Noto K, Ruiz L, Pavlovic M, Hong EL, Rand K, Girshick A, Guturu H, Baltzell AH, Niemi MEK, Rahmouni S, Guntz J, Beguin Y, Cordioli M, Pigazzini S, Nkambule L, Georges M, Moutschen M, Misset B, Darcis G, Guiot J, Azarzar S, Gofflot S, Claassen S, Malaise O, Huynen P, Meuris C, Thys M, Jacques J, Léonard P, Frippiat F, Giot JB, Sauvage AS, Frenckell CV, Belhaj Y, Lambermont B, Nakanishi T, Morrison DR, Mooser V, Richards JB, Butler-Laporte G, Forgetta V, Li R, Ghosh B, Laurent L, Belisle A, Henry D, Abdullah T, Adeleye O, Mamlouk N, Kimchi N, Afrasiabi Z, Rezk N, Vulesevic B, Bouab M, Guzman C, Petitjean L, Tselios C, Xue X, Afilalo J, Afilalo M, Oliveira M, Brenner B, Brassard N, Durand M, Schurr E, Lepage P, Ragoussis J, Auld D, Chassé M, Kaufmann DE, Lathrop GM, Adra D, Hayward C, Glessner JT, Shaw DM, Campbell A, Morris M, Hakonarson H, Porteous DJ, Below J, Richmond A, Chang X, Polikowski H, Lauren PE, Chen HH, Wanying Z, Fawns-Ritchie C, North K, McCormick JB, Chang X, Glessner JR, Hakonarson H, Gignoux CR, Wicks SJ, Crooks K, Barnes KC, Daya M, Shortt J, Rafaels N, Chavan S, Timmers PRHJ, Wilson JF, Tenesa A, Kerr SM, D’Mellow K, Shahin D, El-Sherbiny YM, von Hohenstaufen KA, Sobh A, Eltoukhy MM, Nkambul L, Elhadidy TA, Abd Elghafar MS, El-Jawhari JJ, Mohamed AAS, Elnagdy MH, Samir A, Abdel-Aziz M, Khafaga WT, El-Lawaty WM, Torky MS, El-shanshory MR, Yassen AM, Hegazy MAF, Okasha K, Eid MA, Moahmed HS, Medina-Gomez C, Ikram MA, Uitterlinden AG, Mägi R, Milani L, Metspalu A, Laisk T, Läll K, Lepamets M, Esko T, Reimann E, Naaber P, Laane E, Pesukova J, Peterson P, Kisand K, Tabri J, Allos R, Hensen K, Starkopf J, Ringmets I, Tamm A, Kallaste A, Alavere H, Metsalu K, Puusepp M, Batini C, Tobin MD, Venn LD, Lee PH, Shrine N, Williams AT, Guyatt AL, John C, Packer RJ, Ali A, Free RC, Wang X, Wain LV, Hollox EJ, Bee CE, Adams EL, Palotie A, Ripatti S, Ruotsalainen S, Kristiansson K, Koskelainen S, Perola M, Donner K, Kivinen K, Palotie A, Kaunisto M, Rivolta C, Bochud PY, Bibert S, Boillat N, Nussle SG, Albrich W, Quinodoz M, Kamdar D, Suh N, Neofytos D, Erard V, Voide C, Bochud PY, Rivolta C, Bibert S, Quinodoz M, Kamdar D, Neofytos D, Erard V, Voide C, Friolet R, Vollenweider P, Pagani JL, Oddo M, zu Bentrup FM, Conen A, Clerc O, Marchetti O, Guillet A, Guyat-Jacques C, Foucras S, Rime M, Chassot J, Jaquet M, Viollet RM, Lannepoudenx Y, Portopena L, Bochud PY, Vollenweider P, Pagani JL, Desgranges F, Filippidis P, Guéry B, Haefliger D, Kampouri EE, Manuel O, Munting A, Papadimitriou-Olivgeris M, Regina J, Rochat-Stettler L, Suttels V, Tadini E, Tschopp J, Van Singer M, Viala B, Boillat-Blanco N, Brahier T, Hügli O, Meuwly JY, Pantet O, Gonseth Nussle S, Bochud M, D’Acremont V, Estoppey Younes S, Albrich WC, Suh N, Cerny A, O’Mahony L, von Mering C, Bochud PY, Frischknecht M, Kleger GR, Filipovic M, Kahlert CR, Wozniak H, Negro TR, Pugin J, Bouras K, Knapp C, Egger T, Perret A, Montillier P, di Bartolomeo C, Barda B, de Cid R, Carreras A, Moreno V, Kogevinas M, Galván-Femenía I, Blay N, Farré X, Sumoy L, Cortés B, Mercader JM, Guindo-Martinez M, Torrents D, Garcia-Aymerich J, Castaño-Vinyals G, Dobaño C, Gori M, Renieri A, Mari F, Mondelli MU, Castelli F, Vaghi M, Rusconi S, Montagnani F, Bargagli E, Franchi F, Mazzei MA, Cantarini L, Tacconi D, Feri M, Scala R, Spargi G, Nencioni C, Bandini M, Caldarelli GP, Canaccini A, Ognibene A, D’Arminio Monforte A, Girardis M, Antinori A, Francisci D, Schiaroli E, Scotton PG, Panese S, Scaggiante R, Monica MD, Capasso M, Fiorentino G, Castori M, Aucella F, Biagio AD, Masucci L, Valente S, Mandalà M, Zucchi P, Giannattasio F, Coviello DA, Mussini C, Tavecchia L, Crotti L, Rizzi M, Rovere MTL, Sarzi-Braga S, Bussotti M, Ravaglia S, Artuso R, Perrella A, Romani D, Bergomi P, Catena E, Vincenti A, Ferri C, Grassi D, Pessina G, Tumbarello M, Pietro MD, Sabrina R, Luchi S, Furini S, Dei S, Benetti E, Picchiotti N, Sanarico M, Ceri S, Pinoli P, Raimondi F, Biscarini F, Stella A, Zguro K, Capitani K, Nkambule L, Tanfoni M, Fallerini C, Daga S, Baldassarri M, Fava F, Frullanti E, Valentino F, Doddato G, Giliberti A, Tita R, Amitrano S, Bruttini M, Croci S, Meloni I, Mencarelli MA, Rizzo CL, Pinto AM, Beligni G, Tommasi A, Sarno LD, Palmieri M, Carriero ML, Alaverdian D, Busani S, Bruno R, Vecchia M, Belli MA, Mantovani S, Ludovisi S, Quiros-Roldan E, Antoni MD, Zanella I, Siano M, Emiliozzi A, Fabbiani M, Rossetti B, Bergantini L, D’Alessandro M, Cameli P, Bennett D, Anedda F, Marcantonio S, Scolletta S, Guerrini S, Conticini E, Frediani B, Spertilli C, Donati A, Guidelli L, Corridi M, Croci L, Piacentini P, Desanctis E, Cappelli S, Verzuri A, Anemoli V, Pancrazzi A, Lorubbio M, Miraglia FG, Venturelli S, Cossarizza A, Vergori A, Gabrieli A, Riva A, Paciosi F, Andretta F, Gatti F, Parisi SG, Baratti S, Piscopo C, Russo R, Andolfo I, Iolascon A, Carella M, Merla G, Squeo GM, Raggi P, Marciano C, Perna R, Bassetti M, Sanguinetti M, Giorli A, Salerni L, Parravicini P, Menatti E, Trotta T, Coiro G, Lena F, Martinelli E, Mancarella S, Gabbi C, Maggiolo F, Ripamonti D, Bachetti T, Suardi C, Parati G, Bottà G, Domenico PD, Rancan I, Bianchi F, Colombo R, Barbieri C, Acquilini D, Andreucci E, Segala FV, Tiseo G, Falcone M, Lista M, Poscente M, Vivo OD, Petrocelli P, Guarnaccia A, Baroni S, Hayward C, Porteous DJ, Fawns-Ritchie C, Richmond A, Campbell A, van Heel DA, Hunt KA, Trembath RC, Huang QQ, Martin HC, Mason D, Trivedi B, Wright J, Finer S, Akhtar S, Anwar M, Arciero E, Ashraf S, Breen G, Chung R, Curtis CJ, Chowdhury M, Colligan G, Deloukas P, Durham C, Finer S, Griffiths C, Huang QQ, Hurles M, Hunt KA, Hussain S, Islam K, Khan A, Khan A, Lavery C, Lee SH, Lerner R, MacArthur D, MacLaughlin B, Martin H, Mason D, Miah S, Newman B, Safa N, Tahmasebi F, Trembath RC, Trivedi B, van Heel DA, Wright J, Griffiths CJ, Smith AV, Boughton AP, Li KW, LeFaive J, Annis A, Niavarani A, Aliannejad R, Sharififard B, Amirsavadkouhi A, Naderpour Z, Tadi HA, Aleagha AE, Ahmadi S, Moghaddam SBM, Adamsara A, Saeedi M, Abdollahi H, Hosseini A, Chariyavilaskul P, Jantarabenjakul W, Hirankarn N, Chamnanphon M, Suttichet TB, Shotelersuk V, Pongpanich M, Phokaew C, Chetruengchai W, Putchareon O, Torvorapanit P, Puthanakit T, Suchartlikitwong P, Nilaratanakul V, Sodsai P, Brumpton BM, Hveem K, Willer C, Wolford B, Zhou W, Rogne T, Solligard E, Åsvold BO, Franke L, Boezen M, Deelen P, Claringbould A, Lopera E, Warmerdam R, Vonk JM, van Blokland I, Lanting P, Ori APS, Feng YCA, Mercader J, Weiss ST, Karlson EW, Smoller JW, Murphy SN, Meigs JB, Woolley AE, Green RC, Perez EF, Wolford B, Zöllner S, Wang J, Beck A, Sloofman LG, Ascolillo S, Sebra RP, Collins BL, Levy T, Buxbaum JD, Sealfon SC, Jordan DM, Thompson RC, Gettler K, Chaudhary K, Belbin GM, Preuss M, Hoggart C, Choi S, Underwood SJ, Salib I, Britvan B, Keller K, Tang L, Peruggia M, Hiester LL, Niblo K, Aksentijevich A, Labkowsky A, Karp A, Zlatopolsky M, Zyndorf M, Charney AW, Beckmann ND, Schadt EE, Abul-Husn NS, Cho JH, Itan Y, Kenny EE, Loos RJF, Nadkarni GN, Do R, O’Reilly P, Huckins LM, Ferreira MAR, Abecasis GR, Leader JB, Cantor MN, Justice AE, Carey DJ, Chittoor G, Josyula NS, Kosmicki JA, Horowitz JE, Baras A, Gass MC, Yadav A, Mirshahi T, Hottenga JJ, Bartels M, de geus EEJC, Nivard MMG, Verma A, Ritchie MD, Rader D, Li B, Verma SS, Lucas A, Bradford Y, Abedalthagafi M, Alaamery M, Alshareef A, Sawaji M, Massadeh S, AlMalik A, Alqahtani S, Baraka D, Harthi FA, Alsolm E, Safieh LA, Alowayn AM, Alqubaishi F, Mutairi AA, Mangul S, Almutairi M, Aljawini N, Albesher N, Arabi YM, Mahmoud ES, Khattab AK, Halawani RT, Alahmadey ZZ, Albakri JK, Felemban WA, Suliman BA, Hasanato R, Al-Awdah L, Alghamdi J, AlZahrani D, AlJohani S, Al-Afghani H, AlDhawi N, AlBardis H, Alkwai S, Alswailm M, Almalki F, Albeladi M, Almohammed I, Barhoush E, Albader A, Alotaibi S, Alghamdi B, Jung J, fawzy MS, Alrashed M, Zeberg H, Nkambul L, Frithiof R, Hultström M, Lipcsey M, Tardif N, Rooyackers O, Grip J, Maricic T, Helgeland Ø, Magnus P, Trogstad LIS, Lee Y, Harris JR, Mangino M, Spector TD, Emma D, Moutsianas L, Caulfield MJ, Scott RH, Kousathanas A, Pasko D, Walker S, Stuckey A, Odhams CA, Rhodes D, Fowler T, Rendon A, Chan G, Arumugam P, Karczewski KJ, Martin AR, Wilson DJ, Spencer CCA, Crook DW, Wyllie DH, O’Connell AM, Atkinson EG, Kanai M, Tsuo K, Baya N, Turley P, Gupta R, Walters RK, Palmer DS, Sarma G, Solomonson M, Cheng N, Lu W, Churchhouse C, Goldstein JI, King D, Zhou W, Seed C, Daly MJ, Neale BM, Finucane H, Bryant S, Satterstrom FK, Band G, Earle SG, Lin SK, Arning N, Koelling N, Armstrong J, Rudkin JK, Callier S, Bryant S, Cusick C, Soranzo N, Zhao JH, Danesh J, Angelantonio ED, Butterworth AS, Sun YV, Huffman JE, Cho K, O’Donnell CJ, Tsao P, Gaziano JM, Peloso G, Ho YL, Smieszek SP, Polymeropoulos C, Polymeropoulos V, Polymeropoulos MH, Przychodzen BP, Fernandez-Cadenas I, Planas AM, Perez-Tur J, Llucià-Carol L, Cullell N, Muiño E, Cárcel-Márquez J, DeDiego ML, Iglesias LL, Soriano A, Rico V, Agüero D, Bedini JL, Lozano F, Domingo C, Robles V, Ruiz-Jaén F, Márquez L, Gomez J, Coto E, Albaiceta GM, García-Clemente M, Dalmau D, Arranz MJ, Dietl B, Serra-Llovich A, Soler P, Colobrán R, Martín-Nalda A, Martínez AP, Bernardo D, Rojo S, Fiz-López A, Arribas E, de la Cal-Sabater P, Segura T, González-Villa E, Serrano-Heras G, Martí-Fàbregas J, Jiménez-Xarrié E, de Felipe Mimbrera A, Masjuan J, García-Madrona S, Domínguez-Mayoral A, Villalonga JM, Menéndez-Valladares P, Chasman DI, Sesso HD, Manson JE, Buring JE, Ridker PM, Franco G, Davis L, Lee S, Priest J, Sankaran VG, van Heel D, Biesecker L, Kerchberger VE, Baillie JK. A first update on mapping the human genetic architecture of COVID-19. Nature 2022; 608:E1-E10. [PMID: 35922517 PMCID: PMC9352569 DOI: 10.1038/s41586-022-04826-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 04/29/2022] [Indexed: 01/04/2023]
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Han JH, Ryan G, Guy A, Liu L, Quinodoz M, Helbling I, Lai-Cheong JE, Barwell J, Folcher M, McGrath JA, Moss C, Rivolta C. Mutations in the ribosome biogenesis factor gene LTV1 are linked to LIPHAK syndrome, a novel poikiloderma-like disorder. Hum Mol Genet 2022; 31:1970-1978. [PMID: 34999892 PMCID: PMC9239743 DOI: 10.1093/hmg/ddab368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/18/2021] [Accepted: 12/13/2021] [Indexed: 11/12/2022] Open
Abstract
In the framework of the UK 100 000 Genomes Project, we investigated the genetic origin of a previously undescribed recessive dermatological condition, which we named LIPHAK (LTV1-associated Inflammatory Poikiloderma with Hair abnormalities and Acral Keratoses), in four affected individuals from two UK families of Pakistani and Indian origins, respectively. Our analysis showed that only one gene, LTV1, carried rare biallelic variants that were shared in all affected individuals, and specifically they bore the NM_032860.5:c.503A > G, p.(Asn168Ser) change, found homozygously in all of them. In addition, high-resolution homozygosity mapping revealed the presence of a small 652-kb stretch on chromosome 6, encompassing LTV1, that was haploidentical and common to all affected individuals. The c.503A > G variant was predicted by in silico tools to affect the correct splicing of LTV1's exon 5. Minigene-driven splicing assays in HEK293T cells and in a skin sample from one of the patients confirmed that this variant was indeed responsible for the creation of a new donor splice site, resulting in aberrant splicing and in a premature termination codon in exon 6 of this gene. LTV1 encodes one of the ribosome biogenesis factors that promote the assembly of the small (40S) ribosomal subunit. In yeast, defects in LTV1 alter the export of nascent ribosomal subunits to the cytoplasm; however, the role of this gene in human pathology is unknown to date. Our data suggest that LIPHAK could be a previously unrecognized ribosomopathy.
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Affiliation(s)
- Ji Hoon Han
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham B15 2TG, UK
| | - Alyson Guy
- Viapath, St Thomas' Hospital, London SE1 7EH, UK
| | - Lu Liu
- Viapath, St Thomas' Hospital, London SE1 7EH, UK
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ingrid Helbling
- Department of Dermatology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | | | | | - Julian Barwell
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Department of Clinical Genetics, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, UK
| | - Marc Folcher
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
| | - John A McGrath
- NIHR Biomedical Research Centre, Guy's and St Thomas' NHS Foundation Trust and King's College London, London SE1 9RT, UK
- St John's Institute of Dermatology, King's College London (Guy's campus), London SE1 9RT, UK
| | - Celia Moss
- Department of Paediatric Dermatology, Birmingham Women’s and Children’s Hospital NHS FT, Birmingham B4 6NH, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031 Basel, Switzerland
- Department of Ophthalmology, University of Basel, 4031 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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18
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Hahaut V, Pavlinic D, Carbone W, Schuierer S, Balmer P, Quinodoz M, Renner M, Roma G, Cowan CS, Picelli S. Fast and highly sensitive full-length single-cell RNA sequencing using FLASH-seq. Nat Biotechnol 2022; 40:1447-1451. [PMID: 35637419 PMCID: PMC9546769 DOI: 10.1038/s41587-022-01312-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 04/08/2022] [Indexed: 12/29/2022]
Abstract
We present FLASH-seq (FS), a full-length single-cell RNA sequencing (scRNA-seq) method with increased sensitivity and reduced hands-on time compared to Smart-seq3. The entire FS protocol can be performed in ~4.5 hours, is simple to automate and can be easily miniaturized to decrease resource consumption. The FS protocol can also use unique molecular identifiers (UMIs) for molecule counting while displaying reduced strand-invasion artifacts. FS will be especially useful for characterizing gene expression at high resolution across multiple samples. FLASH-seq speeds up high-sensitivity scRNA-seq while sparing resources.
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19
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Nardou K, Nicolas M, Kuttler F, Cisarova K, Celik E, Quinodoz M, Riggi N, Michielin O, Rivolta C, Turcatti G, Moulin AP. Identification of New Vulnerabilities in Conjunctival Melanoma Using Image-Based High Content Drug Screening. Cancers (Basel) 2022; 14:cancers14061575. [PMID: 35326726 PMCID: PMC8946509 DOI: 10.3390/cancers14061575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 02/05/2023] Open
Abstract
Recent evidence suggests that numerous similarities exist between the genomic landscapes of both conjunctival and cutaneous melanoma. Since alterations of several components of the MAP kinases, PI3K/mTOR, and cell cycle pathways have been reported in conjunctival melanoma, we decided to assess the sensitivity of conjunctival melanoma to targeted inhibition mostly of kinase inhibitors. A high content drug screening assay based on automated fluorescence microscopy was performed in three conjunctival melanoma cell lines with different genomic backgrounds with 489 kinase inhibitors and 53 other inhibitors. IC50 and apoptosis induction were respectively assessed for 53 and 48 compounds. The genomic background influenced the response to MAK and PI3K/mTOR inhibition, more specifically cell lines with BRAF V600E mutations were more sensitive to BRAF/MEK inhibition, while CRMM2 bearing the NRASQ61L mutation was more sensitive to PI3k/mTOR inhibition. All cell lines demonstrated sensitivity to cell cycle inhibition, being more pronounced in CRMM2, especially with polo-like inhibitors. Our data also revealed new vulnerabilities to Hsp90 and Src inhibition. This study demonstrates that the genomic background partially influences the response to targeted therapy and uncovers a large panel of potential vulnerabilities in conjunctival melanoma that may expand available options for the management of this tumor.
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Affiliation(s)
- Katya Nardou
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
| | - Michael Nicolas
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
| | - Fabien Kuttler
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (F.K.); (G.T.)
| | - Katarina Cisarova
- Medical Genetics Unit, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland;
| | - Elifnaz Celik
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Nicolo Riggi
- Experimental Pathology, Institute of Pathology, Lausanne University, 1011 Lausanne, Switzerland;
| | - Olivier Michielin
- Oncology Department, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland;
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel, 4031 Basel, Switzerland; (E.C.); (M.Q.); (C.R.)
- Department of Ophthalmology, University of Basel, 4056 Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; (F.K.); (G.T.)
| | - Alexandre Pierre Moulin
- Jules-Gonin Eye Hospital, University of Lausanne, 1004 Lausanne, Switzerland; (K.N.); (M.N.)
- Correspondence:
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20
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Dentici ML, Alesi V, Quinodoz M, Robens B, Guerin A, Lebon S, Poduri A, Travaglini L, Graziola F, Afenjar A, Keren B, Licursi V, Capuano A, Dallapiccola B, Superti-Furga A, Novelli A. Biallelic variants in ZNF526 cause a severe neurodevelopmental disorder with microcephaly, bilateral cataract, epilepsy and simplified gyration. J Med Genet 2022; 59:262-269. [PMID: 33397746 DOI: 10.1136/jmedgenet-2020-107430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/04/2020] [Accepted: 12/19/2020] [Indexed: 11/03/2022]
Abstract
BACKGROUND Next-generation sequencing, combined with international pooling of cases, has impressively enhanced the discovery of genes responsible for Mendelian neurodevelopmental disorders, particularly in individuals affected by clinically undiagnosed diseases. To date, biallelic missense variants in ZNF526 gene, encoding a Krüppel-type zinc-finger protein, have been reported in three families with non-syndromic intellectual disability. METHODS Here, we describe five individuals from four unrelated families with an undiagnosed neurodevelopmental disorder in which we performed exome sequencing, on a combination of trio-based (4 subjects) or single probands (1 subject). RESULTS We identified five patients from four unrelated families with homozygous ZNF526 variants by whole exome sequencing. Four had variants resulting in truncation of ZNF526; they were affected by severe prenatal and postnatal microcephaly (ranging from -4 SD to -8 SD), profound psychomotor delay, hypertonic-dystonic movements, epilepsy and simplified gyral pattern on MRI. All of them also displayed bilateral progressive cataracts. A fifth patient had a homozygous missense variant and a slightly less severe disorder, with postnatal microcephaly (-2 SD), progressive bilateral cataracts, severe intellectual disability and unremarkable brain MRI.Mutant znf526 zebrafish larvae had notable malformations of the eye and central nervous system, resembling findings seen in the human holoprosencephaly spectrum. CONCLUSION Our findings support the role of ZNF526 biallelic variants in a complex neurodevelopmental disorder, primarily affecting brain and eyes, resulting in severe microcephaly, simplified gyral pattern, epileptic encephalopathy and bilateral cataracts.
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Affiliation(s)
- Maria Lisa Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, Rome, Italy
| | - Viola Alesi
- Medical Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Barbara Robens
- Department of Neurology, F.M. Kirby Neurobiology Center, Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Guerin
- Division of Medical Genetics, Department of Pediatrics, Kingston Health Sciences Centre, Queen's University, Kingston, Ontario, Canada
| | - Sébastien Lebon
- Unit of Pediatric Neurology and Neurorehabilitation Unit, Division of Pediatrics, Department Woman-Mother-Child, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Annapurna Poduri
- Department of Neurology, F.M. Kirby Neurobiology Center, Division of Epilepsy and Clinical Neurophysiology and Epilepsy Genetics Program, Boston Children's Hospital, Boston, Massachusetts, USA
- Division of Epilepsy and Clinical Neurophysiology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Lorena Travaglini
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Federica Graziola
- Neurology Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Neuroscience department, Tor Vergata University, Rome, Italy
| | - Alexandra Afenjar
- CRMR Déficiences Intellectuelles de Causes Rares, Département de Génétique, Sorbonne Université, APHP, Hôpital Trousseau, Paris, France
| | - Boris Keren
- APHP, Département de Génétique, Groupe Hospitalier Pitié Salpêtrière, Paris, France
| | - Valerio Licursi
- Dept. of Biology and Biotechnology, "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Alessandro Capuano
- Neurology Unit, Department of Neuroscience, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | | | - Antonio Novelli
- Medical Genetics Laboratory, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
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21
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Azhar Baig HM, Ansar M, Iqbal A, Naeem MA, Quinodoz M, Calzetti G, Iqbal M, Rivolta C. Genetic analysis of consanguineous Pakistani families with congenital stationary night blindness. Ophthalmic Res 2021; 65:104-110. [PMID: 34781300 DOI: 10.1159/000520895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 10/28/2021] [Indexed: 11/19/2022]
Abstract
AIM Congenital stationary night blindness (CSNB) is a rare, largely non progressive, inherited retinal disorder that can be clinically classified on the basis of fundus and electroretinogram (ERG) abnormalities. METHODS We analyzed four large consanguineous families from the Southern Punjab region of Pakistan including multiple individuals affected with CSNB. Exome sequencing (ES) was performed in probands of all four families; Sanger sequencing was performed in additional members to test co-segregation of the variants identified. RESULTS We identified two novel and likely pathogenic variants in two pedigrees, namely NM_002905.4:c.668A>C (p.Gln223Pro) in RDH5, and NM_022567.2:c.908del (p.Gly303ValfsTer45) in NYX. In the two other families, the variants NM_002905.4:c.319G>C (p.Gly107Arg) in RDH5 and NM_000541.5:c.874C>T (p.Arg292Ter) in SAG were identified. These variants have been reported previously, but not in the Pakistani population. CONCLUSIONS Our findings expand the mutational spectrum of CSNB, in particular within the population of Southern Punjab.
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Affiliation(s)
- Hafiz Muhammad Azhar Baig
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Ansar
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Afia Iqbal
- Department of Zoology, Lahore College for Women University, Lahore, Pakistan
| | - Muhammad Asif Naeem
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Giacomo Calzetti
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Muhammad Iqbal
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
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22
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Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Correction: Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:2016. [PMID: 34522029 DOI: 10.1038/s41436-021-01306-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
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23
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Rodan LH, Spillmann RC, Kurata HT, Lamothe SM, Maghera J, Jamra RA, Alkelai A, Antonarakis SE, Atallah I, Bar-Yosef O, Bilan F, Bjorgo K, Blanc X, Van Bogaert P, Bolkier Y, Burrage LC, Christ BU, Granadillo JL, Dickson P, Donald KA, Dubourg C, Eliyahu A, Emrick L, Engleman K, Gonfiantini MV, Good JM, Kalser J, Kloeckner C, Lachmeijer G, Macchiaiolo M, Nicita F, Odent S, O'Heir E, Ortiz-Gonzalez X, Pacio-Miguez M, Palomares-Bralo M, Pena L, Platzer K, Quinodoz M, Ranza E, Rosenfeld JA, Roulet-Perez E, Santani A, Santos-Simarro F, Pode-Shakked B, Skraban C, Slaugh R, Superti-Furga A, Thiffault I, van Jaabrsveld RH, Vincent M, Wang HG, Zacher P, Rush E, Pitt GS, Au PYB, Shashi V. Phenotypic expansion of CACNA1C-associated disorders to include isolated neurological manifestations. Genet Med 2021; 23:1922-1932. [PMID: 34163037 PMCID: PMC8488020 DOI: 10.1038/s41436-021-01232-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 12/09/2020] [Accepted: 05/14/2021] [Indexed: 11/09/2022] Open
Abstract
PURPOSE CACNA1C encodes the alpha-1-subunit of a voltage-dependent L-type calcium channel expressed in human heart and brain. Heterozygous variants in CACNA1C have previously been reported in association with Timothy syndrome and long QT syndrome. Several case reports have suggested that CACNA1C variation may also be associated with a primarily neurological phenotype. METHODS We describe 25 individuals from 22 families with heterozygous variants in CACNA1C, who present with predominantly neurological manifestations. RESULTS Fourteen individuals have de novo, nontruncating variants and present variably with developmental delays, intellectual disability, autism, hypotonia, ataxia, and epilepsy. Functional studies of a subgroup of missense variants via patch clamp experiments demonstrated differential effects on channel function in vitro, including loss of function (p.Leu1408Val), neutral effect (p.Leu614Arg), and gain of function (p.Leu657Phe, p.Leu614Pro). The remaining 11 individuals from eight families have truncating variants in CACNA1C. The majority of these individuals have expressive language deficits, and half have autism. CONCLUSION We expand the phenotype associated with CACNA1C variants to include neurodevelopmental abnormalities and epilepsy, in the absence of classic features of Timothy syndrome or long QT syndrome.
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Affiliation(s)
- Lance H Rodan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Department of Neurology, Boston Children's Hospital, Boston, MA, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Harley T Kurata
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Shawn M Lamothe
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Jasmine Maghera
- Department of Pharmacology, Alberta Diabetes Institute, University of Alberta, Edmonton, AB, Canada
| | - Rami Abou Jamra
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Anna Alkelai
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, Switzerland
| | - Omer Bar-Yosef
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Frédéric Bilan
- CHU de Poitiers, Service de Génétique, EA3808 NEUVACOD, Poitiers, France
| | - Kathrine Bjorgo
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Xavier Blanc
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | | | - Yoav Bolkier
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Pediatric Cardiology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lindsay C Burrage
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Björn U Christ
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Jorge L Granadillo
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Patricia Dickson
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Kirsten A Donald
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, SA, South Africa
| | - Christèle Dubourg
- Service de Génétique Moléculaire et Génomique, CHU, Rennes, France
- University of Rennes, CNRS, IGDR, UMR 6290, Rennes, France
| | - Aviva Eliyahu
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- The Danek Gertner Insitute of Human Genetics, Sheba Medical Center, Tel-Hahsomer, Israel
- Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Lisa Emrick
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kendra Engleman
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Jean-Marc Good
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Judith Kalser
- Pediatric Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Chiara Kloeckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Guus Lachmeijer
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Marina Macchiaiolo
- Rare Diseases and Medical Genetic Unit, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Francesco Nicita
- Unit of Neuromuscular and Neurodegenerative Diseases, Department of Neurosciences and Neurorehabilitation, IRCCS Bambino Gesù Children's Hospital, Rome, Italy
| | - Sylvie Odent
- Service de Génétique Clinique, Centre de référence "Maladies Rares" Anomalies du développement CLAD-Ouest, Hôpital SUD, Échirolles, France
| | - Emily O'Heir
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
- Center for Mendelian Genomics and Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Xilma Ortiz-Gonzalez
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marta Pacio-Miguez
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - María Palomares-Bralo
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Loren Pena
- Cincinnati Children's Hospital and Medical Center Cincinnati, Cincinnati, OH, USA
- University of Cincinnati College of Medicine Cincinnati, Cincinnati, OH, USA
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Emmanuelle Ranza
- Medigenome, Swiss Institute of Genomic Medicine, Geneva, Switzerland
| | - Jill A Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Avni Santani
- Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Fernando Santos-Simarro
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz, IdiPAZ, CIBERER, ISCIII, Madrid, Spain
| | - Ben Pode-Shakked
- Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- Institute of Rare Diseases, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hahsomer, Israel
| | - Cara Skraban
- Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rachel Slaugh
- Division of Genetics and Genomic Medicine, Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | | | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, Kansas City, MO, USA
| | | | - Marie Vincent
- Service de Génétique Médicale, CHU Nantes, France; Inserm, CNRS, Univ Nantes, l'institut du thorax, Nantes, France
| | - Hong-Gang Wang
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Pia Zacher
- The Saxon Epilepsy Center Kleinwachau, Radeberg, Germany
| | - Eric Rush
- The Children's Mercy Hospital, Kansas City, MO, USA
- Department of Pediatrics University of Missouri-Kansas City, Kansas City, MO, USA
- Department of Internal Medicine, University of Kansas Medical Center, Kansas City, MO, USA
| | - Geoffrey S Pitt
- Cardiovascular Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ping Yee Billie Au
- Alberta Children's Hospital Research Institute, Department of Genetics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA.
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24
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Rehman AU, Sepahi N, Bedoni N, Ravesh Z, Salmaninejad A, Cancellieri F, Peter VG, Quinodoz M, Mojarrad M, Pasdar A, Asad AG, Ghalamkari S, Piran M, Piran M, Superti-Furga A, Rivolta C. Whole exome sequencing in 17 consanguineous Iranian pedigrees expands the mutational spectrum of inherited retinal dystrophies. Sci Rep 2021; 11:19332. [PMID: 34588515 PMCID: PMC8481312 DOI: 10.1038/s41598-021-98677-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 09/06/2021] [Indexed: 11/24/2022] Open
Abstract
Inherited retinal dystrophies (IRDs) constitute one of the most heterogeneous groups of Mendelian human disorders. Using autozygome-guided next-generation sequencing methods in 17 consanguineous pedigrees of Iranian descent with isolated or syndromic IRD, we identified 17 distinct genomic variants in 11 previously-reported disease genes. Consistent with a recessive inheritance pattern, as suggested by pedigrees, variants discovered in our study were exclusively bi-allelic and mostly in a homozygous state (in 15 families out of 17, or 88%). Out of the 17 variants identified, 5 (29%) were never reported before. Interestingly, two mutations (GUCY2D:c.564dup, p.Ala189ArgfsTer130 and TULP1:c.1199G > A, p.Arg400Gln) were also identified in four separate pedigrees (two pedigrees each). In addition to expanding the mutational spectrum of IRDs, our findings confirm that the traditional practice of endogamy in the Iranian population is a prime cause for the appearance of IRDs.
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Affiliation(s)
- Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Nicola Bedoni
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Zeinab Ravesh
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Arash Salmaninejad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Francesca Cancellieri
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Virginie G Peter
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Majid Mojarrad
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics and Molecular Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Medical Genetics Research Centre, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | | | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Mehrdad Piran
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK. .,Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland.
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25
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Perea-Romero I, Blanco-Kelly F, Sanchez-Navarro I, Lorda-Sanchez I, Tahsin-Swafiri S, Avila-Fernandez A, Martin-Merida I, Trujillo-Tiebas MJ, Lopez-Rodriguez R, Rodriguez de Alba M, Iancu IF, Romero R, Quinodoz M, Hakonarson H, Garcia-Sandova B, Minguez P, Corton M, Rivolta C, Ayuso C. NGS and phenotypic ontology-based approaches increase the diagnostic yield in syndromic retinal diseases. Hum Genet 2021; 140:1665-1678. [PMID: 34448047 PMCID: PMC8553673 DOI: 10.1007/s00439-021-02343-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/10/2021] [Indexed: 02/08/2023]
Abstract
Syndromic retinal diseases (SRDs) are a group of complex inherited systemic disorders, with challenging molecular underpinnings and clinical management. Our main goal is to improve clinical and molecular SRDs diagnosis, by applying a structured phenotypic ontology and next-generation sequencing (NGS)-based pipelines. A prospective and retrospective cohort study was performed on 100 probands with an a priori diagnosis of non-Usher SRDs, using available clinical data, including Human Phenotype Ontology annotation, and further classification into seven clinical categories (ciliopathies, specific syndromes and five others). Retrospective molecular diagnosis was assessed using different molecular and bioinformatic methods depending on availability. Subsequently, uncharacterized probands were prospectively screened using other NGS approaches to extend the number of analyzed genes. After phenotypic classification, ciliopathies were the most common SRD (35%). A global characterization rate of 52% was obtained, with six cases incompletely characterized for a gene that partially explained the phenotype. An improved characterization rate was achieved addressing prospective cases (83%) and well-recognizable syndrome (62%) subgroups. The 27% of the fully characterized cases were reclassified into a different clinical category after identification of the disease-causing gene. Clinical-exome sequencing is the most appropriate first-tier approach for prospective cases, whereas whole-exome sequencing and bioinformatic reanalysis increases the diagnosis of uncharacterized retrospective cases to 45%, mostly those with unspecific symptoms. Our study describes a comprehensive approach to SRDs in daily clinical practice and the importance of thorough clinical assessment and selection of the most appropriate molecular test to be used to solve these complex cases and elucidate novel associations.
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Affiliation(s)
- I Perea-Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - F Blanco-Kelly
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Sanchez-Navarro
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I Lorda-Sanchez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - S Tahsin-Swafiri
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - A Avila-Fernandez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - I Martin-Merida
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M J Trujillo-Tiebas
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Lopez-Rodriguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Rodriguez de Alba
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - I F Iancu
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - R Romero
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - H Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Blanca Garcia-Sandova
- Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.,Department of Ophthalmology, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - P Minguez
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - M Corton
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain.,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - C Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - C Ayuso
- Department of Genetics, Health Research Institute-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain. .,Center for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain.
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26
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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Gonçalves AB, Hasselbalch SK, Joensen BB, Patzke S, Martens P, Ohlsen SK, Quinodoz M, Nikopoulos K, Suleiman R, Damsø Jeppesen MP, Weiss C, Christensen ST, Rivolta C, Andersen JS, Farinelli P, Pedersen LB. CEP78 functions downstream of CEP350 to control biogenesis of primary cilia by negatively regulating CP110 levels. eLife 2021; 10:63731. [PMID: 34259627 PMCID: PMC8354638 DOI: 10.7554/elife.63731] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 07/13/2021] [Indexed: 12/12/2022] Open
Abstract
CEP78 is a centrosomal protein implicated in ciliogenesis and ciliary length control, and mutations in the CEP78 gene cause retinal cone-rod dystrophy associated with hearing loss. However, the mechanism by which CEP78 affects cilia formation is unknown. Based on a recently discovered disease-causing CEP78 p.L150S mutation, we identified the disease-relevant interactome of CEP78. We confirmed that CEP78 interacts with the EDD1-DYRK2-DDB1VPRBP E3 ubiquitin ligase complex, which is involved in CP110 ubiquitination and degradation, and identified a novel interaction between CEP78 and CEP350 that is weakened by the CEP78L150S mutation. We show that CEP350 promotes centrosomal recruitment and stability of CEP78, which in turn leads to centrosomal recruitment of EDD1. Consistently, cells lacking CEP78 display significantly increased cellular and centrosomal levels of CP110, and depletion of CP110 in CEP78-deficient cells restored ciliation frequency to normal. We propose that CEP78 functions downstream of CEP350 to promote ciliogenesis by negatively regulating CP110 levels via an EDD1-dependent mechanism.
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Affiliation(s)
- André Brás Gonçalves
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sarah Kirstine Hasselbalch
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Beinta Biskopstø Joensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Sebastian Patzke
- Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Pernille Martens
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Signe Krogh Ohlsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | | | - Reem Suleiman
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Magnus Per Damsø Jeppesen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Catja Weiss
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Søren Tvorup Christensen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Pietro Farinelli
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
| | - Lotte Bang Pedersen
- Department of Biology, Section for Cell Biology and Physiology, University of Copenhagen, Copenhagen, Denmark
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28
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Bibert S, Guex N, Lourenco J, Brahier T, Papadimitriou-Olivgeris M, Damonti L, Manuel O, Liechti R, Götz L, Tschopp J, Quinodoz M, Vollenweider P, Pagani JL, Oddo M, Hügli O, Lamoth F, Erard V, Voide C, Delorenzi M, Rufer N, Candotti F, Rivolta C, Boillat-Blanco N, Bochud PY. Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. Front Immunol 2021; 12:666163. [PMID: 34135895 PMCID: PMC8202013 DOI: 10.3389/fimmu.2021.666163] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/10/2021] [Indexed: 12/19/2022] Open
Abstract
The reason why most individuals with COVID-19 have relatively limited symptoms while other develop respiratory distress with life-threatening complications remains unknown. Increasing evidence suggests that COVID-19 associated adverse outcomes mainly rely on dysregulated immunity. Here, we compared transcriptomic profiles of blood cells from 103 patients with different severity levels of COVID-19 with that of 27 healthy and 22 influenza-infected individuals. Data provided a complete overview of SARS-CoV-2-induced immune signature, including a dramatic defect in IFN responses, a reduction of toxicity-related molecules in NK cells, an increased degranulation of neutrophils, a dysregulation of T cells, a dramatic increase in B cell function and immunoglobulin production, as well as an important over-expression of genes involved in metabolism and cell cycle in patients infected with SARS-CoV-2 compared to those infected with influenza viruses. These features also differed according to COVID-19 severity. Overall and specific gene expression patterns across groups can be visualized on an interactive website (https://bix.unil.ch/covid/). Collectively, these transcriptomic host responses to SARS-CoV-2 infection are discussed in the context of current studies, thereby improving our understanding of COVID-19 pathogenesis and shaping the severity level of COVID-19.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Nicolas Guex
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
| | - Joao Lourenco
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Thomas Brahier
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Lauro Damonti
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Oriol Manuel
- Infectious Diseases Service and Transplantation Center, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Robin Liechti
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Lou Götz
- Bioinformatics Competence Center, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
| | - Jonathan Tschopp
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Peter Vollenweider
- Internal Medicine Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jean-Luc Pagani
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mauro Oddo
- Department of Adult Intensive Care Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Olivier Hügli
- Emergency Department, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Frédéric Lamoth
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Department of Laboratory Medicine, Institute of Microbiology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Véronique Erard
- Clinique de Médecine et spécialités, Infectiologie, Hôpital Fribourgeois-Fribourg, Fribourg, Switzerland
| | - Cathy Voide
- Department of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland
| | - Mauro Delorenzi
- SIB Swiss Institute of Bioinformatics and Department of Fundamenal Oncology, University of Lausanne, Lausanne, Switzerland
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Nathalie Rufer
- Department of Oncology, University Hospital and University of Lausanne, Epalinges, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Basel, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Noémie Boillat-Blanco
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
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Atallah I, Quinodoz M, Campos-Xavier B, Peter VG, Fouriki A, Bonvin C, Bottani A, Kumps C, Angelini F, Bellutti Enders F, Christen-Zaech S, Rizzi M, Renella R, Beck-Popovic M, Poloni C, Frossard V, Blouin JL, Rivolta C, Riccio O, Candotti F, Hofer M, Unger S, Superti-Furga A. Immune deficiency, autoimmune disease and intellectual disability: A pleiotropic disorder caused by biallelic variants in the TPP2 gene. Clin Genet 2021; 99:780-788. [PMID: 33586135 DOI: 10.1111/cge.13942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/20/2021] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022]
Abstract
Four individuals from two families presented with a multisystemic condition of suspected genetic origin that was diagnosed only after genome analysis. The main phenotypic features were immune system dysregulation (severe immunodeficiency with autoimmunity) and intellectual disability. The four individuals were found to be homozygous for a 4.4 Kb deletion removing exons 20-23 (NM_003291.4) of the TPP2 gene, predicting a frameshift with premature termination of the protein. The deletion was located on a shared chromosome 13 haplotype indicating a Swiss founder mutation. Tripeptidyl peptidase 2 (TPP2) is a protease involved in HLA/antigen complex processing and amino acid homeostasis. Biallelic variants in TPP2 have been described in 10 individuals with variable features including immune deficiency, autoimmune cytopenias, and intellectual disability or chronic sterile brain inflammation mimicking multiple sclerosis. Our observations further delineate this severe condition not yet included in the OMIM catalog. Timely recognition of TPP2 deficiency is crucial since (1) immune surveillance is needed and hematopoietic stem cell transplantation may be necessary, and (2) for provision of genetic counselling. Additionally, enzyme replacement therapy, as already established for TPP1 deficiency, might be an option in the future.
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Affiliation(s)
- Isis Atallah
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Belinda Campos-Xavier
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Athina Fouriki
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Christophe Bonvin
- Division of Neurology, Lausanne University Hospital, Lausanne, Switzerland
| | - Armand Bottani
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Camille Kumps
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Federica Angelini
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Felicitas Bellutti Enders
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Mattia Rizzi
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Raffaele Renella
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Maja Beck-Popovic
- Pediatric Hemato-Oncology Unit, Lausanne University Hospital, Lausanne, Switzerland
| | - Claudia Poloni
- Pediatric Neurology Unit, Sion Hospital, Sion, Switzerland
| | | | - Jean-Louis Blouin
- Division of Genetic Medicine, Geneva University Hospitals, Geneva, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Orbicia Riccio
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabio Candotti
- Division of Immunology and Allergy, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Michael Hofer
- Pediatric Immunology Unit, Division of Pediatrics, Lausanne University Hospital, Lausanne, Switzerland
| | - Sheila Unger
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
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30
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Allou L, Balzano S, Magg A, Quinodoz M, Royer-Bertrand B, Schöpflin R, Chan WL, Speck-Martins CE, Carvalho DR, Farage L, Lourenço CM, Albuquerque R, Rajagopal S, Nampoothiri S, Campos-Xavier B, Chiesa C, Niel-Bütschi F, Wittler L, Timmermann B, Spielmann M, Robson MI, Ringel A, Heinrich V, Cova G, Andrey G, Prada-Medina CA, Pescini-Gobert R, Unger S, Bonafé L, Grote P, Rivolta C, Mundlos S, Superti-Furga A. Non-coding deletions identify Maenli lncRNA as a limb-specific En1 regulator. Nature 2021; 592:93-98. [DOI: 10.1038/s41586-021-03208-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2019] [Accepted: 01/07/2021] [Indexed: 11/09/2022]
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31
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Quinodoz M, Peter VG, Bedoni N, Royer Bertrand B, Cisarova K, Salmaninejad A, Sepahi N, Rodrigues R, Piran M, Mojarrad M, Pasdar A, Ghanbari Asad A, Sousa AB, Coutinho Santos L, Superti-Furga A, Rivolta C. AutoMap is a high performance homozygosity mapping tool using next-generation sequencing data. Nat Commun 2021; 12:518. [PMID: 33483490 PMCID: PMC7822856 DOI: 10.1038/s41467-020-20584-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Homozygosity mapping is a powerful method for identifying mutations in patients with recessive conditions, especially in consanguineous families or isolated populations. Historically, it has been used in conjunction with genotypes from highly polymorphic markers, such as DNA microsatellites or common SNPs. Traditional software performs rather poorly with data from Whole Exome Sequencing (WES) and Whole Genome Sequencing (WGS), which are now extensively used in medical genetics. We develop AutoMap, a tool that is both web-based or downloadable, to allow performing homozygosity mapping directly on VCF (Variant Call Format) calls from WES or WGS projects. Following a training step on WES data from 26 consanguineous families and a validation procedure on a matched cohort, our method shows higher overall performances when compared with eight existing tools. Most importantly, when tested on real cases with negative molecular diagnosis from an internal set, AutoMap detects three gene-disease and multiple variant-disease associations that were previously unrecognized, projecting clear benefits for both molecular diagnosis and research activities in medical genetics. Homozygosity mapping is a useful tool for identifying candidate mutations in recessive conditions, however application to next generation sequencing data has been sub-optimal. Here, the authors present AutoMap, which efficiently identifies runs of homozygosity in whole exome/genome sequencing data.
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Affiliation(s)
- Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Nicola Bedoni
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Béryl Royer Bertrand
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Katarina Cisarova
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Arash Salmaninejad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Neda Sepahi
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Raquel Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Mehran Piran
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran.,Bioinformatics and Computational Biology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Majid Mojarrad
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Alireza Pasdar
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.,Division of Applied Medicine, Medical School, University of Aberdeen, Aberdeen, UK
| | - Ali Ghanbari Asad
- Noncommunicable Diseases Research Center, Fasa University of Sciences, Fasa, Iran
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Medical Faculty, Lisbon University, Lisbon, Portugal
| | | | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland. .,Department of Ophthalmology, University of Basel, Basel, Switzerland. .,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK.
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Janeschitz‐Kriegl L, Rivolta C, György B, Quinodoz M, Meyer P, Wild A, Escher P, Scholl H, Goldblum D. c.‐61G>A in OVOL2 is a pathogenic variant in posterior polymorphous corneal dystrophy 1—a case report. Acta Ophthalmol 2021. [DOI: 10.1111/j.1755-3768.2020.0178] [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: 11/27/2022]
Affiliation(s)
- Lucas Janeschitz‐Kriegl
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Bence György
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
| | - Peter Meyer
- Eye Clinic University Hospital Basel Basel Switzerland
| | | | - Pascal Escher
- Inselspital Universitätsklinik für Augenheilkunde Bern Switzerland
| | - Hendrik Scholl
- Eye Clinic University Hospital Basel Basel Switzerland
- Institute of Molecular and Clinical Ophthalmology Basel (IOB) Basel Switzerland
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Peter VG, Quinodoz M, Sadio S, Held S, Rodrigues M, Soares M, Sousa AB, Coutinho Santos L, Damme M, Rivolta C. New clinical and molecular evidence linking mutations in ARSG to Usher syndrome type IV. Hum Mutat 2020; 42:261-271. [PMID: 33300174 DOI: 10.1002/humu.24150] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [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: 07/17/2020] [Revised: 11/11/2020] [Accepted: 12/06/2020] [Indexed: 11/11/2022]
Abstract
In murine and canine animal models, mutations in the Arylsulfatase G gene (ARSG) cause a particular lysosomal storage disorder characterized by neurological phenotypes. Recently, two variants in the same gene were found to be associated with an atypical form of Usher syndrome in humans, leading to visual and auditory impairment without the involvement of the central nervous system. In this study, we identified three novel pathogenic variants in ARSG, which segregated recessively with the disease in two families from Portugal. The probands were affected with retinitis pigmentosa and sensorineural hearing loss, generally with an onset of symptoms in their fourth decade of life. Functional experiments showed that these pathogenic variants abolish the sulfatase activity of the Arylsulfatase G enzyme and impede the appropriate lysosomal localization of the protein product, which appears to be retained in the endoplasmic reticulum. Our data enable to definitely confirm that different biallelic variants in ARSG cause a specific deaf-blindness syndrome, by abolishing the activity of the enzyme it encodes.
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Affiliation(s)
- Virginie G Peter
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Institute of Experimental Pathology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Mathieu Quinodoz
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Silvia Sadio
- Department of Ophthalmology, Instituto de Oftalmologia Dr. Gama Pinto, Lisbon, Portugal
| | - Sebastian Held
- Department of Biochemistry, University of Kiel, Kiel, Germany
| | - Márcia Rodrigues
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Marta Soares
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal
| | - Ana Berta Sousa
- Department of Medical Genetics, Hospital Santa Maria, Centro Hospitalar Universitário Lisboa Norte (CHULN), Lisbon Academic Medical Center (CAML), Lisbon, Portugal.,Department of Basic Immunology, Medical Faculty, University of Lisbon, Lisbon, Portugal
| | - Luisa Coutinho Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr. Gama Pinto, Lisbon, Portugal
| | - Markus Damme
- Department of Biochemistry, University of Kiel, Kiel, Germany
| | - Carlo Rivolta
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland.,Department of Ophthalmology, University of Basel, Basel, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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Panagiotou ES, Papathomas T, Nikopoulos K, Koukoula S, Quinodoz M, Rehman AU, Giannopoulos T, Rivolta C, Konstas AG. Management of Full-Thickness Macular Hole in A Genetically Confirmed Case with Usher Syndrome. Ophthalmol Ther 2020; 9:677-684. [PMID: 32566994 PMCID: PMC7406580 DOI: 10.1007/s40123-020-00276-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Indexed: 11/12/2022] Open
Abstract
INTRODUCTION Full-thickness macular hole (FTMH) formation is rarely seen in patients with retinitis pigmentosa (RP) and can have an adverse impact on their residual visual function. The underlying mechanisms are unknown, and clinical experience is limited regarding surgical outcomes. Here, we describe the surgical management of FTMH in a young patient with genetically confirmed Usher syndrome, the most common form of syndromic RP. CASE REPORT A 28-year-old woman presented with blurred vision in her right eye (RE). She had a history of RP and bilateral hearing impairment since childhood. Fundoscopy and spectral-domain optical coherence tomography revealed a FTMH in the RE along with typical RP features bilaterally. After pars plana vitrectomy (PPV) with internal limiting membrane peel and gas tamponade, the FTMH closed. Six months after PPV the patient underwent cataract surgery in the affected eye, and the visual acuity remained stable compared to baseline. The clinical diagnosis of Usher syndrome was genetically confirmed by whole exome sequencing (WES), which revealed the presence of two pathogenic nucleotide variants in trans (compound heterozygosity) in the gene USH2A. CONCLUSION We report a rare case of successful closure of a FTMH in a patient with Usher syndrome. Surgical treatment of FTMH can help preserve the central vision in RP patients, whose peripheral vision is severely affected.
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Affiliation(s)
- Evangelia S Panagiotou
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Thomas Papathomas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Konstantinos Nikopoulos
- Laboratory of Oncogenomics, Department of Hematology, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | | | - Mathieu Quinodoz
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Atta Ur Rehman
- Division of Genetic Medicine, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Theodoros Giannopoulos
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Carlo Rivolta
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University of Basel, Basel, Switzerland
| | - Anastasios G Konstas
- 1st Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
- 3rd Department of Ophthalmology, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece.
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Bastos F, Quinodoz M, Addor MC, Royer-Bertrand B, Fodstad H, Rivolta C, Poloni C, Superti-Furga A, Roulet-Perez E, Lebon S. Childhood neurodegeneration associated with a specific UBTF variant: a new case report and review of the literature. BMC Neurol 2020; 20:17. [PMID: 31931739 PMCID: PMC6958716 DOI: 10.1186/s12883-019-1586-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 12/22/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND A new monogenic neurodegenerative disease affecting ribosomal metabolism has recently been identified in association with a monoallelic UBTF putative gain of function variant (NM_001076683.1:c.628G>A, hg19). Phenotype is consistent among these probands with progressive motor, cognitive, and behavioural regression in early to middle childhood. CASE PRESENTATION We report on a child with this monoallelic UBTF variant who presented with progressive disease including regression, episodes of subacute deterioration during febrile illnesses and a remarkable EEG pattern with a transient pattern of semi-periodic slow waves. CONCLUSIONS This case further supports the phenotype-genotype correlation of neurodegeneration associated with UBTF c.628G>A. Moreover, it brings new insights into the clinical features and EEG that could possibly serve as diagnostic markers of this otherwise nonspecific phenotype.
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Affiliation(s)
- Filipa Bastos
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland. .,Great Ormond Street Hospital Institute of Child Health, University College London, 30 Guilford Steet, London, WC1N 1EH, United Kingdom.
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland
| | - Marie-Claude Addor
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Beryl Royer-Bertrand
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Heidi Fodstad
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Rue du Bugnon 27, 1011, Lausanne, Switzerland.,Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, LE1 7RH, United Kingdom
| | - Claudia Poloni
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland.,Department of Paediatrics, Sion Hospital, Avenue Grand-Champsec 80, 1950, Sion, Switzerland
| | - Andrea Superti-Furga
- Department of Medecine, Division of Genetic Medicine, Lausanne University Hospital (CHUV), Rue du Bugnon 46, 1011, Lausanne, Switzerland
| | - Eliane Roulet-Perez
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland
| | - Sebastien Lebon
- Department woman-mother-child, Unit of Paediatric Neurology and Neurorehabilitation, Lausanne University Hospital (CHUV), Rue du Bugnon 21, 1011, Lausanne, Switzerland
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Bibert S, Piret J, Quinodoz M, Collinet E, Zoete V, Michielin O, Menasria R, Meylan P, Bihl T, Erard V, Fellmann F, Rivolta C, Boivin G, Bochud PY. Herpes simplex encephalitis in adult patients with MASP-2 deficiency. PLoS Pathog 2019; 15:e1008168. [PMID: 31869396 PMCID: PMC6944389 DOI: 10.1371/journal.ppat.1008168] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 01/06/2020] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
We report here two cases of Herpes simplex virus encephalitis (HSE) in adult patients with very rare, previously uncharacterized, non synonymous heterozygous G634R and R203W substitution in mannan-binding lectin serine protease 2 (MASP2), a gene encoding a key protease of the lectin pathway of the complement system. None of the 2 patients had variants in genes involved in the TLR3-interferon signaling pathway. Both MASP2 variants induced functional defects in vitro, including a reduced (R203W) or abolished (G634R) protein secretion, a lost capability to cleave MASP-2 precursor into its active form (G634R) and an in vivo reduced antiviral activity (G634R). In a murine model of HSE, animals deficient in mannose binding lectins (MBL, the main pattern recognition molecule associated with MASP-2) had a decreased survival rate and an increased brain burden of HSV-1 compared to WT C57BL/6J mice. Altogether, these data suggest that MASP-2 deficiency can increase susceptibility to adult HSE. Human herpes virus type 1 (HSV-1) infects a large number of individuals during their life, with manifestations usually limited to mild and self-limiting inflammation of the oral mucosa (cold sore). However, HSV-1 can cause a very severe disease of the brain called Herpes simplex encephalitis (HSE) in 1 out of 250’000–500’000 individuals per year. The reasons why HSV-1 can cause such a devastating disease in a very limited number of individuals are unknown. Increasing evidence suggests that susceptibility to HSE in children can results from genetic variations in the immune system, in particular in a viral detection pathway called the Toll-like receptor 3 (TLR3)–interferon (IFN) axis. Fewer data are available to explain HSE in adult patients. Here, we describe two adult patients with HSE who carry mutations in a gene called mannan-binding lectin serine protease 2 (MASP2), which is part of an immune pathway different from the TLR3-IFN axis, called the lectin pathway of the complement system. We demonstrate that MASP2 mutations induce functional defects in immune defense against HSV-1 that prevent viral replication. Mice deficient in the lectin pathway have higher mortality compared to wild-type mice after HSV-1 infection. Altogether, our study suggests that susceptibility to HSE in adults relies of immune deficiencies that are different from those causing HSE in children.
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Affiliation(s)
- Stéphanie Bibert
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Jocelyne Piret
- Research center in Infectious Diseases, CHU of Quebec and Laval University, Quebec city, Canada
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne Switzerland
| | - Emilie Collinet
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Vincent Zoete
- Ludwig Institute for Cancer research, University of Lausanne, Lausanne, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier Sorge, Génopode, Lausanne, Switzerland
| | - Olivier Michielin
- Ludwig Institute for Cancer research, University of Lausanne, Lausanne, Switzerland
- Molecular Modeling Group, Swiss Institute of Bioinformatics, Quartier Sorge, Génopode, Lausanne, Switzerland
- Department of Oncology, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Rafik Menasria
- Research center in Infectious Diseases, CHU of Quebec and Laval University, Quebec city, Canada
| | - Pascal Meylan
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- Institute of Microbiology, Department of Laboratory Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Titus Bihl
- Canton Hospital of Fribourg, Fribourg, Switzerland
| | | | - Florence Fellmann
- Department of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Guy Boivin
- Research center in Infectious Diseases, CHU of Quebec and Laval University, Quebec city, Canada
| | - Pierre-Yves Bochud
- Infectious Diseases Service, Department of Medicine, University Hospital and University of Lausanne, Lausanne, Switzerland
- * E-mail:
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Moye AR, Bedoni N, Cunningham JG, Sanzhaeva U, Tucker ES, Mathers P, Peter VG, Quinodoz M, Paris LP, Coutinho-Santos L, Camacho P, Purcell MG, Winkelmann AC, Foster JA, Pugacheva EN, Rivolta C, Ramamurthy V. Mutations in ARL2BP, a protein required for ciliary microtubule structure, cause syndromic male infertility in humans and mice. PLoS Genet 2019; 15:e1008315. [PMID: 31425546 PMCID: PMC6715254 DOI: 10.1371/journal.pgen.1008315] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 08/29/2019] [Accepted: 07/17/2019] [Indexed: 12/30/2022] Open
Abstract
Cilia are evolutionarily conserved hair-like structures with a wide spectrum of key biological roles, and their dysfunction has been linked to a growing class of genetic disorders, known collectively as ciliopathies. Many strides have been made towards deciphering the molecular causes for these diseases, which have in turn expanded the understanding of cilia and their functional roles. One recently-identified ciliary gene is ARL2BP, encoding the ADP-Ribosylation Factor Like 2 Binding Protein. In this study, we have identified multiple ciliopathy phenotypes associated with mutations in ARL2BP in human patients and in a mouse knockout model. Our research demonstrates that spermiogenesis is impaired, resulting in abnormally shaped heads, shortened and mis-assembled sperm tails, as well as in loss of axonemal doublets. Additional phenotypes in the mouse included enlarged ventricles of the brain and situs inversus. Mouse embryonic fibroblasts derived from knockout animals revealed delayed depolymerization of primary cilia. Our results suggest that ARL2BP is required for the structural maintenance of cilia as well as of the sperm flagellum, and that its deficiency leads to syndromic ciliopathy. The flagellated tails of sperm cells require a stringent developmental process that is essential for motility and fertility. The components that comprise the sperm tail assemble in regulated steps with protein processing, transport, and structural assembly dependent on each other for sperm tail maturity. In this work, we have identified ARL2BP, a previously retinal-associated protein, to be essential for sperm tail development and assembly. We show that without functional ARL2BP in humans or mice, sperm tails fail to develop, starting with the assembly of the core microtubular structure within the tail. Loss of ARL2BP also effects other ciliated cells, indicating a unique role for ARL2BP in ciliary microtubule formation. This research on ARL2BP provides further understanding on the links between vision and fertility. This work also demonstrates how genomic studies for human patients and murine models can coincide to provide greater insight into disease.
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Affiliation(s)
- Abigail R. Moye
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Nicola Bedoni
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Jessica G. Cunningham
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Urikhan Sanzhaeva
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Eric S. Tucker
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Peter Mathers
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
| | - Virginie G. Peter
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Liliana P. Paris
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Luísa Coutinho-Santos
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Pedro Camacho
- Department of Ophthalmology, Instituto de Oftalmologia Dr Gama Pinto, Lisbon, Portugal
| | - Madeleine G. Purcell
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - Abbie C. Winkelmann
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - James A. Foster
- Department of Biology, Randolph-Macon College, Ashland, VA, United States of America
| | - Elena N. Pugacheva
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
- Clinical Research Center, Institute of Molecular and Clinical Ophthalmology Basel (IOB), Basel, Switzerland
- Department of Ophthalmology, University Hospital Basel, Switzerland
- * E-mail: (CR); (VR)
| | - Visvanathan Ramamurthy
- Department of Ophthalmology, West Virginia University, Morgantown, United States of America
- Department of Biochemistry, West Virginia University, Morgantown, United States of America
- Rockefeller Neurosciences Institute, West Virginia University, Morgantown, WV, United States of America
- * E-mail: (CR); (VR)
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Nikopoulos K, Cisarova K, Quinodoz M, Koskiniemi-Kuendig H, Miyake N, Farinelli P, Rehman AU, Khan MI, Prunotto A, Akiyama M, Kamatani Y, Terao C, Miya F, Ikeda Y, Ueno S, Fuse N, Murakami A, Wada Y, Terasaki H, Sonoda KH, Ishibashi T, Kubo M, Cremers FPM, Kutalik Z, Matsumoto N, Nishiguchi KM, Nakazawa T, Rivolta C. A frequent variant in the Japanese population determines quasi-Mendelian inheritance of rare retinal ciliopathy. Nat Commun 2019; 10:2884. [PMID: 31253780 PMCID: PMC6599023 DOI: 10.1038/s41467-019-10746-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 09/21/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Hereditary retinal degenerations (HRDs) are Mendelian diseases characterized by progressive blindness and caused by ultra-rare mutations. In a genomic screen of 331 unrelated Japanese patients, we identify a disruptive Alu insertion and a nonsense variant (p.Arg1933*) in the ciliary gene RP1, neither of which are rare alleles in Japan. p.Arg1933* is almost polymorphic (frequency = 0.6%, amongst 12,000 individuals), does not cause disease in homozygosis or heterozygosis, and yet is significantly enriched in HRD patients (frequency = 2.1%, i.e., a 3.5-fold enrichment; p-value = 9.2 × 10-5). Familial co-segregation and association analyses show that p.Arg1933* can act as a Mendelian mutation in trans with the Alu insertion, but might also associate with disease in combination with two alleles in the EYS gene in a non-Mendelian pattern of heredity. Our results suggest that rare conditions such as HRDs can be paradoxically determined by relatively common variants, following a quasi-Mendelian model linking monogenic and complex inheritance.
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Affiliation(s)
- Konstantinos Nikopoulos
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
- Service of Medical Genetics, Lausanne University Hospital (CHUV), 1011, Lausanne, Switzerland
| | - Katarina Cisarova
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Mathieu Quinodoz
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Hanna Koskiniemi-Kuendig
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Pietro Farinelli
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Atta Ur Rehman
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Muhammad Imran Khan
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Andrea Prunotto
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland
| | - Masato Akiyama
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, 113-8510, Japan
| | - Yasuhiro Ikeda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Shinji Ueno
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Nobuo Fuse
- Department of Integrative Genomics, Tohoku Medical Megabank Organization, Sendai, 980-8573, Japan
| | - Akira Murakami
- Department of Ophthalmology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan
| | - Yuko Wada
- Yuko Wada Eye Clinic, Sendai, 980-0011, Japan
| | - Hiroko Terasaki
- Department of Ophthalmology, Nagoya University Graduate School of Medicine, Nagoya, 466-8550, Japan
| | - Koh-Hei Sonoda
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Tatsuro Ishibashi
- Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan
| | - Frans P M Cremers
- Department of Human Genetics, Radboud University Medical Center, 6500 HB, Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 GA, Nijmegen, The Netherlands
| | - Zoltán Kutalik
- Institute of Social and Preventive Medicine, Lausanne University Hospital, 1011, Lausanne, Switzerland
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, 236-0004, Japan
| | - Koji M Nishiguchi
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
| | - Toru Nakazawa
- Department of Ophthalmology, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
- Department of Advanced Ophthalmic Medicine, Tohoku University Graduate School of Medicine, Sendai, 980-8574, Japan
| | - Carlo Rivolta
- Unit of Medical Genetics, Department of Computational Biology, University of Lausanne, 1015, Lausanne, Switzerland.
- Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK.
- Institute of Molecular and Clinical Ophthalmology Basel (IOB), 4031, Basel, Switzerland.
- University of Basel, 4001, Basel, Switzerland.
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Peter VG, Nikopoulos K, Quinodoz M, Granse L, Farinelli P, Superti-Furga A, Andréasson S, Rivolta C. A novel missense variant in IDH3A causes autosomal recessive retinitis pigmentosa. Ophthalmic Genet 2019; 40:177-181. [DOI: 10.1080/13816810.2019.1605391] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Virginie G. Peter
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Konstantinos Nikopoulos
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Lotta Granse
- Department of Ophthalmology, University of Lund, Lund, Sweden
| | - Pietro Farinelli
- Department of Biology, University of Copenhagen, Copenhagen, OE, Denmark
| | - Andrea Superti-Furga
- Service of Medical Genetics, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Sten Andréasson
- Department of Ophthalmology, University of Lund, Lund, Sweden
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
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40
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Fregni G, Quinodoz M, Möller E, Vuille J, Galland S, Fusco C, Martin P, Letovanec I, Provero P, Rivolta C, Riggi N, Stamenkovic I. Reciprocal modulation of mesenchymal stem cells and tumor cells promotes lung cancer metastasis. EBioMedicine 2018; 29:128-145. [PMID: 29503225 PMCID: PMC5925622 DOI: 10.1016/j.ebiom.2018.02.017] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 02/14/2018] [Accepted: 02/19/2018] [Indexed: 12/15/2022] Open
Abstract
Metastasis is a multi-step process in which direct crosstalk between cancer cells and their microenvironment plays a key role. Here, we assessed the effect of paired tumor-associated and normal lung tissue mesenchymal stem cells (MSCs) on the growth and dissemination of primary human lung carcinoma cells isolated from the same patients. We show that the tumor microenvironment modulates MSC gene expression and identify a four-gene MSC signature that is functionally implicated in promoting metastasis. We also demonstrate that tumor-associated MSCs induce the expression of genes associated with an aggressive phenotype in primary lung cancer cells and selectively promote their dissemination rather than local growth. Our observations provide insight into mechanisms by which the stroma promotes lung cancer metastasis. Distinct gene expression profiles distinguish normal lung and tumor-associated MSCs. MSCs induce EMT- and hypoxia-related genes in primary tumor cells and promote their metastatic potential. A 4-gene T-MSC signature is involved in MSC-induced metastasis promotion.
The tumor microenvironment, which includes mesenchymal stem cells (MSCs) among many other stromal cell types, plays a fundamental role in cancer metastasis. Although MSCs are suggested to participate in tumor progression, most studies thus far have been performed on bone marrow-derived MSCs and cancer cell lines. Using primary human pulmonary MSCs and paired lung cancer cells, we show that tumor cells modulate MSCs to acquire properties, including a four-gene signature, which allow them to promote tumor dissemination. Our results provide insight into the mutual cancer cell-stromal cell modulation that drives tumor dissemination.
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Affiliation(s)
- Giulia Fregni
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011, Switzerland
| | - Emely Möller
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Joanna Vuille
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Sabine Galland
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Carlo Fusco
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Patricia Martin
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Igor Letovanec
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Paolo Provero
- Center for Translational Genomics and Bioinformatics, San Raffaele Scientific Institute, IRCCS, Milan20132, Italy; Dept. of Molecular Biotechnology and Health Sciences, University of Turin, 10126 Turin, Italy
| | - Carlo Rivolta
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011, Switzerland; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 9HN, UK
| | - Nicolo Riggi
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland
| | - Ivan Stamenkovic
- Experimental Pathology Service, CHUV and University of Lausanne, 1011, Switzerland.
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Astuti GDN, van den Born LI, Khan MI, Hamel CP, Bocquet B, Manes G, Quinodoz M, Ali M, Toomes C, McKibbin M, El-Asrag ME, Haer-Wigman L, Inglehearn CF, Black GCM, Hoyng CB, Cremers FPM, Roosing S. Identification of Inherited Retinal Disease-Associated Genetic Variants in 11 Candidate Genes. Genes (Basel) 2018; 9:genes9010021. [PMID: 29320387 PMCID: PMC5793174 DOI: 10.3390/genes9010021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 12/31/2017] [Accepted: 01/03/2018] [Indexed: 01/09/2023] Open
Abstract
Inherited retinal diseases (IRDs) display an enormous genetic heterogeneity. Whole exome sequencing (WES) recently identified genes that were mutated in a small proportion of IRD cases. Consequently, finding a second case or family carrying pathogenic variants in the same candidate gene often is challenging. In this study, we searched for novel candidate IRD gene-associated variants in isolated IRD families, assessed their causality, and searched for novel genotype-phenotype correlations. Whole exome sequencing was performed in 11 probands affected with IRDs. Homozygosity mapping data was available for five cases. Variants with minor allele frequencies ≤ 0.5% in public databases were selected as candidate disease-causing variants. These variants were ranked based on their: (a) presence in a gene that was previously implicated in IRD; (b) minor allele frequency in the Exome Aggregation Consortium database (ExAC); (c) in silico pathogenicity assessment using the combined annotation dependent depletion (CADD) score; and (d) interaction of the corresponding protein with known IRD-associated proteins. Twelve unique variants were found in 11 different genes in 11 IRD probands. Novel autosomal recessive and dominant inheritance patterns were found for variants in Small Nuclear Ribonucleoprotein U5 Subunit 200 (SNRNP200) and Zinc Finger Protein 513 (ZNF513), respectively. Using our pathogenicity assessment, a variant in DEAH-Box Helicase 32 (DHX32) was the top ranked novel candidate gene to be associated with IRDs, followed by eight medium and lower ranked candidate genes. The identification of candidate disease-associated sequence variants in 11 single families underscores the notion that the previously identified IRD-associated genes collectively carry > 90% of the defects implicated in IRDs. To identify multiple patients or families with variants in the same gene and thereby provide extra proof for pathogenicity, worldwide data sharing is needed.
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Affiliation(s)
- Galuh D. N. Astuti
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Radboud Institute for Molecular Life Sciences, Radboud University, 6525 GA Nijmegen, The Netherlands
| | | | - M. Imran Khan
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Christian P. Hamel
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Béatrice Bocquet
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
- CHRU, Genetics of Sensory Diseases, 34295 Montpellier, France
| | - Gaël Manes
- Institut National de la Santé et de la Recherche Médicale, Institute for Neurosciences of Montpellier, 34080 Montpellier, France; (B.B.); (G.M.)
- University of Montpellier, 34090 Montpellier, France
| | - Mathieu Quinodoz
- Department of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1015 Lausanne, Switzerland;
| | - Manir Ali
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Carmel Toomes
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Martin McKibbin
- Department of Ophthalmology, St. James’s University Hospital, LS9 7TF Leeds, UK;
| | - Mohammed E. El-Asrag
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
- Department of Zoology, Faculty of Science, Benha University, 13511 Benha, Egypt
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
| | - Chris F. Inglehearn
- Section of Ophthalmology & Neuroscience, Leeds Institute of Biomedical & Clinical Sciences, University of Leeds, St. James’s University Hospital, LS9 7TF Leeds, UK; (M.A.); (C.T.); (M.E.E.-A.); (C.F.I.)
| | - Graeme C. M. Black
- Centre for Genomic Medicine, St. Mary’s Hospital, Manchester Academic Health Science Centre, University of Manchester, M13 9PL Manchester, UK;
| | - Carel B. Hoyng
- Department of Ophthalmology, Radboud University Medical Center, 6525 EX Nijmegen, The Netherlands;
| | - Frans P. M. Cremers
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
| | - Susanne Roosing
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (G.D.N.A.); (M.I.K.); (L.H.-W.); (F.P.M.C.)
- Donders Institute for Brain, Cognition and Behaviour, Radboud University Nijmegen, 6525 EN Nijmegen, The Netherlands
- Correspondence: ; Tel.: +31-(0)24-365-5266
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Quinodoz M, Royer-Bertrand B, Cisarova K, Di Gioia SA, Superti-Furga A, Rivolta C. DOMINO: Using Machine Learning to Predict Genes Associated with Dominant Disorders. Am J Hum Genet 2017; 101:623-629. [PMID: 28985496 DOI: 10.1016/j.ajhg.2017.09.001] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 09/01/2017] [Indexed: 10/18/2022] Open
Abstract
In contrast to recessive conditions with biallelic inheritance, identification of dominant (monoallelic) mutations for Mendelian disorders is more difficult, because of the abundance of benign heterozygous variants that act as massive background noise (typically, in a 400:1 excess ratio). To reduce this overflow of false positives in next-generation sequencing (NGS) screens, we developed DOMINO, a tool assessing the likelihood for a gene to harbor dominant changes. Unlike commonly-used predictors of pathogenicity, DOMINO takes into consideration features that are the properties of genes, rather than of variants. It uses a machine-learning approach to extract discriminant information from a broad array of features (N = 432), including: genomic data, intra-, and interspecies conservation, gene expression, protein-protein interactions, protein structure, etc. DOMINO's iterative architecture includes a training process on 985 genes with well-established inheritance patterns for Mendelian conditions, and repeated cross-validation that optimizes its discriminant power. When validated on 99 newly-discovered genes with pathogenic mutations, the algorithm displays an excellent final performance, with an area under the curve (AUC) of 0.92. Furthermore, unsupervised analysis by DOMINO of real sets of NGS data from individuals with intellectual disability or epilepsy correctly recognizes known genes and predicts 9 new candidates, with very high confidence. In summary, DOMINO is a robust and reliable tool that can infer dominance of candidate genes with high sensitivity and specificity, making it a useful complement to any NGS pipeline dealing with the analysis of the morbid human genome.
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Kousathanas A, Leuenberger C, Helfer J, Quinodoz M, Foll M, Wegmann D. Likelihood-Free Inference in High-Dimensional Models. Genetics 2016; 203:893-904. [PMID: 27052569 PMCID: PMC4896201 DOI: 10.1534/genetics.116.187567] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 04/04/2016] [Indexed: 11/18/2022] Open
Abstract
Methods that bypass analytical evaluations of the likelihood function have become an indispensable tool for statistical inference in many fields of science. These so-called likelihood-free methods rely on accepting and rejecting simulations based on summary statistics, which limits them to low-dimensional models for which the value of the likelihood is large enough to result in manageable acceptance rates. To get around these issues, we introduce a novel, likelihood-free Markov chain Monte Carlo (MCMC) method combining two key innovations: updating only one parameter per iteration and accepting or rejecting this update based on subsets of statistics approximately sufficient for this parameter. This increases acceptance rates dramatically, rendering this approach suitable even for models of very high dimensionality. We further derive that for linear models, a one-dimensional combination of statistics per parameter is sufficient and can be found empirically with simulations. Finally, we demonstrate that our method readily scales to models of very high dimensionality, using toy models as well as by jointly inferring the effective population size, the distribution of fitness effects (DFE) of segregating mutations, and selection coefficients for each locus from data of a recent experiment on the evolution of drug resistance in influenza.
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Affiliation(s)
- Athanasios Kousathanas
- Department of Biology and Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
| | | | - Jonas Helfer
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge Massachusetts 02139
| | - Mathieu Quinodoz
- Department of Computational Biology, University of Lausanne, 1200 Lausanne, Switzerland
| | - Matthieu Foll
- International Agency for Research on Cancer, 69372 Lyon, France
| | - Daniel Wegmann
- Department of Biology and Biochemistry, University of Fribourg, 1700 Fribourg, Switzerland Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
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Quinodoz M, Gobet C, Naef F, Gustafson KB. Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters. Genome Biol 2014; 15:R85. [PMID: 24972996 PMCID: PMC4197824 DOI: 10.1186/gb-2014-15-6-r85] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 06/12/2014] [Indexed: 01/15/2023] Open
Abstract
Background In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. Results Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3. Conclusions We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.
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Slosman D, Fréneaux E, Quinodoz M, Helg C. 6000 ORAL Quality assessment of FDG PET imaging in clinical trials: definition of standard indicators and longitudinal assessment in patients treated for lymphoma. EJC Suppl 2007. [DOI: 10.1016/s1359-6349(07)71291-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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Quinodoz P, Quinodoz M, Nussbaum JL, Montandon D, Pittet B. Barium sulphate and soft-tissue radiology: allying the old and the new for the investigation of animal cutaneous microcirculation. Br J Plast Surg 2002; 55:664-7. [PMID: 12550120 DOI: 10.1054/bjps.2002.3949] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The study of microcirculation using angiography is essential to the advancement of flap and angiogenesis research in plastic surgery. Until the mid-1980s, barium sulphate was the most commonly used contrast material, although it did not provide optimal visualisation of the vascular tree. In 1986, a new technique using lead oxide was proposed, which permitted very high-quality imaging and rapidly became the technique of choice, despite its high toxicity. We reconsider the former technique of barium-sulphate injection and combine it with soft-tissue radiology using mammographic film to achieve a radiological definition similar to that obtained with lead oxide, and discuss the advantages and disadvantages of the two methods. We conclude that barium sulphate and the use of mammographic film is an accurate, simple and non-toxic method of analysing the cutaneous circulation in small animals.
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Affiliation(s)
- P Quinodoz
- Division of Plastic and Reconstructive Surgery, Department of Surgery, Geneva University Hospitals, Geneva, Switzerland
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Bieri S, Quinodoz M, Balmer-Majno S, Kurtz J. 684 Is postoperative mammography prior to definitive breast irradiation therapy useful? Eur J Cancer 1995. [DOI: 10.1016/0959-8049(95)95934-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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