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Vong KI, Lee S, Au KS, Crowley TB, Capra V, Martino J, Haller M, Araújo C, Machado HR, George R, Gerding B, James KN, Stanley V, Jiang N, Alu K, Meave N, Nidhiry AS, Jiwani F, Tang I, Nisal A, Jhamb I, Patel A, Patel A, McEvoy-Venneri J, Barrows C, Shen C, Ha YJ, Howarth R, Strain M, Ashley-Koch AE, Azam M, Mumtaz S, Bot GM, Finnell RH, Kibar Z, Marwan AI, Melikishvili G, Meltzer HS, Mutchinick OM, Stevenson DA, Mroczkowski HJ, Ostrander B, Schindewolf E, Moldenhauer J, Zackai EH, Emanuel BS, Garcia-Minaur S, Nowakowska BA, Stevenson RE, Zaki MS, Northrup H, McNamara HK, Aldinger KA, Phelps IG, Deng M, Glass IA, Morrow B, McDonald-McGinn DM, Sanna-Cherchi S, Lamb DJ, Gleeson JG. Risk of meningomyelocele mediated by the common 22q11.2 deletion. Science 2024; 384:584-590. [PMID: 38696583 DOI: 10.1126/science.adl1624] [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: 10/08/2023] [Accepted: 03/27/2024] [Indexed: 05/04/2024]
Abstract
Meningomyelocele is one of the most severe forms of neural tube defects (NTDs) and the most frequent structural birth defect of the central nervous system. We assembled the Spina Bifida Sequencing Consortium to identify causes. Exome and genome sequencing of 715 parent-offspring trios identified six patients with chromosomal 22q11.2 deletions, suggesting a 23-fold increased risk compared with the general population. Furthermore, analysis of a separate 22q11.2 deletion cohort suggested a 12- to 15-fold increased NTD risk of meningomyelocele. The loss of Crkl, one of several neural tube-expressed genes within the minimal deletion interval, was sufficient to replicate NTDs in mice, where both penetrance and expressivity were exacerbated by maternal folate deficiency. Thus, the common 22q11.2 deletion confers substantial meningomyelocele risk, which is partially alleviated by folate supplementation.
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Affiliation(s)
- Keng Ioi Vong
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Sangmoon Lee
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kit Sing Au
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - T Blaine Crowley
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Valeria Capra
- Genomics and Clinical Genetics Unit, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | - Jeremiah Martino
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Meade Haller
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
| | - Camila Araújo
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Hélio R Machado
- Department of Surgery and Anatomy, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14040-900, Brazil
| | - Renee George
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Bryn Gerding
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kiely N James
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Valentina Stanley
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Nan Jiang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Kameron Alu
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Naomi Meave
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Anna S Nidhiry
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Fiza Jiwani
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Isaac Tang
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ashna Nisal
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Ishani Jhamb
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Arzoo Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Aakash Patel
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Jennifer McEvoy-Venneri
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Chelsea Barrows
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Celina Shen
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Yoo-Jin Ha
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Robyn Howarth
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
| | - Madison Strain
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | | | - Matloob Azam
- Pediatrics and Child Neurology, Wah Medical College, Wah Cantt, Punjab 47000, Pakistan
| | - Sara Mumtaz
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Punjab 46000, Pakistan
| | - Gyang Markus Bot
- Neurosurgery Division, Department of Surgery, Jos University Teaching Hospital, Jos 930105, Nigeria
| | - Richard H Finnell
- Center for Precision Environmental Health, Departments of Molecular and Human Genetics, Molecular and Cellular Biology and Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zoha Kibar
- Department of Neurosciences, University of Montreal and CHU Sainte Justine Research Center, Montreal, QC H3T 1C5, Canada
| | - Ahmed I Marwan
- Division of Pediatric Surgery, University of Colorado School of Medicine, Children's Hospital of Colorado, Colorado Fetal Care Center, Aurora, CO 80045, USA
| | - Gia Melikishvili
- Department of Pediatrics, MediClubGeorgia Medical Center, Tbilisi 0160, Georgia
| | - Hal S Meltzer
- Department of Neurosurgery, University of California San Diego, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Osvaldo M Mutchinick
- Department of Genetics, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, 14080 Mexico City, Mexico
| | - David A Stevenson
- Division of Medical Genetics, Stanford University, Palo Alto, CA 94305, USA
| | - Henry J Mroczkowski
- Division of Medical Genetics, University of Tennessee Health Science Campus, Memphis, TN 38163, USA
| | - Betsy Ostrander
- Division of Pediatric Neurology, Primary Children's Hospital, University of Utah, Salt Lake City, UT 84113, USA
| | - Erica Schindewolf
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Julie Moldenhauer
- Center for Fetal Diagnosis and Treatment, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Elaine H Zackai
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Beverly S Emanuel
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sixto Garcia-Minaur
- Clinical Genetics Section, Institute of Medical and Molecular Genetics, University Hospital La Paz, 28046 Madrid, Spain
| | - Beata A Nowakowska
- Department of Medical Genetics, Institute of Mother and Child, Kasprzaka, 01-211 Warsaw, Poland
| | - Roger E Stevenson
- JC Self Research Institute of Human Genetics, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Maha S Zaki
- Clinical Genetics Department, Human Genetics and Genome Research Division, National Research Centre, Cairo 12311, Egypt
| | - Hope Northrup
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston (UTHealth) and Children's Memorial Hermann Hospital, Houston, TX 77030, USA
| | - Hanna K McNamara
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
- Department of Neurology, University of Washington, Seattle, WA 98105, USA
| | - Ian G Phelps
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Mei Deng
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Ian A Glass
- Departments of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Bernice Morrow
- Division of Translational Genetics, Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Donna M McDonald-McGinn
- 22q and You Center, Division of Human Genetics, Children's Hospital of Philadelphia and Department of Pediatrics, Perelman School of Medicine of the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Human Biology and Medical Genetics, Sapienza University, 00185-Rome RM, Italy
| | - Simone Sanna-Cherchi
- Division of Nephrology, Department of Medicine, Columbia University, NY 10027, USA
| | - Dolores J Lamb
- Center for Reproductive Medicine, Department of Molecular and Cellular Biology and Scott Department of Urology, Baylor College of Medicine, TX 77030, USA
- Department of Urology, Center for Reproductive Genomics, Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Joseph G Gleeson
- Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
- Rady Children's Institute for Genomic Medicine, San Diego, CA 92123, USA
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Aldinger KA, Thomson Z, Phelps IG, Haldipur P, Deng M, Timms AE, Hirano M, Santpere G, Roco C, Rosenberg AB, Lorente-Galdos B, Gulden FO, O'Day D, Overman LM, Lisgo SN, Alexandre P, Sestan N, Doherty D, Dobyns WB, Seelig G, Glass IA, Millen KJ. Spatial and cell type transcriptional landscape of human cerebellar development. Nat Neurosci 2021; 24:1163-1175. [PMID: 34140698 PMCID: PMC8338761 DOI: 10.1038/s41593-021-00872-y] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [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: 07/06/2020] [Accepted: 05/10/2021] [Indexed: 02/05/2023]
Abstract
The human neonatal cerebellum is one-fourth of its adult size yet contains the blueprint required to integrate environmental cues with developing motor, cognitive and emotional skills into adulthood. Although mature cerebellar neuroanatomy is well studied, understanding of its developmental origins is limited. In this study, we systematically mapped the molecular, cellular and spatial composition of human fetal cerebellum by combining laser capture microscopy and SPLiT-seq single-nucleus transcriptomics. We profiled functionally distinct regions and gene expression dynamics within cell types and across development. The resulting cell atlas demonstrates that the molecular organization of the cerebellar anlage recapitulates cytoarchitecturally distinct regions and developmentally transient cell types that are distinct from the mouse cerebellum. By mapping genes dominant for pediatric and adult neurological disorders onto our dataset, we identify relevant cell types underlying disease mechanisms. These data provide a resource for probing the cellular basis of human cerebellar development and disease.
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Affiliation(s)
- Kimberly A Aldinger
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
| | - Zachary Thomson
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Ian G Phelps
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Parthiv Haldipur
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Mei Deng
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Andrew E Timms
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA, USA
| | - Matthew Hirano
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Gabriel Santpere
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
- Neurogenomics Group, Research Programme on Biomedical Informatics, Hospital del Mar Medical Research Institute, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Charles Roco
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Alexander B Rosenberg
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
| | - Belen Lorente-Galdos
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Forrest O Gulden
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Diana O'Day
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Lynne M Overman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Steven N Lisgo
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Paula Alexandre
- University College London Great Ormond Street Institute of Child Health, London, UK
| | - Nenad Sestan
- Department of Neuroscience and Kavli Institute for Neuroscience, Yale School of Medicine, New Haven, CT, USA
| | - Dan Doherty
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - William B Dobyns
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA, USA
| | - Georg Seelig
- Department of Electrical and Computer Engineering, University of Washington, Seattle, WA, USA
- School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Ian A Glass
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Kathleen J Millen
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, USA.
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3
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Epting D, Senaratne LDS, Ott E, Holmgren A, Sumathipala D, Larsen SM, Wallmeier J, Bracht D, Frikstad KM, Crowley S, Sikiric A, Barøy T, Käsmann‐Kellner B, Decker E, Decker C, Bachmann N, Patzke S, Phelps IG, Katsanis N, Giles R, Schmidts M, Zucknick M, Lienkamp SS, Omran H, Davis EE, Doherty D, Strømme P, Frengen E, Bergmann C, Misceo D. Loss of CBY1 results in a ciliopathy characterized by features of Joubert syndrome. Hum Mutat 2020; 41:2179-2194. [PMID: 33131181 PMCID: PMC7756669 DOI: 10.1002/humu.24127] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/31/2020] [Accepted: 10/04/2020] [Indexed: 12/17/2022]
Abstract
Ciliopathies are clinically and genetically heterogeneous diseases. We studied three patients from two independent families presenting with features of Joubert syndrome: abnormal breathing pattern during infancy, developmental delay/intellectual disability, cerebellar ataxia, molar tooth sign on magnetic resonance imaging scans, and polydactyly. We identified biallelic loss-of-function (LOF) variants in CBY1, segregating with the clinical features of Joubert syndrome in the families. CBY1 localizes to the distal end of the mother centriole, contributing to the formation and function of cilia. In accordance with the clinical and mutational findings in the affected individuals, we demonstrated that depletion of Cby1 in zebrafish causes ciliopathy-related phenotypes. Levels of CBY1 transcript were found reduced in the patients compared with controls, suggesting degradation of the mutated transcript through nonsense-mediated messenger RNA decay. Accordingly, we could detect CBY1 protein in fibroblasts from controls, but not from patients by immunofluorescence. Furthermore, we observed reduced ability to ciliate, increased ciliary length, and reduced levels of the ciliary proteins AHI1 and ARL13B in patient fibroblasts. Our data show that CBY1 LOF-variants cause a ciliopathy with features of Joubert syndrome.
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Affiliation(s)
- Daniel Epting
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
| | | | - Elisabeth Ott
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
| | - Asbjørn Holmgren
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Dulika Sumathipala
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Selma M. Larsen
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Julia Wallmeier
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Diana Bracht
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Kari‐Anne M. Frikstad
- Department of Radiation Biology, Division of Cancer Medicine, Surgery and Transplantation, Institute for Cancer ResearchOslo University Hospitals–Norwegian Radium HospitalOsloNorway
| | - Suzanne Crowley
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Alma Sikiric
- Department of NeurohabilitationOslo University HospitalOsloNorway
| | - Tuva Barøy
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Barbara Käsmann‐Kellner
- Section of Pediatric Ophthalmology and Low Vision, Department of OphthalmologyUniversity of SaarlandHomburgGermany
| | - Eva Decker
- Medizinische Genetik MainzLimbach GeneticsMainzGermany
| | | | | | - Sebastian Patzke
- Department of Radiation Biology, Division of Cancer Medicine, Surgery and Transplantation, Institute for Cancer ResearchOslo University Hospitals–Norwegian Radium HospitalOsloNorway
| | - Ian G. Phelps
- Department of Pediatrics, Seattle Children's Research InstituteUniversity of WashingtonSeattleWashingtonUSA
| | - Nicholas Katsanis
- Center for Human Disease ModelingDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Rachel Giles
- Department of Nephrology and HypertensionUniversity Medical Center UtrechtUtrechtThe Netherlands
| | - Miriam Schmidts
- International Radboud Institute for Molecular Life SciencesRadboud University NijmegenNijmegenThe Netherlands
| | - Manuela Zucknick
- Oslo Centre for Biostatistics and Epidemiology, Institute for Basic Medical SciencesUniversity of OsloOsloNorway
| | | | - Heymut Omran
- Klinik für Kinder‐ und JugendmedizinUniversitätsklinikum MünsterMünsterGermany
| | - Erica E. Davis
- Center for Human Disease ModelingDuke University Medical CenterDurhamNorth CarolinaUSA
| | - Dan Doherty
- Department of Pediatrics, Seattle Children's Research InstituteUniversity of WashingtonSeattleWashingtonUSA
| | - Petter Strømme
- Division of Pediatric and Adolescent MedicineOslo University Hospital, University of OsloOsloNorway
| | - Eirik Frengen
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
| | - Carsten Bergmann
- Department of Medicine IV, Faculty of MedicineMedical Center‐University of FreiburgFreiburgGermany
- Medizinische Genetik MainzLimbach GeneticsMainzGermany
| | - Doriana Misceo
- Department of Medical GeneticsOslo University Hospital, University of OsloOsloNorway
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4
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Phelps IG, Dempsey JC, Grout ME, Isabella CR, Tully HM, Doherty D, Bachmann-Gagescu R. Interpreting the clinical significance of combined variants in multiple recessive disease genes: systematic investigation of Joubert syndrome yields little support for oligogenicity. Genet Med 2018; 20:223-233. [PMID: 28771248 PMCID: PMC5797514 DOI: 10.1038/gim.2017.94] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 01/18/2017] [Accepted: 05/19/2017] [Indexed: 01/11/2023] Open
Abstract
PurposeNext-generation sequencing (NGS) often identifies multiple rare predicted-deleterious variants (RDVs) in different genes associated with a recessive disorder in a given patient. Such variants have been proposed to contribute to digenicity/oligogenicity or "triallelism" or to act as genetic modifiers.MethodsUsing the recessive ciliopathy Joubert syndrome (JBTS) as a model, we investigated these possibilities systematically, relying on NGS of known JBTS genes in a large JBTS and two control cohorts.Results65% of affected individuals had a recessive genetic cause, while 4.9% were candidates for di-/oligogenicity, harboring heterozygous RDVs in two or more genes, compared with 4.2-8% in controls (P = 0.66-0.21). Based on Exome Aggregation Consortium (ExAC) allele frequencies, the probability of cumulating RDVs in any two JBTS genes is 9.3%. We found no support for triallelism, as no unaffected siblings carried the same biallelic RDVs as their affected relative. Sixty percent of individuals sharing identical causal RDVs displayed phenotypic discordance. Although 38% of affected individuals harbored RDVs in addition to the causal mutations, their presence did not correlate with phenotypic severity.ConclusionOur data offer little support for triallelism or digenicity/oligogenicity as clinically relevant inheritance modes in JBTS. While phenotypic discordance supports the existence of genetic modifiers, identifying clinically relevant modifiers remains challenging.
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Affiliation(s)
- Ian G. Phelps
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Megan E. Grout
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | | | - Hannah M. Tully
- Department of Neurology, University of Washington, Seattle, Washington
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington
| | - Ruxandra Bachmann-Gagescu
- Institute of Medical Genetics, University of Zurich, Switzerland
- Institute of Molecular Life Sciences, University of Zurich, Switzerland
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5
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Van De Weghe JC, Rusterholz TD, Latour B, Grout ME, Aldinger KA, Shaheen R, Dempsey JC, Maddirevula S, Cheng YHH, Phelps IG, Gesemann M, Goel H, Birk OS, Alanzi T, Rawashdeh R, Khan AO, Bamshad MJ, Nickerson DA, Neuhauss SC, Dobyns WB, Alkuraya FS, Roepman R, Bachmann-Gagescu R, Doherty D, Doherty D. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Am J Hum Genet 2017. [PMID: 28625504 DOI: 10.1016/j.ajhg.2017.05.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
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6
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Dempsey JC, Phelps IG, Bachmann-Gagescu R, Glass IA, Tully HM, Doherty D. Mortality in Joubert syndrome. Am J Med Genet A 2017; 173:1237-1242. [PMID: 28371402 DOI: 10.1002/ajmg.a.38158] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 08/04/2016] [Accepted: 01/08/2017] [Indexed: 11/05/2022]
Abstract
Joubert syndrome (JS) is a rare, recessively inherited neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. Little is known about mortality in affected individuals. Identifying the timing and causes of death will allow for development of healthcare guidelines for families and providers and, thus, help to prolong and improve the lives of patients with JS. We evaluated information on 40 deceased individuals with JS to characterize age and cause of death. We compared this population with 525 living individuals with JS to estimate associations between risk of death and extra-neurological features. Genetic causes were examined in both groups. Mean age of death in this cohort was 7.2 years, and the most prevalent causes of death were respiratory failure (35%), particularly in individuals younger than 6 years, and kidney failure (37.5%), which was more common in older individuals. We identified possible associations between risk of death and kidney disease, liver fibrosis, polydactyly, occipital encephalocele, and genetic cause. This work highlights factors (genetic cause, extra-neurological organ involvement, and other malformations) likely to be associated with higher risk of mortality in JS, which should prompt increased monitoring for respiratory issues, kidney disease, and liver fibrosis.
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Affiliation(s)
| | - Ian G Phelps
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Ruxandra Bachmann-Gagescu
- Institute for Molecular Life Sciences and Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Ian A Glass
- Department of Pediatrics, University of Washington, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
| | - Hannah M Tully
- Seattle Children's Research Institute, Seattle, Washington.,Department of Neurology, University of Washington, Seattle, Washington
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington.,Seattle Children's Research Institute, Seattle, Washington
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7
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Kane MS, Davids M, Bond MR, Adams CJ, Grout ME, Phelps IG, O'Day DR, Dempsey JC, Li X, Golas G, Vezina G, Gunay-Aygun M, Hanover JA, Doherty D, He M, Malicdan MCV, Gahl WA, Boerkoel CF. Abnormal glycosylation in Joubert syndrome type 10. Cilia 2017; 6:2. [PMID: 28344780 PMCID: PMC5364566 DOI: 10.1186/s13630-017-0048-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The discovery of disease pathogenesis requires systematic agnostic screening of multiple homeostatic processes that may become deregulated. We illustrate this principle in the evaluation and diagnosis of a 5-year-old boy with Joubert syndrome type 10 (JBTS10). He carried the OFD1 mutation p.Gln886Lysfs*2 (NM_003611.2: c.2656del) and manifested features of Joubert syndrome. METHODS We integrated exome sequencing, MALDI-TOF mass spectrometry analyses of plasma and cultured dermal fibroblasts glycomes, and full clinical evaluation of the proband. Analyses of cilia formation and lectin staining were performed by immunofluorescence. Measurement of cellular nucleotide sugar levels was performed with high-performance anion-exchange chromatography with pulsed amperometric detection. Statistical analyses utilized the Student's and Fisher's exact t tests. RESULTS Glycome analyses of plasma and cultured dermal fibroblasts identified abnormal N- and O-linked glycosylation profiles. These findings replicated in two unrelated males with OFD1 mutations. Cultured fibroblasts from affected individuals had a defect in ciliogenesis. The proband's fibroblasts also had an abnormally elevated nuclear sialylation signature and increased total cellular levels of CMP-sialic acid. Ciliogenesis and each glycosylation anomaly were rescued by expression of wild-type OFD1. CONCLUSIONS The rescue of ciliogenesis and glycosylation upon reintroduction of WT OFD1 suggests that both contribute to the pathogenesis of JBTS10.
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Affiliation(s)
- Megan S Kane
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA.,Inova Translational Medicine Institute, Inova Health System, Falls Church, VA USA
| | - Mariska Davids
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Michelle R Bond
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Christopher J Adams
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Megan E Grout
- Department of Pediatrics, University of Washington, Seattle, WA USA
| | - Ian G Phelps
- Department of Pediatrics, University of Washington, Seattle, WA USA
| | - Diana R O'Day
- Department of Pediatrics, University of Washington, Seattle, WA USA
| | | | - Xeuli Li
- The Michael J Palmieri Metabolic Laboratory, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - Gretchen Golas
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | | | - Meral Gunay-Aygun
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA.,Office of the Clinical Director, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA.,Johns Hopkins University School of Medicine, Department of Pediatrics and McKusick-Nathans Institute of Genetic Medicine, Baltimore, MD USA
| | - John A Hanover
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA USA
| | - Miao He
- The Michael J Palmieri Metabolic Laboratory, Children's Hospital of Philadelphia, Philadelphia, PA USA
| | - May Christine V Malicdan
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - William A Gahl
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Disease Program, Common Fund, Office of the Director, and National Human Genome Research Institute, National Institutes of Health, Bethesda, MD USA.,Department of Medical Genetics, University of British Columbia, Vancouver, BC Canada
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8
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Slaats GG, Isabella CR, Kroes HY, Dempsey JC, Gremmels H, Monroe GR, Phelps IG, Duran KJ, Adkins J, Kumar SA, Knutzen DM, Knoers NV, Mendelsohn NJ, Neubauer D, Mastroyianni SD, Vogt J, Worgan L, Karp N, Bowdin S, Glass IA, Parisi MA, Otto EA, Johnson CA, Hildebrandt F, van Haaften G, Giles RH, Doherty D. MKS1 regulates ciliary INPP5E levels in Joubert syndrome. J Med Genet 2016; 53:62-72. [PMID: 26490104 PMCID: PMC5060087 DOI: 10.1136/jmedgenet-2015-103250] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [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: 05/06/2015] [Accepted: 09/23/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Joubert syndrome (JS) is a recessive ciliopathy characterised by a distinctive brain malformation 'the molar tooth sign'. Mutations in >27 genes cause JS, and mutations in 12 of these genes also cause Meckel-Gruber syndrome (MKS). The goals of this work are to describe the clinical features of MKS1-related JS and determine whether disease causing MKS1 mutations affect cellular phenotypes such as cilium number, length and protein content as potential mechanisms underlying JS. METHODS We measured cilium number, length and protein content (ARL13B and INPP5E) by immunofluorescence in fibroblasts from individuals with MKS1-related JS and in a three-dimensional (3D) spheroid rescue assay to test the effects of disease-related MKS1 mutations. RESULTS We report MKS1 mutations (eight of them previously unreported) in nine individuals with JS. A minority of the individuals with MKS1-related JS have MKS features. In contrast to the truncating mutations associated with MKS, all of the individuals with MKS1-related JS carry ≥ 1 non-truncating mutation. Fibroblasts from individuals with MKS1-related JS make normal or fewer cilia than control fibroblasts, their cilia are more variable in length than controls, and show decreased ciliary ARL13B and INPP5E. Additionally, MKS1 mutant alleles have similar effects in 3D spheroids. CONCLUSIONS MKS1 functions in the transition zone at the base of the cilium to regulate ciliary INPP5E content, through an ARL13B-dependent mechanism. Mutations in INPP5E also cause JS, so our findings in patient fibroblasts support the notion that loss of INPP5E function, due to either mutation or mislocalisation, is a key mechanism underlying JS, downstream of MKS1 and ARL13B.
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Affiliation(s)
- Gisela G. Slaats
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hester Y. Kroes
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | | | - Hendrik Gremmels
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Glen R. Monroe
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Karen J. Duran
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Jonathan Adkins
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Sairam A. Kumar
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Dana M. Knutzen
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Nine V. Knoers
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nancy J. Mendelsohn
- Department of Medical Genetics, Children’s Hospitals & Clinics of Minnesota, Minneapolis, MN, USA
| | - David Neubauer
- Department of Child, Adolescent and Developmental Neurology, University Children’s Hospital Ljubljana, Ljubljana, Slovenia
| | | | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women’s Hospital, Birmingham, UK
| | - Lisa Worgan
- Department of Clinical Genetics, Liverpool Hospital, Liverpool, Australia
| | - Natalya Karp
- Medical Genetics Program, Department of Pediatrics, London Health Science Centre, University of Western Ontario, London, Ontario, Canada
| | - Sarah Bowdin
- Division of Clinical and Metabolic Genetics, Department of Paediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ian A. Glass
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Melissa A. Parisi
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Edgar A. Otto
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - Colin A. Johnson
- Section of Ophthalmology and Neuroscience, Leeds Institutes of Molecular Medicine, University of Leeds, Leeds, UK
| | - Friedhelm Hildebrandt
- Division of Nephrology, Boston Children’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Gijs van Haaften
- Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Rachel H. Giles
- Department of Nephrology and Hypertension, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Seattle Children’s Research Institute, Seattle, WA, USA
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9
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Schueler M, Halbritter J, Phelps IG, Braun DA, Otto EA, Porath JD, Gee HY, Shendure J, O'Roak BJ, Lawson JA, Nabhan MM, Soliman NA, Doherty D, Hildebrandt F. Large-scale targeted sequencing comparison highlights extreme genetic heterogeneity in nephronophthisis-related ciliopathies. J Med Genet 2015; 53:208-14. [PMID: 26673778 DOI: 10.1136/jmedgenet-2015-103304] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [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: 06/09/2015] [Accepted: 11/13/2015] [Indexed: 02/07/2023]
Abstract
BACKGROUND The term nephronophthisis-related ciliopathies (NPHP-RC) describes a group of rare autosomal-recessive cystic kidney diseases, characterised by broad genetic and clinical heterogeneity. NPHP-RC is frequently associated with extrarenal manifestations and accounts for the majority of genetically caused chronic kidney disease (CKD) during childhood and adolescence. Generation of a molecular diagnosis has been impaired by this broad genetic heterogeneity. However, recently developed high-throughput exon sequencing techniques represent powerful and efficient tools to screen large cohorts for dozens of causative genes. METHODS Therefore, we performed massively multiplexed targeted sequencing using the modified molecular inversion probe strategy (MIPs) in an international cohort of 384 patients diagnosed with NPHP-RC. RESULTS As a result, we established the molecular diagnoses in 81/384 unrelated individuals (21.1%). We detected 127 likely disease-causing mutations in 18 of 34 evaluated NPHP-RC genes, 22 of which were novel. We further compared a subgroup of current findings to the results of a previous study in which we used an array-based microfluidic PCR technology in the same cohort. While 78 likely disease-causing mutations were previously detected by the array-based microfluidic PCR, the MIPs approach identified 94 likely pathogenic mutations. Compared with the previous approach, MIPs redetected 66 out of 78 variants and 28 previously unidentified variants, for a total of 94 variants. CONCLUSIONS In summary, we demonstrate that the modified MIPs technology is a useful approach to screen large cohorts for a multitude of established NPHP genes in order to identify the underlying molecular cause. Combined application of two independent library preparation and sequencing techniques, however, may still be indicated for Mendelian diseases with extensive genetic heterogeneity in order to further increase diagnostic sensitivity.
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Affiliation(s)
- Markus Schueler
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jan Halbritter
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Divison of Nephrology, Department of Internal Medicine, University Clinic Leipzig, Leipzig, Germany
| | - Ian G Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Daniela A Braun
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Edgar A Otto
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan, USA
| | - Jonathan D Porath
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Heon Yung Gee
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Jay Shendure
- University of Washington, Genome Sciences, Seattle, Washington, USA
| | - Brian J O'Roak
- Oregon Health and Science University, Molecular and Medical Genetics, Portland, Oregon, USA
| | - Jennifer A Lawson
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Marwa M Nabhan
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Neveen A Soliman
- Department of Pediatrics, Kasr Al Ainy School of Medicine, Cairo University, Cairo, Egypt Egyptian Group for Orphan Renal Diseases (EGORD), Cairo, Egypt
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Friedhelm Hildebrandt
- Divison of Nephology, Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
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10
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Bachmann-Gagescu R, Dempsey J, Phelps IG, Isabella C, O'Day D, O'Roak B, Shendure J, Glass I, Doherty D. Genotype-Phenotype correlations in Joubert Syndrome in the Era of Next Generation Sequencing. Cilia 2015. [PMCID: PMC4518614 DOI: 10.1186/2046-2530-4-s1-p8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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11
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Bachmann-Gagescu R, Dona M, Hetterschijt L, Tonnaer E, Peters T, de Vrieze E, Mans DA, van Beersum SEC, Phelps IG, Arts HH, Keunen JE, Ueffing M, Roepman R, Boldt K, Doherty D, Moens CB, Neuhauss SCF, Kremer H, van Wijk E. The Ciliopathy Protein CC2D2A Associates with NINL and Functions in RAB8-MICAL3-Regulated Vesicle Trafficking. PLoS Genet 2015; 11:e1005575. [PMID: 26485645 PMCID: PMC4617701 DOI: 10.1371/journal.pgen.1005575] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 02/26/2015] [Accepted: 09/16/2015] [Indexed: 12/16/2022] Open
Abstract
Ciliopathies are a group of human disorders caused by dysfunction of primary cilia, ubiquitous microtubule-based organelles involved in transduction of extra-cellular signals to the cell. This function requires the concentration of receptors and channels in the ciliary membrane, which is achieved by complex trafficking mechanisms, in part controlled by the small GTPase RAB8, and by sorting at the transition zone located at the entrance of the ciliary compartment. Mutations in the transition zone gene CC2D2A cause the related Joubert and Meckel syndromes, two typical ciliopathies characterized by central nervous system malformations, and result in loss of ciliary localization of multiple proteins in various models. The precise mechanisms by which CC2D2A and other transition zone proteins control protein entrance into the cilium and how they are linked to vesicular trafficking of incoming cargo remain largely unknown. In this work, we identify the centrosomal protein NINL as a physical interaction partner of CC2D2A. NINL partially co-localizes with CC2D2A at the base of cilia and ninl knockdown in zebrafish leads to photoreceptor outer segment loss, mislocalization of opsins and vesicle accumulation, similar to cc2d2a-/- phenotypes. Moreover, partial ninl knockdown in cc2d2a-/- embryos enhances the retinal phenotype of the mutants, indicating a genetic interaction in vivo, for which an illustration is found in patients from a Joubert Syndrome cohort. Similar to zebrafish cc2d2a mutants, ninl morphants display altered Rab8a localization. Further exploration of the NINL-associated interactome identifies MICAL3, a protein known to interact with Rab8 and to play an important role in vesicle docking and fusion. Together, these data support a model where CC2D2A associates with NINL to provide a docking point for cilia-directed cargo vesicles, suggesting a mechanism by which transition zone proteins can control the protein content of the ciliary compartment.
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Affiliation(s)
- Ruxandra Bachmann-Gagescu
- Institute for Molecular Life Sciences, University of Zurich, Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Margo Dona
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
| | - Lisette Hetterschijt
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
| | - Edith Tonnaer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Theo Peters
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Erik de Vrieze
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
| | - Dorus A. Mans
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Sylvia E. C. van Beersum
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Heleen H. Arts
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
- Department of Biochemistry, University of Western Ontario, London, Ontario, Canada
| | - Jan E. Keunen
- Department of Ophthalmology, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Marius Ueffing
- Division of Experimental Ophthalmology and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Germany
| | - Ronald Roepman
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Karsten Boldt
- Division of Experimental Ophthalmology and Medical Proteome Center, Centre for Ophthalmology, Eberhard Karls University Tuebingen, Germany
| | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, United States of America
| | - Cecilia B. Moens
- Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | | | - Hannie Kremer
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Centre, Nijmegen, the Netherlands
| | - Erwin van Wijk
- Department of Otorhinolaryngology, Radboud University Medical Centre, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, the Netherlands
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12
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Bachmann-Gagescu R, Phelps IG, Dempsey JC, Sharma VA, Ishak GE, Boyle EA, Wilson M, Lourenço CM, Arslan M, Shendure J, Doherty D. KIAA0586 is Mutated in Joubert Syndrome. Hum Mutat 2015; 36:831-5. [PMID: 26096313 PMCID: PMC4537327 DOI: 10.1002/humu.22821] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [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: 04/27/2015] [Accepted: 06/08/2015] [Indexed: 12/26/2022]
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by a distinctive mid-hindbrain malformation. JS is part of a group of disorders called ciliopathies based on their overlapping phenotypes and common underlying pathophysiology linked to primary cilium dysfunction. Biallelic mutations in one of 28 genes, all encoding proteins localizing to the primary cilium or basal body, can cause JS. Despite this large number of genes, the genetic cause can currently be determined in about 62% of individuals with JS. To identify novel JS genes, we performed whole exome sequencing on 35 individuals with JS and found biallelic rare deleterious variants (RDVs) in KIAA0586, encoding a centrosomal protein required for ciliogenesis, in one individual. Targeted next-generation sequencing in a large JS cohort identified biallelic RDVs in eight additional families for an estimated prevalence of 2.5% (9/366 JS families). All affected individuals displayed JS phenotypes toward the mild end of the spectrum.
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Affiliation(s)
- Ruxandra Bachmann-Gagescu
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
- Institute of Medical Genetics, University of Zurich, 8603 Zurich, Switzerland
| | - Ian G. Phelps
- Dept. of Pediatrics, University of Washington, Seattle, WA
| | | | | | - Gisele E. Ishak
- Department of Radiology, University of Washington, Seattle Children’s Hospital, Seattle, WA
| | - Evan A Boyle
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Department of Genetics, Stanford University, Stanford, CA, USA
| | - Meredith Wilson
- Department of Clinical Genetics, Children’s Hospital at Westmead, Sydney, NSW, Australia
| | - Charles Marques Lourenço
- Department of Neurosciences and Behavior Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Mutluay Arslan
- Gulhane Military Medical School, Division of Child Neurology, Ankara, Turkey
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Dan Doherty
- Dept. of Pediatrics, University of Washington, Seattle, WA
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13
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Bachmann-Gagescu R, Dempsey JC, Phelps IG, O'Roak BJ, Knutzen DM, Rue TC, Ishak GE, Isabella CR, Gorden N, Adkins J, Boyle EA, de Lacy N, O'Day D, Alswaid A, Ramadevi A R, Lingappa L, Lourenço C, Martorell L, Garcia-Cazorla À, Ozyürek H, Haliloğlu G, Tuysuz B, Topçu M, Chance P, Parisi MA, Glass IA, Shendure J, Doherty D. Joubert syndrome: a model for untangling recessive disorders with extreme genetic heterogeneity. J Med Genet 2015; 52:514-22. [PMID: 26092869 PMCID: PMC5082428 DOI: 10.1136/jmedgenet-2015-103087] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [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: 02/23/2015] [Accepted: 06/01/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterised by hypotonia, ataxia, cognitive impairment, abnormal eye movements, respiratory control disturbances and a distinctive mid-hindbrain malformation. JS demonstrates substantial phenotypic variability and genetic heterogeneity. This study provides a comprehensive view of the current genetic basis, phenotypic range and gene-phenotype associations in JS. METHODS We sequenced 27 JS-associated genes in 440 affected individuals (375 families) from a cohort of 532 individuals (440 families) with JS, using molecular inversion probe-based targeted capture and next-generation sequencing. Variant pathogenicity was defined using the Combined Annotation Dependent Depletion algorithm with an optimised score cut-off. RESULTS We identified presumed causal variants in 62% of pedigrees, including the first B9D2 mutations associated with JS. 253 different mutations in 23 genes highlight the extreme genetic heterogeneity of JS. Phenotypic analysis revealed that only 34% of individuals have a 'pure JS' phenotype. Retinal disease is present in 30% of individuals, renal disease in 25%, coloboma in 17%, polydactyly in 15%, liver fibrosis in 14% and encephalocele in 8%. Loss of CEP290 function is associated with retinal dystrophy, while loss of TMEM67 function is associated with liver fibrosis and coloboma, but we observe no clear-cut distinction between JS subtypes. CONCLUSIONS This work illustrates how combining advanced sequencing techniques with phenotypic data addresses extreme genetic heterogeneity to provide diagnostic and carrier testing, guide medical monitoring for progressive complications, facilitate interpretation of genome-wide sequencing results in individuals with a variety of phenotypes and enable gene-specific treatments in the future.
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Affiliation(s)
- R Bachmann-Gagescu
- Institute for Molecular Life Sciences and Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - J C Dempsey
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - I G Phelps
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - B J O'Roak
- Molecular and Medical Genetics, Oregon Health and Science University, Portland, Oregon, USA
| | - D M Knutzen
- Department of Oncology, Franciscan Health System, Tacoma, Washington, USA
| | - T C Rue
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - G E Ishak
- Department of Radiology, University of Washington, Seattle Children's Hospital, Seattle, Washington, USA
| | - C R Isabella
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - N Gorden
- Department of Internal Medicine, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - J Adkins
- Division of Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | - E A Boyle
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - N de Lacy
- Department of Psychiatry, University of Washington, Seattle, Washington, USA
| | - D O'Day
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - A Alswaid
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh, Saudi Arabia
| | | | - L Lingappa
- Department of Child Neurology, Rainbow Children Hospital, Hyderabad, India
| | - C Lourenço
- Department of Neurosciences and Behavior Neurosciences, School of Medicine of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - L Martorell
- Department of Genetica Molecular, Hospital Sant Joan de Deu, Barcelona, Spain
| | - À Garcia-Cazorla
- Department of Neurology, Neurometabolic Unit, Hospital Sant Joan de Déu and CIBERER, ISCIII, Barcelona, Spain
| | - H Ozyürek
- Department of Pediatric Neurology, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - G Haliloğlu
- Department of Pediatric Neurology, Hacettepe University Children's Hospital, Ankara, Turkey
| | - B Tuysuz
- Department of Pediatric Genetics, Cerrahpasa Medical School, Istanbul University, Istanbul, Turkey
| | - M Topçu
- Department of Pediatric Neurology, Hacettepe University Children's Hospital, Ankara, Turkey
| | - P Chance
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - M A Parisi
- National Institute of Child Health and Human Development, NIH, Bethesda, Maryland, USA
| | - I A Glass
- Department of Pediatrics, University of Washington, Seattle, Washington, USA Seattle Children's Research Institute, Seattle, Washington, USA
| | - J Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - D Doherty
- Department of Pediatrics, University of Washington, Seattle, Washington, USA Seattle Children's Research Institute, Seattle, Washington, USA
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14
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Oegema R, Cushion TD, Phelps IG, Chung SK, Dempsey JC, Collins S, Mullins JGL, Dudding T, Gill H, Green AJ, Dobyns WB, Ishak GE, Rees MI, Doherty D. Recognizable cerebellar dysplasia associated with mutations in multiple tubulin genes. Hum Mol Genet 2015; 24:5313-25. [PMID: 26130693 DOI: 10.1093/hmg/ddv250] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023] Open
Abstract
Mutations in alpha- and beta-tubulins are increasingly recognized as a major cause of malformations of cortical development (MCD), typically lissencephaly, pachygyria and polymicrogyria; however, sequencing tubulin genes in large cohorts of MCD patients has detected tubulin mutations in only 1-13%. We identified patients with a highly characteristic cerebellar dysplasia but without lissencephaly, pachygyria and polymicrogyria typically associated with tubulin mutations. Remarkably, in seven of nine patients (78%), targeted sequencing revealed mutations in three different tubulin genes (TUBA1A, TUBB2B and TUBB3), occurring de novo or inherited from a mosaic parent. Careful re-review of the cortical phenotype on brain imaging revealed only an irregular pattern of gyri and sulci, for which we propose the term tubulinopathy-related dysgyria. Basal ganglia (100%) and brainstem dysplasia (80%) were common features. On the basis of in silico structural predictions, the mutations affect amino acids in diverse regions of the alpha-/beta-tubulin heterodimer, including the nucleotide binding pocket. Cell-based assays of tubulin dynamics reveal various effects of the mutations on incorporation into microtubules: TUBB3 p.Glu288Lys and p.Pro357Leu do not incorporate into microtubules at all, whereas TUBB2B p.Gly13Ala shows reduced incorporation and TUBA1A p.Arg214His incorporates fully, but at a slower rate than wild-type. The broad range of effects on microtubule incorporation is at odds with the highly stereotypical clinical phenotype, supporting differential roles for the three tubulin genes involved. Identifying this highly characteristic phenotype is important due to the low recurrence risk compared with the other (recessive) cerebellar dysplasias and the apparent lack of non-neurological medical issues.
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Affiliation(s)
- Renske Oegema
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, The Netherlands,
| | | | | | - Seo-Kyung Chung
- Institute of Life Science, College of Medicine and Wales Epilepsy Research Network (WERN), College of Medicine, Swansea University, Swansea SA2 8PP, UK
| | | | - Sarah Collins
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | | | - Tracy Dudding
- Hunter Genetics, Waratah, New South Wales, Australia, University of Newcastle, Callaghan, New South Wales, Australia
| | - Harinder Gill
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland and
| | - Andrew J Green
- National Centre for Medical Genetics, Our Lady's Children's Hospital, Dublin 12, Ireland and School of Medicine and Medical Science, University College Dublin, Dublin 4, Ireland
| | - William B Dobyns
- Department of Pediatrics, Department of Neurology and Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Gisele E Ishak
- Department of Radiology, Seattle Children's Hospital and University of Washington, Seattle, WA 98195, USA
| | - Mark I Rees
- Institute of Life Science, College of Medicine and Wales Epilepsy Research Network (WERN), College of Medicine, Swansea University, Swansea SA2 8PP, UK
| | - Dan Doherty
- Department of Pediatrics, Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA,
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15
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Pan L, Shah AN, Phelps IG, Doherty D, Johnson EA, Moens CB. Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis. BMC Genomics 2015; 16:83. [PMID: 25886285 PMCID: PMC4457992 DOI: 10.1186/s12864-015-1263-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [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: 07/30/2014] [Accepted: 01/22/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Targeting Induced Local Lesions IN Genomes (TILLING) is a reverse genetics approach to directly identify point mutations in specific genes of interest in genomic DNA from a large chemically mutagenized population. Classical TILLING processes, based on enzymatic detection of mutations in heteroduplex PCR amplicons, are slow and labor intensive. RESULTS Here we describe a new TILLING strategy in zebrafish using direct next generation sequencing (NGS) of 250 bp amplicons followed by Paired-End Low-Error (PELE) sequence analysis. By pooling a genomic DNA library made from over 9,000 N-ethyl-N-nitrosourea (ENU) mutagenized F1 fish into 32 equal pools of 288 fish, each with a unique Illumina barcode, we reduce the complexity of the template to a level at which we can detect mutations that occur in a single heterozygous fish in the entire library. MiSeq sequencing generates 250 base-pair overlapping paired-end reads, and PELE analysis aligns the overlapping sequences to each other and filters out any imperfect matches, thereby eliminating variants introduced during the sequencing process. We find that this filtering step reduces the number of false positive calls 50-fold without loss of true variant calls. After PELE we were able to validate 61.5% of the mutant calls that occurred at a frequency between 1 mutant call:100 wildtype calls and 1 mutant call:1000 wildtype calls in a pool of 288 fish. We then use high-resolution melt analysis to identify the single heterozygous mutation carrier in the 288-fish pool in which the mutation was identified. CONCLUSIONS Using this NGS-TILLING protocol we validated 28 nonsense or splice site mutations in 20 genes, at a two-fold higher efficiency than using traditional Cel1 screening. We conclude that this approach significantly increases screening efficiency and accuracy at reduced cost and can be applied in a wide range of organisms.
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Affiliation(s)
- Luyuan Pan
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Current Address: China Zebrafish Resource Center, Institute of Hydrobiology CAS, 430072, Wuhan, China.
| | - Arish N Shah
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA.
| | - Ian G Phelps
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA, USA.
| | - Eric A Johnson
- Institute of Molecular Biology, University of Oregon, Eugene, OR, USA.
| | - Cecilia B Moens
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA, USA. .,Biology Department, University of Washington, Seattle, WA, USA.
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16
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Tuz K, Bachmann-Gagescu R, O'Day DR, Hua K, Isabella CR, Phelps IG, Stolarski AE, O'Roak BJ, Dempsey JC, Lourenco C, Alswaid A, Bönnemann CG, Medne L, Nampoothiri S, Stark Z, Leventer RJ, Topçu M, Cansu A, Jagadeesh S, Done S, Ishak GE, Glass IA, Shendure J, Neuhauss SCF, Haldeman-Englert CR, Doherty D, Ferland RJ. Mutations in CSPP1 cause primary cilia abnormalities and Joubert syndrome with or without Jeune asphyxiating thoracic dystrophy. Am J Hum Genet 2014; 94:62-72. [PMID: 24360808 DOI: 10.1016/j.ajhg.2013.11.019] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 11/13/2013] [Indexed: 12/26/2022] Open
Abstract
Joubert syndrome (JBTS) is a recessive ciliopathy in which a subset of affected individuals also have the skeletal dysplasia Jeune asphyxiating thoracic dystrophy (JATD). Here, we have identified biallelic truncating CSPP1 (centrosome and spindle pole associated protein 1) mutations in 19 JBTS-affected individuals, four of whom also have features of JATD. CSPP1 mutations explain ∼5% of JBTS in our cohort, and despite truncating mutations in all affected individuals, the range of phenotypic severity is broad. Morpholino knockdown of cspp1 in zebrafish caused phenotypes reported in other zebrafish models of JBTS (curved body shape, pronephric cysts, and cerebellar abnormalities) and reduced ciliary localization of Arl13b, further supporting loss of CSPP1 function as a cause of JBTS. Fibroblasts from affected individuals with CSPP1 mutations showed reduced numbers of primary cilia and/or short primary cilia, as well as reduced axonemal localization of ciliary proteins ARL13B and adenylyl cyclase III. In summary, CSPP1 mutations are a major cause of the Joubert-Jeune phenotype in humans; however, the mechanism by which these mutations lead to both JBTS and JATD remains unknown.
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Affiliation(s)
- Karina Tuz
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
| | - Ruxandra Bachmann-Gagescu
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland; Institute of Medical Genetics, University of Zurich, 8603 Zurich, Switzerland
| | - Diana R O'Day
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Kiet Hua
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
| | - Christine R Isabella
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Ian G Phelps
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Allan E Stolarski
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health Sciences University, Portland, OR 97239, USA
| | - Jennifer C Dempsey
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Charles Lourenco
- Neurogenetics Division, Clinics Hospital, School of Medicine of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14049-900, Brazil
| | - Abdulrahman Alswaid
- Department of Pediatrics, King Abdulaziz Medical City, Riyadh 11426, Saudi Arabia
| | - Carsten G Bönnemann
- Neuromuscular and Neurogenetic Disorders of Childhood Section, John Edward Porter Neuroscience Research Center, National Institutes of Health, Bethesda, MD 20892, USA
| | - Livija Medne
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Center, AIMS Ponekkara Post Office, Kochi, Kerala 682041, India
| | - Zornitza Stark
- Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, Parkville, VIC 3052, Australia
| | - Richard J Leventer
- Departments of Neurology and Pediatrics, Murdoch Childrens Research Institute, Royal Children's Hospital and University of Melbourne, Parkville, VIC 3052, Australia
| | - Meral Topçu
- Department of Child Neurology, Hacettepe University Medical Faculty, Ihsan Dogramacı Children's Hospital, Ankara 06100, Turkey
| | - Ali Cansu
- Pediatric Neurology Unit, De Karadeniz Technical University, Trabzon 61080, Turkey
| | | | - Stephen Done
- Department of Radiology, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Gisele E Ishak
- Department of Radiology, University of Washington and Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Ian A Glass
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Hospital Research Institute, Seattle, WA 98105, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Stephan C F Neuhauss
- Institute of Molecular Life Sciences, University of Zurich, 8057 Zurich, Switzerland
| | - Chad R Haldeman-Englert
- Department of Pediatrics, Section on Medical Genetics, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Dan Doherty
- Divisions of Genetic Medicine and Developmental Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Hospital Research Institute, Seattle, WA 98105, USA.
| | - Russell J Ferland
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, NY 12208, USA; Department of Neurology, Albany Medical College, Albany, NY 12208, USA.
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17
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Tuz K, Hsiao YC, Juárez O, Shi B, Harmon EY, Phelps IG, Lennartz MR, Glass IA, Doherty D, Ferland RJ. The Joubert syndrome-associated missense mutation (V443D) in the Abelson-helper integration site 1 (AHI1) protein alters its localization and protein-protein interactions. J Biol Chem 2013; 288:13676-94. [PMID: 23532844 DOI: 10.1074/jbc.m112.420786] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Missense mutations in AHI1 result in the neurodevelopmental ciliopathy called Joubert syndrome. RESULTS Mutations in AHI1 decrease cilia formation, alter its localization and stability, and change its binding to HAP1 and NPHP1. CONCLUSION Mutations in AHI1 affect ciliogenesis, AHI1 protein localization, and AHI1-protein interactions. SIGNIFICANCE This study begins to describe how missense mutations in AHI1 can cause Joubert syndrome. Mutations in AHI1 cause Joubert syndrome (JBTS), a neurodevelopmental ciliopathy, characterized by midbrain-hindbrain malformations and motor/cognitive deficits. Here, we show that primary cilia (PC) formation is decreased in fibroblasts from individuals with JBTS and AHI1 mutations. Most missense mutations in AHI1, causing JBTS, occur in known protein domains, however, a common V443D mutation in AHI1 is found in a region with no known protein motifs. We show that cells transfected with AHI1-V443D, or a new JBTS-causing mutation, AHI1-R351L, have aberrant localization of AHI1 at the basal bodies of PC and at cell-cell junctions, likely through decreased binding of mutant AHI1 to NPHP1 (another JBTS-causing protein). The AHI1-V443D mutation causes decreased AHI1 stability because there is a 50% reduction in AHI1-V443D protein levels compared with wild type AHI1. Huntingtin-associated protein-1 (Hap1) is a regulatory protein that binds Ahi1, and Hap1 knock-out mice have been reported to have JBTS-like phenotypes, suggesting a role for Hap1 in ciliogenesis. Fibroblasts and neurons with Hap1 deficiency form PC with normal growth factor-induced ciliary signaling, indicating that the Hap1 JBTS phenotype is likely not through effects at PC. These results also suggest that the binding of Ahi1 and Hap1 may not be critical for ciliary function. However, we show that HAP1 has decreased binding to AHI1-V443D indicating that this altered binding could be responsible for the JBTS-like phenotype through an unknown pathway. Thus, these JBTS-associated missense mutations alter their subcellular distribution and protein interactions, compromising functions of AHI1 in cell polarity and cilium-mediated signaling, thereby contributing to JBTS.
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Affiliation(s)
- Karina Tuz
- Center for Neuropharmacology and Neuroscience, Albany Medical College, Albany, New York 12208, USA
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18
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O’Roak BJ, Vives L, Fu W, Egertson JD, Stanaway IB, Phelps IG, Carvill G, Kumar A, Lee C, Ankenman K, Munson J, Hiatt JB, Turner EH, Levy R, O’Day DR, Krumm N, Coe BP, Martin BK, Borenstein E, Nickerson DA, Mefford HC, Doherty D, Akey JM, Bernier R, Eichler EE, Shendure J. Multiplex targeted sequencing identifies recurrently mutated genes in autism spectrum disorders. Science 2012; 338:1619-22. [PMID: 23160955 PMCID: PMC3528801 DOI: 10.1126/science.1227764] [Citation(s) in RCA: 922] [Impact Index Per Article: 76.8] [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] [Indexed: 12/17/2022]
Abstract
Exome sequencing studies of autism spectrum disorders (ASDs) have identified many de novo mutations but few recurrently disrupted genes. We therefore developed a modified molecular inversion probe method enabling ultra-low-cost candidate gene resequencing in very large cohorts. To demonstrate the power of this approach, we captured and sequenced 44 candidate genes in 2446 ASD probands. We discovered 27 de novo events in 16 genes, 59% of which are predicted to truncate proteins or disrupt splicing. We estimate that recurrent disruptive mutations in six genes-CHD8, DYRK1A, GRIN2B, TBR1, PTEN, and TBL1XR1-may contribute to 1% of sporadic ASDs. Our data support associations between specific genes and reciprocal subphenotypes (CHD8-macrocephaly and DYRK1A-microcephaly) and replicate the importance of a β-catenin-chromatin-remodeling network to ASD etiology.
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Affiliation(s)
- Brian J. O’Roak
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Laura Vives
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Wenqing Fu
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Jarrett D. Egertson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian B. Stanaway
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ian G. Phelps
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Gemma Carvill
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Akash Kumar
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Choli Lee
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Katy Ankenman
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jeff Munson
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Joseph B. Hiatt
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Emily H. Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Roie Levy
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Diana R. O’Day
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Beth K. Martin
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Elhanan Borenstein
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Department of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Heather C. Mefford
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Dan Doherty
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98195, USA
- Seattle Children’s Hospital, Seattle, WA 98105, USA
| | - Joshua M. Akey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Raphael Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
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19
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Bachmann-Gagescu R, Phelps IG, Forbes A, Doherty D, Moens CB. Live imaging of Rab8 trafficking defects in cc2d2a mutant zebrafish. Cilia 2012. [PMCID: PMC3555742 DOI: 10.1186/2046-2530-1-s1-o29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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20
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Bachmann-Gagescu R, Ishak GE, Dempsey JC, Adkins J, O'Day D, Phelps IG, Gunay-Aygun M, Kline AD, Szczaluba K, Martorell L, Alswaid A, Alrasheed S, Pai S, Izatt L, Ronan A, Parisi MA, Mefford H, Glass I, Doherty D. Genotype-phenotype correlation in CC2D2A-related Joubert syndrome reveals an association with ventriculomegaly and seizures. J Med Genet 2012; 49:126-37. [PMID: 22241855 DOI: 10.1136/jmedgenet-2011-100552] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
BACKGROUND Joubert syndrome (JS) is a ciliopathy characterised by a distinctive brain malformation (the 'molar tooth sign'), developmental delay, abnormal eye movements and abnormal breathing pattern. Retinal dystrophy, cystic kidney disease, liver fibrosis and polydactyly are variably present, resulting in significant phenotypic heterogeneity and overlap with other ciliopathies. JS is also genetically heterogeneous, resulting from mutations in 13 genes. These factors render clinical/molecular diagnosis and management challenging. CC2D2A mutations are a relatively common cause of JS and also cause Meckel syndrome. The clinical consequences of CC2D2A mutations in patients with JS have been incompletely reported. METHODS Subjects with JS from 209 families were evaluated to identify mutations in CC2D2A. Clinical and imaging features in subjects with CC2D2A mutations were compared with those in subjects without CC2D2A mutations and reports in the literature. RESULTS 10 novel CC2D2A mutations in 20 subjects were identified; a summary is provided of all published CC2D2A mutations. Subjects with CC2D2A-related JS were more likely to have ventriculomegaly (p<0.0001) and seizures (p=0.024) than subjects without CC2D2A mutations. No mutation-specific genotype-phenotype correlations could be identified, but the findings confirm the observation that mutations that cause CC2D2A-related JS are predicted to be less deleterious than mutations that cause CC2D2A-related Meckel syndrome. Missense variants in the coiled-coil and C2 domains, as well as the C-terminal region, identify these regions as important for the biological mechanisms underlying JS. CONCLUSIONS CC2D2A testing should be prioritised in patients with JS and ventriculomegaly and/or seizures. Patients with CC2D2A-related JS should be monitored for hydrocephalus and seizures.
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Affiliation(s)
- Ruxandra Bachmann-Gagescu
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington 98195-6320, USA
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21
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Bachmann-Gagescu R, Phelps IG, Stearns G, Link BA, Brockerhoff SE, Moens CB, Doherty D. The ciliopathy gene cc2d2a controls zebrafish photoreceptor outer segment development through a role in Rab8-dependent vesicle trafficking. Hum Mol Genet 2011; 20:4041-55. [PMID: 21816947 PMCID: PMC3177654 DOI: 10.1093/hmg/ddr332] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [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] [Indexed: 01/24/2023] Open
Abstract
Ciliopathies are a genetically and phenotypically heterogeneous group of human developmental disorders whose root cause is the absence or dysfunction of primary cilia. Joubert syndrome is characterized by a distinctive hindbrain malformation variably associated with retinal dystrophy and cystic kidney disease. Mutations in CC2D2A are found in ∼10% of patients with Joubert syndrome. Here we describe the retinal phenotype of cc2d2a mutant zebrafish consisting of disorganized rod and cone photoreceptor outer segments resulting in abnormal visual function as measured by electroretinogram. Our analysis reveals trafficking defects in mutant photoreceptors affecting transmembrane outer segment proteins (opsins) and striking accumulation of vesicles, suggesting a role for Cc2d2a in vesicle trafficking and fusion. This is further supported by mislocalization of Rab8, a key regulator of opsin carrier vesicle trafficking, in cc2d2a mutant photoreceptors and by enhancement of the cc2d2a retinal and kidney phenotypes with partial knockdown of rab8. We demonstrate that Cc2d2a localizes to the connecting cilium in photoreceptors and to the transition zone in other ciliated cell types and that cilia are present in these cells in cc2d2a mutants, arguing against a primary function for Cc2d2a in ciliogenesis. Our data support a model where Cc2d2a, localized at the photoreceptor connecting cilium/transition zone, facilitates protein transport through a role in Rab8-dependent vesicle trafficking and fusion.
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Affiliation(s)
- Ruxandra Bachmann-Gagescu
- HHMI and Division of Basic Science, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.
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