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Ebstein F, Latypova X, Sharon Hung KY, Prado MA, Lee BH, Möller S, Wendlandt M, Zieba BA, Florenceau L, Vignard V, Poirier L, Toutain B, Moroni I, Dubucs C, Chassaing N, Horvath J, Prokisch H, Küry S, Bézieau S, Paulo JA, Finley D, Krüger E, Ghezzi D, Isidor B. Biallelic USP14 variants cause a syndromic neurodevelopmental disorder. Genet Med 2024; 26:101120. [PMID: 38469793 DOI: 10.1016/j.gim.2024.101120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024] Open
Abstract
PURPOSE Imbalances in protein homeostasis affect human brain development, with the ubiquitin-proteasome system (UPS) and autophagy playing crucial roles in neurodevelopmental disorders (NDD). This study explores the impact of biallelic USP14 variants on neurodevelopment, focusing on its role as a key hub connecting UPS and autophagy. METHODS Here, we identified biallelic USP14 variants in 4 individuals from 3 unrelated families: 1 fetus, a newborn with a syndromic NDD and 2 siblings affected by a progressive neurological disease. Specifically, the 2 siblings from the latter family carried 2 compound heterozygous variants c.8T>C p.(Leu3Pro) and c.988C>T p.(Arg330∗), whereas the fetus had a homozygous frameshift c.899_902del p.(Lys300Serfs∗24) variant, and the newborn patient harbored a homozygous frameshift c.233_236del p.(Leu78Glnfs∗11) variant. Functional studies were conducted using sodium dodecyl-sulfate polyacrylamide gel electrophoresis, western blotting, and mass spectrometry analyses in both patient-derived and CRISPR-Cas9-generated cells. RESULTS Our investigations indicated that the USP14 variants correlated with reduced N-terminal methionine excision, along with profound alterations in proteasome, autophagy, and mitophagy activities. CONCLUSION Biallelic USP14 variants in NDD patients perturbed protein degradation pathways, potentially contributing to disorder etiology. Altered UPS, autophagy, and mitophagy activities underscore the intricate interplay, elucidating their significance in maintaining proper protein homeostasis during brain development.
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Affiliation(s)
- Frédéric Ebstein
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany; Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France.
| | - Xenia Latypova
- Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | | | - Miguel A Prado
- Dept of Cell Biology, Harvard Medical School, Boston, MA; Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Byung-Hoon Lee
- Dept of Cell Biology, Harvard Medical School, Boston, MA; Dept of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Korea
| | - Sophie Möller
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Martin Wendlandt
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Barbara A Zieba
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | | | - Virginie Vignard
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Léa Poirier
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Bérénice Toutain
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France
| | - Isabella Moroni
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Charlotte Dubucs
- Département anatomie et cytologie pathologiques, CHU Toulouse, Toulouse, France; Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
| | - Sébastien Küry
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Stéphane Bézieau
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France
| | - Joao A Paulo
- Dept of Cell Biology, Harvard Medical School, Boston, MA
| | - Daniel Finley
- Dept of Cell Biology, Harvard Medical School, Boston, MA
| | - Elke Krüger
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy; Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Bertrand Isidor
- Nantes Université, CNRS, INSERM, L'Institut du Thorax, Nantes, France; Nantes Université, Service de Génétique Médicale, CHU Nantes, Nantes Cedex 1, France.
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2
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Romano F, Haanpää MK, Pomianowski P, Peraino AR, Pollard JR, Di Feo MF, Traverso M, Severino M, Derchi M, Henzen E, Zara F, Faravelli F, Capra V, Scala M. Expanding the phenotype of UPF3B-related disorder: Case reports and literature review. Am J Med Genet A 2024; 194:e63534. [PMID: 38318947 DOI: 10.1002/ajmg.a.63534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 02/07/2024]
Abstract
UPF3B encodes the Regulator of nonsense transcripts 3B protein, a core-member of the nonsense-mediated mRNA decay pathway, protecting the cells from the potentially deleterious actions of transcripts with premature termination codons. Hemizygous variants in the UPF3B gene cause a spectrum of neuropsychiatric issues including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, and schizophrenia/childhood-onset schizophrenia (COS). The number of patients reported to date is very limited, often lacking an extensive phenotypical and neuroradiological description of this ultra-rare syndrome. Here we report three subjects harboring UPF3B variants, presenting with variable clinical pictures, including cognitive impairment, central hypotonia, and syndromic features. Patients 1 and 2 harbored novel UPF3B variants-the p.(Lys207*) and p.(Asp429Serfs*27) ones, respectively-while the p.(Arg225Lysfs*229) variant, identified in Patient 3, was already reported in the literature. Novel features in our patients are represented by microcephaly, midface hypoplasia, and brain malformations. Then, we reviewed pertinent literature and compared previously reported subjects to our cases, providing possible insights into genotype-phenotype correlations in this emerging condition. Overall, the detailed phenotypic description of three patients carrying UPF3B variants is useful not only to expand the genotypic and phenotypic spectrum of UPF3B-related disorders, but also to ameliorate the clinical management of affected individuals.
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Affiliation(s)
- Ferruccio Romano
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Maria K Haanpää
- Department of Genomics and Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Pawel Pomianowski
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
| | - Amanda Rose Peraino
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
| | - John R Pollard
- Epilepsy Center, Christiana Care Health System, Newark, Delaware, USA
| | - Maria Francesca Di Feo
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Genomics and Clinical Genetics, Turku University Hospital, Turku, Finland
- Center for Medical Genetics and Genomics, Christiana Care Health System, Newark, Delaware, USA
- Epilepsy Center, Christiana Care Health System, Newark, Delaware, USA
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Monica Traverso
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | | | - Maria Derchi
- Cardiology Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Edoardo Henzen
- Genomics Facility, Italian Institute of Technology (IIT), Genoa, Italy
| | - Federico Zara
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
| | - Francesca Faravelli
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Valeria Capra
- Clinical Genomics and Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Marcello Scala
- Medical Genetics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy
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3
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He H, Li X, Guzman GA, Bungert-Plümke S, Franzen A, Lin X, Zhu H, Peng G, Zhang H, Yu Y, Sun S, Huang Z, Zhai Q, Chen Z, Peng J, Guzman RE. Expanding the genetic and phenotypic relevance of CLCN4 variants in neurodevelopmental condition: 13 new patients. J Neurol 2024:10.1007/s00415-024-12383-4. [PMID: 38758281 DOI: 10.1007/s00415-024-12383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 04/02/2024] [Accepted: 04/09/2024] [Indexed: 05/18/2024]
Abstract
OBJECTIVES CLCN4 variations have recently been identified as a genetic cause of X-linked neurodevelopmental disorders. This study aims to broaden the phenotypic spectrum of CLCN4-related condition and correlate it with functional consequences of CLCN4 variants. METHODS We described 13 individuals with CLCN4-related neurodevelopmental disorder. We analyzed the functional consequence of the unreported variants using heterologous expression, biochemistry, confocal fluorescent microscopy, patch-clamp electrophysiology, and minigene splicing assay. RESULTS We identified five novel (p.R41W, p.L348V, p.G480R, p.R603W, c.1576 + 5G > A) and three known (p.T203I, p.V275M, p.A555V) pathogenic CLCN4 variants in 13 Chinese patients. The p.V275M variant is found at high frequency and seen in four unrelated individuals. All had global developmental delay (GDD)/intellectual disability (ID). Seizures were present in eight individuals, and 62.5% of them developed refractory epilepsy. Five individuals without seizures showed moderate to severe GDD/ID. Developmental delay precedes seizure onset in most patients. The variants p.R41W, p.L348V, and p.R603W compromise the anion/exchange function of ClC-4. p.R41W partially impairs ClC-3/ClC-4 association. p.G480R reduces ClC-4 expression levels and impairs the heterodimerization with ClC-3. The c.1576 + 5G > A variant causes 22 bp deletion of exon 10. CONCLUSIONS We further define and broaden the clinical and mutational spectrum of CLCN4-related neurodevelopmental conditions. The p.V275M variant may be a potential hotspot CLCN4 variant in Chinese patients. The five novel variants cause loss of function of ClC-4. Transport dysfunction, protein instability, intracellular trafficking defect, or failure of ClC-4 to oligomerize may contribute to the pathophysiological events leading to CLCN4-related neurodevelopmental disorder.
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Affiliation(s)
- Hailan He
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Xinyi Li
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - G A Guzman
- Institute of Biological Information Processing (IBI-7), Structural Biochemistry, Jülich Research Center, Jülich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing (IBI-1), Molecular and Cell Physiology, Jülich Research Center, Jülich, Germany
| | - Arne Franzen
- Institute of Biological Information Processing (IBI-1), Molecular and Cell Physiology, Jülich Research Center, Jülich, Germany
| | - XueQin Lin
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China
| | - Hongmin Zhu
- Department of Rehabilitation, Wuhan Children's Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Guilan Peng
- Department of Neurology, Xiamen Maternal and Child Health Care Hospital, Xiamen, China
| | - Hongwei Zhang
- Epilepsy Center, Children's Hospital Affiliated to Shandong University, Jinan, China
| | - Yonglin Yu
- Department of Rehabilitation, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Suzhen Sun
- Department of Pediatric Neurology, Hebei Children's Hospital, Hebei Medical University, Shijiazhuang, China
| | - Zhongqin Huang
- Department of Neurology, Xiamen Maternal and Child Health Care Hospital, Xiamen, China
| | - Qiongxiang Zhai
- Department of Pediatrics, Guangdong Provincial People's Hospital, Guangzhou, China
| | - Zheng Chen
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Peng
- Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.
| | - Raul E Guzman
- Institute of Biological Information Processing (IBI-1), Molecular and Cell Physiology, Jülich Research Center, Jülich, Germany.
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4
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Rinaldi B, Bayat A, Zachariassen LG, Sun JH, Ge YH, Zhao D, Bonde K, Madsen LH, Awad IAA, Bagiran D, Sbeih A, Shah SM, El-Sayed S, Lyngby SM, Pedersen MG, Stenum-Berg C, Walker LC, Krey I, Delahaye-Duriez A, Emrick LT, Sully K, Murali CN, Burrage LC, Plaud Gonzalez JA, Parnes M, Friedman J, Isidor B, Lefranc J, Redon S, Heron D, Mignot C, Keren B, Fradin M, Dubourg C, Mercier S, Besnard T, Cogne B, Deb W, Rivier C, Milani D, Bedeschi MF, Di Napoli C, Grilli F, Marchisio P, Koudijs S, Veenma D, Argilli E, Lynch SA, Au PYB, Ayala Valenzuela FE, Brown C, Masser-Frye D, Jones M, Patron Romero L, Li WL, Thorpe E, Hecher L, Johannsen J, Denecke J, McNiven V, Szuto A, Wakeling E, Cruz V, Sency V, Wang H, Piard J, Kortüm F, Herget T, Bierhals T, Condell A, Ben-Zeev B, Kaur S, Christodoulou J, Piton A, Zweier C, Kraus C, Micalizzi A, Trivisano M, Specchio N, Lesca G, Møller RS, Tümer Z, Musgaard M, Gerard B, Lemke JR, Shi YS, Kristensen AS. Gain-of-function and loss-of-function variants in GRIA3 lead to distinct neurodevelopmental phenotypes. Brain 2024; 147:1837-1855. [PMID: 38038360 PMCID: PMC11068105 DOI: 10.1093/brain/awad403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/17/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
AMPA (α-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid) receptors (AMPARs) mediate fast excitatory neurotransmission in the brain. AMPARs form by homo- or heteromeric assembly of subunits encoded by the GRIA1-GRIA4 genes, of which only GRIA3 is X-chromosomal. Increasing numbers of GRIA3 missense variants are reported in patients with neurodevelopmental disorders (NDD), but only a few have been examined functionally. Here, we evaluated the impact on AMPAR function of one frameshift and 43 rare missense GRIA3 variants identified in patients with NDD by electrophysiological assays. Thirty-one variants alter receptor function and show loss-of-function or gain-of-function properties, whereas 13 appeared neutral. We collected detailed clinical data from 25 patients (from 23 families) harbouring 17 of these variants. All patients had global developmental impairment, mostly moderate (9/25) or severe (12/25). Twelve patients had seizures, including focal motor (6/12), unknown onset motor (4/12), focal impaired awareness (1/12), (atypical) absence (2/12), myoclonic (5/12) and generalized tonic-clonic (1/12) or atonic (1/12) seizures. The epilepsy syndrome was classified as developmental and epileptic encephalopathy in eight patients, developmental encephalopathy without seizures in 13 patients, and intellectual disability with epilepsy in four patients. Limb muscular hypotonia was reported in 13/25, and hypertonia in 10/25. Movement disorders were reported in 14/25, with hyperekplexia or non-epileptic erratic myoclonus being the most prevalent feature (8/25). Correlating receptor functional phenotype with clinical features revealed clinical features for GRIA3-associated NDDs and distinct NDD phenotypes for loss-of-function and gain-of-function variants. Gain-of-function variants were associated with more severe outcomes: patients were younger at the time of seizure onset (median age: 1 month), hypertonic and more often had movement disorders, including hyperekplexia. Patients with loss-of-function variants were older at the time of seizure onset (median age: 16 months), hypotonic and had sleeping disturbances. Loss-of-function and gain-of-function variants were disease-causing in both sexes but affected males often carried de novo or hemizygous loss-of-function variants inherited from healthy mothers, whereas affected females had mostly de novo heterozygous gain-of-function variants.
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Affiliation(s)
- Berardo Rinaldi
- Medical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Allan Bayat
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5230Denmark
| | - Linda G Zachariassen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jia-Hui Sun
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Department of Neurology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210032, China
- Zhejiang Key Laboratory of Organ Development and Regeneration, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310030, China
| | - Yu-Han Ge
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Department of Neurology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210032, China
- Ministry of Education Key Laboratory of Model Animal for Disease Study, National Resource Center for Mutant Mice, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210032, China
| | - Dan Zhao
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Kristine Bonde
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Laura H Madsen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | | | - Duygu Bagiran
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Amal Sbeih
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Syeda Maidah Shah
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Shaymaa El-Sayed
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Signe M Lyngby
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Miriam G Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Charlotte Stenum-Berg
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
| | - Louise Claudia Walker
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Ilona Krey
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Andrée Delahaye-Duriez
- Unité fonctionnelle de médecine génomique et génétique clinique, Hôpital Jean Verdier, Assistance Publique des Hôpitaux de Paris, Bondy 93140, France
- NeuroDiderot, UMR 1141, Inserm, Université Paris Cité, Paris 75019, France
- UFR SMBH, Université Sorbonne Paris Nord, Bobigny 93000, France
| | - Lisa T Emrick
- Division of Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Krystal Sully
- Division of Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Julie Ana Plaud Gonzalez
- Division of Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Mered Parnes
- Division of Neurology and Developmental Neurosciences, Department of Pediatrics, Baylor College of Medicine, Texas Children’s Hospital, Houston, TX 77030, USA
- Pediatric Movement Disorders Clinic, Texas Children’s Hospital and Baylor College of Medicine, Houston, TX 77030, USA
| | - Jennifer Friedman
- Rady Children’s Institute for Genomic Medicine, San Diego, CA 92123, USA
- Department of Neurosciences, University of California San Diego, San Diego, CA 92123, USA
- Department of Pediatrics, University of California San Diego, San Diego, CA 92123, USA
| | - Bertrand Isidor
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes 44000, France
| | - Jérémie Lefranc
- Pediatric Neurophysiology Department, CHU de Brest, Brest 29200, France
| | - Sylvia Redon
- Service de Génétique Médicale, CHU de Brest, Brest 29200, France
- Université de Brest, CHU de Brest, UMR 1078, Brest F29200, France
| | - Delphine Heron
- APHP Sorbonne Université, Département de Génétique, Hôpital Armand Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Paris 75013, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Cyril Mignot
- APHP Sorbonne Université, Département de Génétique, Hôpital Armand Trousseau and Groupe Hospitalier Pitié-Salpêtrière, Paris 75013, France
- Centre de Référence Déficiences Intellectuelles de Causes Rares, Paris 75013, France
| | - Boris Keren
- Genetic Department, APHP, Sorbonne Université, Pitié-Salpêtrière Hospital, Paris 75013, France
| | - Mélanie Fradin
- Service de Génétique Médicale, Hôpital Sud, CHU de Rennes, Rennes 35200, France
| | - Christele Dubourg
- Service de Génétique Moléculaire et Génomique, CHU de Rennes, Rennes 35200, France
- Université de Rennes, CNRS, Institut de Genetique et Developpement de Rennes, UMR 6290, Rennes 35200, France
| | - Sandra Mercier
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes 44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Thomas Besnard
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes 44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Benjamin Cogne
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes 44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Wallid Deb
- Nantes Université, CHU Nantes, Service de Génétique Médicale, Nantes 44000, France
- Nantes Université, CHU Nantes, CNRS, INSERM, l’institut du thorax, Nantes 44000, France
| | - Clotilde Rivier
- Department of Paediatrics, Villefranche-sur-Saône Hospital, Villefranche-sur-Saône 69655, France
| | - Donatella Milani
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Maria Francesca Bedeschi
- Medical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Claudia Di Napoli
- Medical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Federico Grilli
- Medical Genetics Unit, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan 20122, Italy
| | - Paola Marchisio
- Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Pediatria Pneumoinfettivologia, Milan 20122, Italy
- University of Milan, Milan 20122, Italy
| | - Suzanna Koudijs
- Department of Neurology, ENCORE, Erasmus Medical Center-Sophia Children’s Hospital, Rotterdam 3015, The Netherlands
| | - Danielle Veenma
- Department of Pediatrics, ENCORE, Erasmus Medical Center-Sophia Children’s Hospital, Rotterdam 3015, The Netherlands
| | - Emanuela Argilli
- Institute of Human Genetics, University of California, San Francisco, CA 94143, USA
- Department of Neurology, Weill Institute for Neurosciences, University of California, San Francisco, CA 94143, USA
| | - Sally Ann Lynch
- Department of Clinical Genetics, Children’s Health Ireland Crumlin, Dublin D12 N512, Ireland
| | - Ping Yee Billie Au
- Department of Medical Genetics, Alberta Children’s Hospital Research Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | | | | | - Diane Masser-Frye
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Marilyn Jones
- Division of Genetics, Department of Pediatrics, UC San Diego School of Medicine, Rady Children’s Hospital, San Diego, CA 92123, USA
| | - Leslie Patron Romero
- Facultad de Medicina y Psicología, Universidad Autónoma de Baja California, Tijuana 22010, Mexico
| | | | | | - Laura Hecher
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg 20215, Germany
| | - Jessika Johannsen
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg 20215, Germany
| | - Jonas Denecke
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg 20215, Germany
| | - Vanda McNiven
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1E8, Canada
- Fred A Litwin Family Centre in Genetic Medicine, University Health Network and Mount Sinai Hospital, Toronto, ON M5G 2C4, Canada
| | - Anna Szuto
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, ON M5G 1E8, Canada
- Department of Paediatrics, Hospital for Sick Children and University of Toronto, Toronto, ON M5G 1E8, Canada
| | - Emma Wakeling
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
| | - Vincent Cruz
- DDC Clinic Center for Special Needs Children, Middlefield, OH 44062, USA
| | - Valerie Sency
- DDC Clinic Center for Special Needs Children, Middlefield, OH 44062, USA
| | - Heng Wang
- DDC Clinic Center for Special Needs Children, Middlefield, OH 44062, USA
| | - Juliette Piard
- Centre de Génétique Humaine, Centre Hospitalier Universitaire, Université de Franche-Comté, Besançon 25000, France
- UMR 1231 GAD, Inserm, Université de Bourgogne Franche-Comté, Dijon 21000, France
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Angelo Condell
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia
| | - Bruria Ben-Zeev
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan 52621, Israel
- Faculty of Medicine, Tel Aviv University, Tel Aviv 4R73+8Q, Israel
| | - Simranpreet Kaur
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, Melbourne Medical School, University of Melbourne, Melbourne, Victoria 3052, Australia
| | - John Christodoulou
- Brain and Mitochondrial Research Group, Murdoch Children’s Research Institute, Melbourne, Victoria 3052, Australia
- Department of Paediatrics, Melbourne Medical School, University of Melbourne, Melbourne, Victoria 3052, Australia
- Discipline of Genetic Medicine, Sydney Medical School, University of Sydney, Sydney, New South Wales 2050, Australia
- Discipline of Child and Adolescent Health, Sydney Medical School, University of Sydney, Sydney, NewSouth Wales 2050, Australia
| | - Amelie Piton
- Hôpitaux Universitaires de Strasbourg, Laboratoire de Diagnostic Génétique, Strasbourg 67000, France
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
- Department of Human Genetics, Inselspital Bern, University of Bern, Bern 3010, Switzerland
| | - Cornelia Kraus
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen 91054, Germany
| | - Alessia Micalizzi
- Translational Cytogenomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome 00165, Italy
| | - Marina Trivisano
- Neurology, Epilepsy and Movement Disorders, Bambino Gesù Children's Hospital, IRCCS, Full Member of European Reference Network EpiCARE, Rome 00165, Italy
| | - Nicola Specchio
- Neurology, Epilepsy and Movement Disorders, Bambino Gesù Children's Hospital, IRCCS, Full Member of European Reference Network EpiCARE, Rome 00165, Italy
| | - Gaetan Lesca
- Department of Medical Genetics, University Hospital of Lyon and Claude Bernard Lyon I University, Lyon 69100, France
- Pathophysiology and Genetics of Neuron and Muscle (PNMG), UCBL, CNRS UMR5261 - INSERM U1315, Lyon 69100, France
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5230Denmark
| | - Zeynep Tümer
- Kennedy Center, Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen 2100, Denmark
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Maria Musgaard
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa K1H 8M5, Canada
| | - Benedicte Gerard
- Laboratoires de diagnostic genetique, Institut de genetique Medicale d'Alsace, Hopitaux Universitaires de Strasbourg, Strasbourg 67000, France
| | - Johannes R Lemke
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Yun Stone Shi
- State Key Laboratory of Pharmaceutical Biotechnology, Model Animal Research Center, Department of Neurology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing 210032, China
- Ministry of Education Key Laboratory of Model Animal for Disease Study, National Resource Center for Mutant Mice, Jiangsu Key Laboratory of Molecular Medicine, Medical School, Nanjing University, Nanjing 210032, China
- Guangdong Institute of Intelligence Science and Technology, Zhuhai 519031, China
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen 2100, Denmark
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5
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Sahly AN, Sierra-Marquez J, Bungert-Plümke S, Franzen A, Mougharbel L, Berrahmoune S, Dassi C, Poulin C, Srour M, Guzman RE, Myers KA. Genotype-phenotype correlation in CLCN4-related developmental and epileptic encephalopathy. Hum Genet 2024; 143:667-681. [PMID: 38578438 DOI: 10.1007/s00439-024-02668-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024]
Abstract
CLCN4-related disorder is a rare X-linked neurodevelopmental condition with a pathogenic mechanism yet to be elucidated. CLCN4 encodes the vesicular 2Cl-/H+ exchanger ClC-4, and CLCN4 pathogenic variants frequently result in altered ClC-4 transport activity. The precise cellular and molecular function of ClC-4 remains unknown; however, together with ClC-3, ClC-4 is thought to have a role in the ion homeostasis of endosomes and intracellular trafficking. We reviewed our research database for patients with CLCN4 variants and epilepsy, and performed thorough phenotyping. We examined the functional properties of the variants in mammalian cells using patch-clamp electrophysiology, protein biochemistry, and confocal fluorescence microscopy. Three male patients with developmental and epileptic encephalopathy were identified, with differing phenotypes. Patients #1 and #2 had normal growth parameters and normal-appearing brains on MRI, while patient #3 had microcephaly, microsomia, complete agenesis of the corpus callosum and cerebellar and brainstem hypoplasia. The p.(Gly342Arg) variant of patient #1 significantly impaired ClC-4's heterodimerization capability with ClC-3 and suppressed anion currents. The p.(Ile549Leu) variant of patient #2 and p.(Asp89Asn) variant of patient #3 both shift the voltage dependency of transport activation by 20 mV to more hyperpolarizing potentials, relative to the wild-type, with p.(Asp89Asn) favouring higher transport activity. We concluded that p.(Gly342Arg) carried by patient #1 and the p.(Ile549Leu) expressed by patient #2 impair ClC-4 transport function, while the p.(Asp89Asn) variant results in a gain-of-transport function; all three variants result in epilepsy and global developmental impairment, but with differences in epilepsy presentation, growth parameters, and presence or absence of brain malformations.
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Affiliation(s)
- Ahmed N Sahly
- Division of Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, Canada
- Department of Neurosciences, King Faisal Specialist Hospital & Research Centre, Jeddah, Saudi Arabia
| | - Juan Sierra-Marquez
- Institute of Biological Information Processing; Biological Molecular and Cell Physiology (IBI-1), Molecular and Cell Physiology, Research Center Jülich , GmbH Leo-Brandt-Strasse 1, 52428, Jülich, Germany
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing; Biological Molecular and Cell Physiology (IBI-1), Molecular and Cell Physiology, Research Center Jülich , GmbH Leo-Brandt-Strasse 1, 52428, Jülich, Germany
| | - Arne Franzen
- Institute of Biological Information Processing; Biological Molecular and Cell Physiology (IBI-1), Molecular and Cell Physiology, Research Center Jülich , GmbH Leo-Brandt-Strasse 1, 52428, Jülich, Germany
| | - Lina Mougharbel
- Research Institute of the McGill University Medical Centre, Montreal, QC, Canada
| | - Saoussen Berrahmoune
- Research Institute of the McGill University Medical Centre, Montreal, QC, Canada
| | - Christelle Dassi
- Research Institute of the McGill University Medical Centre, Montreal, QC, Canada
| | - Chantal Poulin
- Division of Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, Montreal Children's Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montreal, PQ, H4A 3J1, Canada
| | - Myriam Srour
- Division of Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, Canada
- Research Institute of the McGill University Medical Centre, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, Montreal Children's Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montreal, PQ, H4A 3J1, Canada
| | - Raul E Guzman
- Institute of Biological Information Processing; Biological Molecular and Cell Physiology (IBI-1), Molecular and Cell Physiology, Research Center Jülich , GmbH Leo-Brandt-Strasse 1, 52428, Jülich, Germany.
| | - Kenneth A Myers
- Division of Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre, Montreal, QC, Canada.
- Research Institute of the McGill University Medical Centre, Montreal, QC, Canada.
- Department of Neurology and Neurosurgery, Montreal Children's Hospital, McGill University Health Centre, 1001 Boulevard Décarie, Montreal, PQ, H4A 3J1, Canada.
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6
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Yang JH, Liu ZG, Liu CL, Zhang MR, Jia YL, Zhai QX, He MF, He N, Qiao JD. MED12 variants associated with X-linked recessive partial epilepsy without intellectual disability. Seizure 2024; 116:30-36. [PMID: 36894399 DOI: 10.1016/j.seizure.2023.02.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/03/2023] Open
Abstract
OBJECTIVES The MED12 gene encodes mediator complex subunit 12, which is a component of the mediator complex involved in the transcriptional regulation of nearly all RNA polymerase II-dependent genes. MED12 variants have previously been associated with developmental disorders with or without nonspecific intellectual disability. This study aims to explore the association between MED12 variants and epilepsy. MATERIALS AND METHODS Trios-based whole-exome sequencing was performed in a cohort of 349 unrelated cases with partial (focal) epilepsy without acquired causes. The genotype-phenotype correlations of MED12 variants were analyzed. RESULTS Five hemizygous missense MED12 variants, including c.958A>G/p.Ile320Val, c.1757G>A/p.Ser586Asn, c.2138C>T/p.Pro713Leu, c.3379T>C/p.Ser1127Pro, and c.4219A>C/p.Met1407Leu were identified in five unrelated males with partial epilepsy. All patients showed infrequent focal seizures and achieved seizure free without developmental abnormalities or intellectual disability. All the hemizygous variants were inherited from asymptomatic mothers (consistent with the X-linked recessive inheritance pattern) and were absent in the general population. The two variants with damaging hydrogen bonds were associated with early-onset seizures. Further genotype-phenotype analysis revealed that congenital anomaly disorder (Hardikar syndrome) was associated with (de novo) destructive variants in an X-linked dominant inheritance pattern, whereas epilepsy was associated with missense variants in an X-linked recessive inheritance pattern. Phenotypic features of intellectual disability appeared as the intermediate phenotype in terms of both genotype and inheritance. Epilepsy-related variants were located at the MED12-LCEWAV domain and the regions between MED12-LCEWAV and MED12-POL. CONCLUSION MED12 is a potentially causative gene for X-linked recessive partial epilepsy without developmental or intellectual abnormalities. The genotype-phenotype correlation of MED12 variants explains the phenotypic variations and can help the genetic diagnosis.
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Affiliation(s)
- Jie-Hua Yang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China; Department of Neurology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Zhi-Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, Guangdong, China
| | - Chun-Ling Liu
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ming-Rui Zhang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yan-Lu Jia
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Qiong-Xiang Zhai
- Department of pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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7
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Espejo-Serrano C, Aitken C, Tan BF, May DG, Chrisopulos RJ, Roux KJ, Demmers JA, Mackintosh SG, Gribnau J, Bustos F, Gontan C, Findlay GM. Chromatin targeting of the RNF12/RLIM E3 ubiquitin ligase controls transcriptional responses. Life Sci Alliance 2024; 7:e202302282. [PMID: 38199845 PMCID: PMC10781586 DOI: 10.26508/lsa.202302282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Protein ubiquitylation regulates key biological processes including transcription. This is exemplified by the E3 ubiquitin ligase RNF12/RLIM, which controls developmental gene expression by ubiquitylating the REX1 transcription factor and is mutated in an X-linked intellectual disability disorder. However, the precise mechanisms by which ubiquitylation drives specific transcriptional responses are not known. Here, we show that RNF12 is recruited to specific genomic locations via a consensus sequence motif, which enables co-localisation with REX1 substrate at gene promoters. Surprisingly, RNF12 chromatin recruitment is achieved via a non-catalytic basic region and comprises a previously unappreciated N-terminal autoinhibitory mechanism. Furthermore, RNF12 chromatin targeting is critical for REX1 ubiquitylation and downstream RNF12-dependent gene regulation. Our results demonstrate a key role for chromatin in regulation of the RNF12-REX1 axis and provide insight into mechanisms by which protein ubiquitylation enables programming of gene expression.
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Affiliation(s)
- Carmen Espejo-Serrano
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Catriona Aitken
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Beatrice F Tan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Danielle G May
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Rachel J Chrisopulos
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
| | - Kyle J Roux
- https://ror.org/00sfn8y78 Enabling Technologies Group, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | - Jeroen Aa Demmers
- https://ror.org/018906e22 Proteomics Center and Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Samuel G Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Joost Gribnau
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Francisco Bustos
- Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, SD, USA
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Cristina Gontan
- https://ror.org/018906e22 Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Greg M Findlay
- https://ror.org/01zg1tt02 MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
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8
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Koch I, Slovik M, Zhang Y, Liu B, Rennie M, Konz E, Cogne B, Daana M, Davids L, Diets IJ, Gold NB, Holtz AM, Isidor B, Mor-Shaked H, Neira Fresneda J, Niederhoffer KY, Nizon M, Pfundt R, Simon M, Stegmann A, Guillen Sacoto MJ, Wevers M, Barakat TS, Yanovsky-Dagan S, Atanassov BS, Toth R, Gao C, Bustos F, Harel T. USP27X variants underlying X-linked intellectual disability disrupt protein function via distinct mechanisms. Life Sci Alliance 2024; 7:e202302258. [PMID: 38182161 PMCID: PMC10770416 DOI: 10.26508/lsa.202302258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/22/2023] [Accepted: 12/22/2023] [Indexed: 01/07/2024] Open
Abstract
Neurodevelopmental disorders with intellectual disability (ND/ID) are a heterogeneous group of diseases driving lifelong deficits in cognition and behavior with no definitive cure. X-linked intellectual disability disorder 105 (XLID105, #300984; OMIM) is a ND/ID driven by hemizygous variants in the USP27X gene encoding a protein deubiquitylase with a role in cell proliferation and neural development. Currently, only four genetically diagnosed individuals from two unrelated families have been described with limited clinical data. Furthermore, the mechanisms underlying the disorder are unknown. Here, we report 10 new XLID105 individuals from nine families and determine the impact of gene variants on USP27X protein function. Using a combination of clinical genetics, bioinformatics, biochemical, and cell biology approaches, we determined that XLID105 variants alter USP27X protein biology via distinct mechanisms including changes in developmentally relevant protein-protein interactions and deubiquitylating activity. Our data better define the phenotypic spectrum of XLID105 and suggest that XLID105 is driven by USP27X functional disruption. Understanding the pathogenic mechanisms of XLID105 variants will provide molecular insight into USP27X biology and may create the potential for therapy development.
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Affiliation(s)
- Intisar Koch
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Maya Slovik
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- https://ror.org/01cqmqj90 Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Yuling Zhang
- https://ror.org/0207yh398 Department of Immunology, School of Biomedical Sciences, Shandong University, Jinan, PR China
| | - Bingyu Liu
- https://ror.org/0207yh398 Department of Immunology, School of Biomedical Sciences, Shandong University, Jinan, PR China
| | - Martin Rennie
- https://ror.org/00vtgdb53 School of Molecular Biosciences, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Emily Konz
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
| | - Benjamin Cogne
- Nantes Université, CHU de Nantes, CNRS, INSERM, L'institut du thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France
| | - Muhannad Daana
- Child Development Centers, Clalit Health Care Services, Jerusalem, Israel
| | - Laura Davids
- Department of Neurosciences, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Illja J Diets
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Nina B Gold
- Massachusetts General Hospital for Children, Boston, MA, USA
- https://ror.org/03wevmz92 Department of Pediatrics, Harvard Medical School, Boston, MA, USA
| | - Alexander M Holtz
- https://ror.org/03wevmz92 Division of Genetics & Genomics, Department of Pediatrics, Boston Children's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Bertrand Isidor
- Nantes Université, CHU de Nantes, CNRS, INSERM, L'institut du thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France
| | - Hagar Mor-Shaked
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- https://ror.org/01cqmqj90 Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Juanita Neira Fresneda
- https://ror.org/03czfpz43 Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Karen Y Niederhoffer
- https://ror.org/0160cpw27 Department of Medical Genetics, University of Alberta, Edmonton, Canada
| | - Mathilde Nizon
- Nantes Université, CHU de Nantes, CNRS, INSERM, L'institut du thorax, Nantes, France
- Nantes Université, CHU de Nantes, Service de Génétique médicale, Nantes, France
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Meh Simon
- https://ror.org/0575yy874 Department of Genetics, University Medical Center Utrecht, Utrecht, Netherlands
| | - Apa Stegmann
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, Netherlands
| | | | - Marijke Wevers
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
- Discovery Unit, Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Shira Yanovsky-Dagan
- https://ror.org/01cqmqj90 Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
| | - Boyko S Atanassov
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chengjiang Gao
- https://ror.org/0207yh398 Department of Immunology, School of Biomedical Sciences, Shandong University, Jinan, PR China
| | - Francisco Bustos
- https://ror.org/00sfn8y78 Pediatrics and Rare Diseases Group, Sanford Research, Sioux Falls, SD, USA
- Department of Pediatrics, University of South Dakota, Sioux Falls, SD, USA
| | - Tamar Harel
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
- https://ror.org/01cqmqj90 Department of Genetics, Hadassah Medical Center, Jerusalem, Israel
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9
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Li RK, Li H, Tian MQ, Li Y, Luo S, Liang XY, Liu WH, Li BM, Shi XQ, Li J, Li B, Shu XM. Investigation of FRMPD4 variants associated with X-linked epilepsy. Seizure 2024; 116:45-50. [PMID: 37330374 DOI: 10.1016/j.seizure.2023.05.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/19/2023] Open
Abstract
BACKGROUND The etiology of unexplained epilepsy in most patients remains unclear. Variants of FRMPD4 are suggested to be associated with neurodevelopmental disorders. Therefore, we screened for disease-causing FRMPD4 variants in patients with epilepsy. METHODS Trios-based whole-exome sequencing was conducted on a cohort of 85 patients with unexplained epilepsy, their parents, and extended family members. Additional cases with FRMPD4 variants were identified from the China Epilepsy Gene Matching Platform V.1.0. The frequency of variants was analyzed, and their subregional effects were predicted using in silico tools. The genotype-phenotype correlation of the newly defined causative genes and protein stability were analyzed using I-Mutant V.3.0 and Grantham scores. RESULTS Two novel missense variants of FRMPD4 were identified in two families. Using the gene matching platform, we identified three additional novel missense variants. These variants presented at low or no allele frequencies in the gnomAD database. All the variants were located outside the three FRMPD4 main domains (WW, PDZ, and FERM). In silico analyses revealed that the variants were damaging and were predicted to be the least stable. All patients eventually became seizure-free. Eight of the 21 patients with FRMPD4 variants had epilepsy, of which five (63%) had missense variants located outside the domains, two had deletions involving exon 2, and one had a frameshift variant located outside the domains. Patients with epilepsy caused by missense variants were often free of intellectual disabilities (4/5), whereas patients with epilepsy caused by truncated variants had intellectual disabilities and structural brain abnormalities (3/3). CONCLUSIONS The FRMPD4 gene is potentially associated with epilepsy. The genotype-phenotype correlation of FRMPD4 variants indicated that differences in variant types and locations of FRMPD4 may explain their phenotypic variation.
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Affiliation(s)
- Ren-Ke Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Huan Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Mao-Qiang Tian
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Yun Li
- Department of Brain Function and Neuroelectrophysiology, the Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421002, China
| | - Sheng Luo
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Xiao-Yu Liang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Wen-Hui Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Bin-Mei Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China
| | - Xiao-Qi Shi
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Juan Li
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China
| | - Bin Li
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical University, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Guangzhou 510260, China.
| | - Xiao-Mei Shu
- Department of Pediatrics, Affiliated Hospital of Zunyi Medical University, Children's Hospital of Guizhou Province, Zunyi 563003, China.
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10
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Huyghebaert J, Mateiu L, Elinck E, Van Rossem KE, Christiaenssen B, D'Incal CP, McCormack MK, Lazzarini A, Vandeweyer G, Kooy RF. Identification of a DLG3 stop mutation in the MRX20 family. Eur J Hum Genet 2024; 32:317-323. [PMID: 38273165 PMCID: PMC10923781 DOI: 10.1038/s41431-024-01537-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 01/27/2024] Open
Abstract
Here, we identified the causal mutation in the MRX20 family, one of the larger X-linked pedigrees that have been described in which no gene had been identified up till now. In 1995, the putative disease gene had been mapped to the pericentromeric region on the X chromosome, but no follow-up studies were performed. Here, whole exome sequencing (WES) on two affected and one unaffected family member revealed the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) that segregated with the affected individuals in the family. DLG3 mutations have been consequently associated with intellectual disability and are a plausible explanation for the clinical abnormalities observed in this family. In addition, we identified two other variants co-segregating with the phenotype: a stop gain mutation in SSX1 (c.358G>T/p.(Glu120Ter)) (NM_001278691.2) and a nonsynonymous SNV in USP27X (c.56 A>G/p.(Gln19Arg)) (NM_001145073.3). RNA sequencing revealed 14 differentially expressed genes (p value < 0.1) in 7 affected males compared to 4 unaffected males of the family, including four genes known to be associated with neurological disorders. Thus, in this paper we identified the c.195del/p.(Thr66ProfsTer55) mutation in the DLG3 gene (NM_021120.4) as likely responsible for the phenotype observed in the MRX20 family.
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Affiliation(s)
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | | | | | | | - Michael K McCormack
- Department of Psychiatry, Rutgers University-Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA
- Department of Cell Biology and Neurosciences, Virtua Health College of Medicine and Life Sciences of Rowan University, Stratford, NJ, 08084, USA
| | - Alice Lazzarini
- Department of Neurology, Rutgers University-Robert Wood Johnson Medical School, New Brunswick, NJ, 08903, USA
| | - Geert Vandeweyer
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Antwerp, Belgium.
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11
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Courraud J, Engel C, Quartier A, Drouot N, Houessou U, Plassard D, Sorlin A, Brischoux-Boucher E, Gouy E, Van Maldergem L, Rossi M, Lesca G, Edery P, Putoux A, Bilan F, Gilbert-Dussardier B, Atallah I, Kalscheuer VM, Mandel JL, Piton A. Molecular consequences of PQBP1 deficiency, involved in the X-linked Renpenning syndrome. Mol Psychiatry 2024; 29:287-296. [PMID: 38030819 DOI: 10.1038/s41380-023-02323-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 10/18/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023]
Abstract
Mutations in the PQBP1 gene (polyglutamine-binding protein-1) are responsible for a syndromic X-linked form of neurodevelopmental disorder (XL-NDD) with intellectual disability (ID), named Renpenning syndrome. PQBP1 encodes a protein involved in transcriptional and post-transcriptional regulation of gene expression. To investigate the consequences of PQBP1 loss, we used RNA interference to knock-down (KD) PQBP1 in human neural stem cells (hNSC). We observed a decrease of cell proliferation, as well as the deregulation of the expression of 58 genes, comprising genes encoding proteins associated with neurodegenerative diseases, playing a role in mRNA regulation or involved in innate immunity. We also observed an enrichment of genes involved in other forms of NDD (CELF2, APC2, etc). In particular, we identified an increase of a non-canonical isoform of another XL-NDD gene, UPF3B, an actor of nonsense mRNA mediated decay (NMD). This isoform encodes a shorter protein (UPF3B_S) deprived from the domains binding NMD effectors, however no notable change in NMD was observed after PQBP1-KD in fibroblasts containing a premature termination codon. We showed that short non-canonical and long canonical UPF3B isoforms have different interactomes, suggesting they could play distinct roles. The link between PQBP1 loss and increase of UPF3B_S expression was confirmed in mRNA obtained from patients with pathogenic variants in PQBP1, particularly pronounced for truncating variants and missense variants located in the C-terminal domain. We therefore used it as a molecular marker of Renpenning syndrome, to test the pathogenicity of variants of uncertain clinical significance identified in PQPB1 in individuals with NDD, using patient blood mRNA and HeLa cells expressing wild-type or mutant PQBP1 cDNA. We showed that these different approaches were efficient to prove a functional effect of variants in the C-terminal domain of the protein. In conclusion, our study provided information on the pathological mechanisms involved in Renpenning syndrome, but also allowed the identification of a biomarker of PQBP1 deficiency useful to test variant effect.
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Affiliation(s)
- Jérémie Courraud
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Camille Engel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Angélique Quartier
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Ursula Houessou
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Damien Plassard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Arthur Sorlin
- National Center of Genetics, Laboratoire national de santé, Dudelange, Luxembourg
| | - Elise Brischoux-Boucher
- Centre de Génétique Humaine, CHU Besançon, Université de Franche-Comté, 25056, Besançon, France
| | - Evan Gouy
- Genetics Department, University Hospital of Lyon, Bron, 69500, France
| | - Lionel Van Maldergem
- Centre de Génétique Humaine, CHU Besançon, Université de Franche-Comté, 25056, Besançon, France
| | - Massimiliano Rossi
- Genetics Department, University Hospital of Lyon, Bron, 69500, France
- Equipe GENDEV, CRNL, Inserm U1028, CNRS UMR 5292, UCB Lyon1, Illkirch, France
| | - Gaetan Lesca
- Genetics Department, University Hospital of Lyon, Bron, 69500, France
- Equipe GENDEV, CRNL, Inserm U1028, CNRS UMR 5292, UCB Lyon1, Illkirch, France
| | - Patrick Edery
- Genetics Department, University Hospital of Lyon, Bron, 69500, France
- Equipe GENDEV, CRNL, Inserm U1028, CNRS UMR 5292, UCB Lyon1, Illkirch, France
| | - Audrey Putoux
- Genetics Department, University Hospital of Lyon, Bron, 69500, France
- Equipe GENDEV, CRNL, Inserm U1028, CNRS UMR 5292, UCB Lyon1, Illkirch, France
| | - Frederic Bilan
- Service de génétique médicale, CHU de Poitiers, 86 000, Poitiers, France
| | | | - Isis Atallah
- Department of Medical Genetics, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | | | - Jean-Louis Mandel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France
- Université de Strasbourg, 67 400, Illkirch, France
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.
- Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.
- Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.
- Université de Strasbourg, 67 400, Illkirch, France.
- Genetic diagnosis laboratory, Strasbourg University Hospital, 67 090, Strasbourg, France.
- Institut Universitaire de France, Paris, France.
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12
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Sahajpal N, Ziats C, Chaubey A, DuPont BR, Abidi F, Schwartz CE, Stevenson RE. Clinical findings in individuals with duplication of genes associated with X-linked intellectual disability. Clin Genet 2024; 105:173-184. [PMID: 37899624 DOI: 10.1111/cge.14445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/25/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Duplication of all genes associated with X-linked intellectual disability (XLID) have been reported but the majority of the duplications include more than one XLID gene. It is exceptional for whole XLID gene duplications to cause the same phenotype as sequence variants or deletions of the same gene. Duplication of PLP1, the gene associated with Pelizaeus-Merzbacher syndrome, is the most notable duplication of this type. More commonly, duplication of XLID genes results in very different phenotypes than sequence alterations or deletions. Duplication of MECP2 is widely recognized as a duplication of this type, but a number of others exist. The phenotypes associated with gene duplications are often milder than those caused by deletions and sequence variants. Among some duplications that are clinically significant, marked skewing of X-inactivation in female carriers has been observed. This report describes the phenotypic consequences of duplication of 22 individual XLID genes, of which 10 are described for the first time.
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Affiliation(s)
- Nikhil Sahajpal
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Catherine Ziats
- Genetics Department, Shodair Children's Hospital, Helena, Montana, USA
| | - Alka Chaubey
- Clinical and Scientific Affairs, Bionano Genomics, San Diego, California, USA
| | - Barbara R DuPont
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Fatima Abidi
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Charles E Schwartz
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
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13
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Templeton KM, Thompson L, Tobias ES, Ahmed SF, McGowan R. Coloboma in a family with Tonne-Kalsheuer syndrome: extending the phenotype of RLIM variants. Clin Dysmorphol 2024; 33:38-42. [PMID: 38038056 DOI: 10.1097/mcd.0000000000000478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2023]
Affiliation(s)
- Kerra M Templeton
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
| | - Louise Thompson
- South East of Scotland Genetics Service, Western General Hospital, Edinburgh
| | - Edward S Tobias
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
- Academic Unit of Medical Genetics and Clinical Pathology, University of Glasgow, Queen Elizabeth University Hospital
| | - S Faisal Ahmed
- Child Health, School of Medicine, Dentistry and Nursing Studies, University of Glasgow, Royal Hospital for Children, Glasgow, UK
| | - Ruth McGowan
- West of Scotland Clinical Genetics Service, Queen Elizabeth University Hospital, Glasgow
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14
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Owens MC, Shen H, Yanas A, Mendoza-Figueroa MS, Lavorando E, Wei X, Shweta H, Tang HY, Goldman YE, Liu KF. Mutant forms of DDX3X with diminished catalysis form hollow condensates that exhibit sex-specific regulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.19.533240. [PMID: 38076929 PMCID: PMC10705264 DOI: 10.1101/2023.03.19.533240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Mutations in the RNA helicase DDX3X, implicated in various cancers and neurodevelopmental disorders, often impair RNA unwinding and translation. However, the mechanisms underlying this impairment and the differential interactions of DDX3X mutants with wild-type (WT) X-linked DDX3X and Y-linked homolog DDX3Y remain elusive. This study reveals that specific DDX3X mutants more frequently found in disease form distinct hollow condensates in cells. Using a combined structural, biochemical, and single-molecule microscopy study, we show that reduced ATPase and RNA release activities contribute to condensate formation and the catalytic deficits result from inhibiting the catalytic cycle at multiple steps. Proteomic investigations further demonstrate that these hollow condensates sequester WT DDX3X/DDX3Y and other proteins crucial for diverse signaling pathways. WT DDX3X enhances the dynamics of heterogeneous mutant/WT hollow condensates more effectively than DDX3Y. These findings offer valuable insights into the catalytic defects of specific DDX3X mutants and their differential interactions with wild-type DDX3X and DDX3Y, potentially explaining sex biases in disease.
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15
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Picollo A. Vesicular CLC chloride/proton exchangers in health and diseases. Front Pharmacol 2023; 14:1295068. [PMID: 38027030 PMCID: PMC10662042 DOI: 10.3389/fphar.2023.1295068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Chloride is one of the most abundant anions in the human body; it is implicated in several physiological processes such as the transmission of action potentials, transepithelial salt transport, maintenance of cellular homeostasis, regulation of osmotic pressure and intracellular pH, and synaptic transmission. The balance between the extracellular and intracellular chloride concentrations is controlled by the interplay of ion channels and transporters embedded in the cellular membranes. Vesicular members of the CLC chloride protein family (vCLCs) are chloride/proton exchangers expressed in the membrane of the intracellular organelles, where they control vesicular acidification and luminal chloride concentration. It is well known that mutations in CLCs cause bone, kidney, and lysosomal genetic diseases. However, the role of CLC exchangers in neurological disorders is only now emerging with the identification of pathogenic CLCN gene variants in patients with severe neuronal and intellectual dysfunctions. This review will provide an overview of the recent advances in understanding the role of the vesicular CLC chloride/proton exchangers in human pathophysiology.
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Affiliation(s)
- Alessandra Picollo
- Institute of Biophysics, National Research Council, Genova, Italy
- RAISE Ecosystem, Genova, Italy
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16
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Mir A, Song Y, Lee H, Khanahmad H, Khorram E, Nasiri J, Tabatabaiefar MA. Whole exome sequencing revealed variants in four genes underlying X-linked intellectual disability in four Iranian families: novel deleterious variants and clinical features with the review of literature. BMC Med Genomics 2023; 16:239. [PMID: 37821930 PMCID: PMC10566173 DOI: 10.1186/s12920-023-01680-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/01/2023] [Indexed: 10/13/2023] Open
Abstract
AIM AND OBJECTIVE Intellectual disability (ID) is a heterogeneous condition affecting brain development, function, and/or structure. The X-linked mode of inheritance of ID (X-linked intellectual disability; XLID) has a prevalence of 1 out of 600 to 1000 males. In the last decades, exome sequencing technology has revolutionized the process of disease-causing gene discovery in XLIDs. Nevertheless, so many of them still remain with unknown etiology. This study investigated four families with severe XLID to identify deleterious variants for possible diagnostics and prevention aims. METHODS Nine male patients belonging to four pedigrees were included in this study. The patients were studied genetically for Fragile X syndrome, followed by whole exome sequencing and analysis of intellectual disability-related genes variants. Sanger sequencing, co-segregation analysis, structural modeling, and in silico analysis were done to verify the causative variants. In addition, we collected data from previous studies to compare and situate our work with existing knowledge. RESULTS In three of four families, novel deleterious variants have been identified in three different genes, including ZDHHC9 (p. Leu189Pro), ATP2B3 (p. Asp847Glu), and GLRA2 (p. Arg350Cys) and also with new clinical features and in another one family, a reported pathogenic variant in the L1CAM (p. Glu309Lys) gene has been identified related to new clinical findings. CONCLUSION The current study's findings expand the existing knowledge of variants of the genes implicated in XLID and broaden the spectrum of phenotypes associated with the related conditions. The data have implications for genetic diagnosis and counseling.
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Affiliation(s)
- Atefeh Mir
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Yongjun Song
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hane Lee
- Division of Medical Genetics, 3Billion Inc, Seoul, South Korea
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Erfan Khorram
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran
| | - Jafar Nasiri
- Child Growth and Development Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Amin Tabatabaiefar
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, 81746 73461, Iran.
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
- Deputy of Research and Technology, GenTArget Corp (GTAC), Isfahan University of Medical Sciences, Isfahan, Iran.
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17
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Petit F, Longoni M, Wells J, Maser RS, Bogenschutz EL, Dysart MJ, Contreras HTM, Frénois F, Pober BR, Clark RD, Giampietro PF, Ropers HH, Hu H, Loscertales M, Wagner R, Ai X, Brand H, Jourdain AS, Delrue MA, Gilbert-Dussardier B, Devisme L, Keren B, McCulley DJ, Qiao L, Hernan R, Wynn J, Scott TM, Calame DG, Coban-Akdemir Z, Hernandez P, Hernandez-Garcia A, Yonath H, Lupski JR, Shen Y, Chung WK, Scott DA, Bult CJ, Donahoe PK, High FA. PLS3 missense variants affecting the actin-binding domains cause X-linked congenital diaphragmatic hernia and body-wall defects. Am J Hum Genet 2023; 110:1787-1803. [PMID: 37751738 PMCID: PMC10577083 DOI: 10.1016/j.ajhg.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 08/31/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
Congenital diaphragmatic hernia (CDH) is a relatively common and genetically heterogeneous structural birth defect associated with high mortality and morbidity. We describe eight unrelated families with an X-linked condition characterized by diaphragm defects, variable anterior body-wall anomalies, and/or facial dysmorphism. Using linkage analysis and exome or genome sequencing, we found that missense variants in plastin 3 (PLS3), a gene encoding an actin bundling protein, co-segregate with disease in all families. Loss-of-function variants in PLS3 have been previously associated with X-linked osteoporosis (MIM: 300910), so we used in silico protein modeling and a mouse model to address these seemingly disparate clinical phenotypes. The missense variants in individuals with CDH are located within the actin-binding domains of the protein but are not predicted to affect protein structure, whereas the variants in individuals with osteoporosis are predicted to result in loss of function. A mouse knockin model of a variant identified in one of the CDH-affected families, c.1497G>C (p.Trp499Cys), shows partial perinatal lethality and recapitulates the key findings of the human phenotype, including diaphragm and abdominal-wall defects. Both the mouse model and one adult human male with a CDH-associated PLS3 variant were observed to have increased rather than decreased bone mineral density. Together, these clinical and functional data in humans and mice reveal that specific missense variants affecting the actin-binding domains of PLS3 might have a gain-of-function effect and cause a Mendelian congenital disorder.
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Affiliation(s)
- Florence Petit
- Clinique de Génétique, CHU de Lille, Lille, France; EA7364 RADEME, Université de Lille, Lille, France
| | - Mauro Longoni
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Matthew J Dysart
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | - Hannah T M Contreras
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA
| | | | - Barbara R Pober
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
| | - Robin D Clark
- Division of Genetics, Department of Pediatrics, Loma Linda University School of Medicine, Loma Linda, CA, USA
| | | | - Hilger H Ropers
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hao Hu
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Maria Loscertales
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Richard Wagner
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA; Department of Pediatric Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Xingbin Ai
- Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA
| | - Harrison Brand
- Department of Neurology, Harvard Medical School, Boston, MA, USA
| | | | | | | | | | - Boris Keren
- Département de Génétique, Hôpital Pitié Salpétrière, CHU de Paris, Paris, France
| | - David J McCulley
- Department of Pediatrics, University of California, San Diego, San Diego, CA, USA
| | - Lu Qiao
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Rebecca Hernan
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Tiana M Scott
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Daniel G Calame
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA
| | - Zeynep Coban-Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, the University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Patricia Hernandez
- IDDRC/TCC, Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Hagith Yonath
- Internal Medicine A and Genetics Institute, Sheba Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA; Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Daryl A Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital, Houston, TX, USA; Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
| | | | - Patricia K Donahoe
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA
| | - Frances A High
- Pediatric Surgical Research Laboratories, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Harvard Medical School, Boston, MA, USA; Department of Pediatrics, Massachusetts General Hospital, Boston, MA, USA; Department of Surgery, Boston Children's Hospital, Boston, MA, USA.
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18
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Kharrat M, Issa AB, Tlili A, Jallouli O, Alila-Fersi O, Maalej M, Chouchen J, Ghouylia Y, Kamoun F, Triki C, Fakhfakh F. A Novel Mutation in the MAP7D3 Gene in Two Siblings with Severe Intellectual Disability and Autistic Traits: Concurrent Assessment of BDNF Functional Polymorphism, X-Inactivation and Oxidative Stress to Explain Disease Severity. J Mol Neurosci 2023; 73:853-864. [PMID: 37817054 DOI: 10.1007/s12031-023-02163-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/27/2023] [Indexed: 10/12/2023]
Abstract
Intellectual disabilities (ID) and autism spectrum disorders (ASD) are characterized by extreme genetic and phenotypic heterogeneity. However, understanding this heterogeneity is difficult due to the intricate interplay among multiple interconnected genes, epigenetic factors, oxidative stress, and environmental factors. Employing next-generation sequencing (NGS), we revealed the genetic cause of ID and autistic traits in two patients from a consanguineous family followed by segregation analysis. Furthermore, in silico prediction methods and 3D modeling were conducted to predict the effect of the variants. To establish genotype-phenotype correlation, X-chromosome inactivation using Methylation-specific PCR and oxidative stress markers were also investigated. By analyzing the NGS data of the two patients, we identified a novel frameshift mutation c.2174_2177del (p.Thr725MetfsTer2) in the MAP7D3 gene inherited from their mother along with the functional BDNF Val66Met polymorphism inherited from their father. The 3D modeling demonstrated that the p.Thr725MetfsTer2 variant led to the loss of the C-terminal tail of the MAP7D3 protein. This change could destabilize its structure and impact kinesin-1's binding to microtubules via an allosteric effect. Moreover, the analysis of oxidative stress biomarkers revealed an elevated oxidative stress in the two patients compared to the controls. To the best of our knowledge, this is the first report describing severe ID and autistic traits in familial cases with novel frameshift mutation c.2174_2177del in the MAP7D3 gene co-occurring with the functional polymorphism Val66M in the BDNF gene. Besides, our study underlines the importance of investigating combined genetic variations, X-chromosome inactivation (XCI) patterns, and oxidative stress markers for a better understanding of ID and autism etiology.
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Affiliation(s)
- Marwa Kharrat
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia.
| | - Abir Ben Issa
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Olfa Jallouli
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Olfa Alila-Fersi
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia
| | - Marwa Maalej
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia
| | - Jihen Chouchen
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates
| | - Yosra Ghouylia
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Fatma Kamoun
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Chahnez Triki
- Child Neurology Department, Hedi Chaker Hospital, Sfax, Tunisia
- Research Laboratory (LR19ES15), Sfax Medical School, Sfax University, Sfax, Tunisia
| | - Faiza Fakhfakh
- Laboratory of Molecular and Functional Genetics, Faculty of Science of Sfax University, Sfax, Tunisia.
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Hogg EKJ, Findlay GM. Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders. FEBS Lett 2023; 597:2375-2415. [PMID: 37607329 PMCID: PMC10952393 DOI: 10.1002/1873-3468.14723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023]
Abstract
Human developmental disorders encompass a wide range of debilitating physical conditions and intellectual disabilities. Perturbation of protein kinase signalling underlies the development of some of these disorders. For example, disrupted SRPK signalling is associated with intellectual disabilities, and the gene dosage of DYRKs can dictate the pathology of disorders including Down's syndrome. Here, we review the emerging roles of the CMGC kinase families SRPK, CLK, DYRK, and sub-family HIPK during embryonic development and in developmental disorders. In particular, SRPK, CLK, and DYRK kinase families have key roles in developmental signalling and stem cell regulation, and can co-ordinate neuronal development and function. Genetic studies in model organisms reveal critical phenotypes including embryonic lethality, sterility, musculoskeletal errors, and most notably, altered neurological behaviours arising from defects of the neuroectoderm and altered neuronal signalling. Further unpicking the mechanisms of specific kinases using human stem cell models of neuronal differentiation and function will improve our understanding of human developmental disorders and may provide avenues for therapeutic strategies.
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Affiliation(s)
- Elizabeth K. J. Hogg
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
| | - Greg M. Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
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20
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Timms RT, Mena EL, Leng Y, Li MZ, Tchasovnikarova IA, Koren I, Elledge SJ. Defining E3 ligase-substrate relationships through multiplex CRISPR screening. Nat Cell Biol 2023; 25:1535-1545. [PMID: 37735597 PMCID: PMC10567573 DOI: 10.1038/s41556-023-01229-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 08/11/2023] [Indexed: 09/23/2023]
Abstract
Specificity within the ubiquitin-proteasome system is primarily achieved through E3 ubiquitin ligases, but for many E3s their substrates-and in particular the molecular features (degrons) that they recognize-remain largely unknown. Current approaches for assigning E3s to their cognate substrates are tedious and low throughput. Here we developed a multiplex CRISPR screening platform to assign E3 ligases to their cognate substrates at scale. A proof-of-principle multiplex screen successfully performed ~100 CRISPR screens in a single experiment, refining known C-degron pathways and identifying an additional pathway through which Cul2FEM1B targets C-terminal proline. Further, by identifying substrates for Cul1FBXO38, Cul2APPBP2, Cul3GAN, Cul3KLHL8, Cul3KLHL9/13 and Cul3KLHL15, we demonstrate that the approach is compatible with pools of full-length protein substrates of varying stabilities and, when combined with site-saturation mutagenesis, can assign E3 ligases to their cognate degron motifs. Thus, multiplex CRISPR screening will accelerate our understanding of how specificity is achieved within the ubiquitin-proteasome system.
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Affiliation(s)
- Richard T Timms
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elijah L Mena
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Yumei Leng
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Mamie Z Li
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA
| | - Iva A Tchasovnikarova
- Wellcome/CRUK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Itay Koren
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Stephen J Elledge
- Department of Genetics, Harvard Medical School, Division of Genetics, Brigham asnd Women's Hospital, Howard Hughes Medical Institute, Boston, MA, USA.
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21
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Li S, Zhang W, Liang P, Zhu M, Zheng B, Zhou W, Wang C, Zhao X. Novel variants in the CLCN4 gene associated with syndromic X-linked intellectual disability. Front Neurol 2023; 14:1096969. [PMID: 37789889 PMCID: PMC10542403 DOI: 10.3389/fneur.2023.1096969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 08/15/2023] [Indexed: 10/05/2023] Open
Abstract
Objective The dysfunction of the CLCN4 gene can lead to X-linked intellectual disability and Raynaud-Claes syndrome (MRXSRC), characterized by severe cognitive impairment and mental disorders. This study aimed to investigate the genetic defects and clinical features of Chinese children with CLCN4 variants and explore the effect of mutant ClC-4 on the protein expression level and subcellular localization through in vitro experiments. Methods A total of 401 children with intellectual disabilities were screened for genetic variability using whole-exome sequencing (WES). Clinical data, including age, sex, perinatal conditions, and environmental exposure, were collected. Cognitive, verbal, motor, and social behavioral abilities were evaluated. Candidate variants were verified using Sanger sequencing, and their pathogenicity and conservation were analyzed using in silico prediction tools. Protein expression and localization of mutant ClC-4 were measured using Western blotting (WB) and immunofluorescence microscopy. The impact of a splice site variant was assessed with a minigene assay. Results Exome analysis identified five rare CLCN4 variants in six unrelated patients with intellectual disabilities, including two recurrent heterozygous de novo missense variants (p.D89N and p.A555V) in three female patients, and two hemizygous missense variants (p.N141S and p.R694Q) and a splicing variant (c.1390-12T > G) that are maternally inherited in three male patients. The p.N141S variant and the splicing variant c.1390-12(T > G were novel, while p.R694Q was identified in two asymptomatic heterozygous female patients. The six children with CLCN4 variants exhibited a neurodevelopmental spectrum disease characterized by intellectual disability (ID), delayed speech, autism spectrum disorders (ASD), microcephaly, hypertonia, and abnormal imaging findings. The minigene splicing result indicated that the c.1390-12T > G did not affect the splicing of CLCN4 mRNA. In vitro experiments showed that the mutant protein level and localization of mutant protein are similar to the wild type. Conclusion The study identified six probands with CLCN4 gene variants associated with X-linked ID. It expanded the gene and phenotype spectrum of CLCN4 variants. The bioinformatic analysis supported the pathogenicity of CLCN4 variants. However, these CLCN4 gene variants did not affect the ClC-4 expression levels and protein location, consistent with previous studies. Further investigations are necessary to investigate the pathogenetic mechanism.
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Affiliation(s)
- Sinan Li
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wenxin Zhang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Piao Liang
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Min Zhu
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Bixia Zheng
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Wei Zhou
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Chunli Wang
- Nanjing Key Laboratory of Pediatrics, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoke Zhao
- Department of Rehabilitation, Children's Hospital of Nanjing Medical University, Nanjing, China
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22
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Wang C, Li J, Liu W, Li S, Zhang Y, Jin Y, Cui J. Comprehensive analysis and experimental validation reveal elevated CLCN4 is a promising biomarker in endometrial cancer. Aging (Albany NY) 2023; 15:8744-8769. [PMID: 37671947 PMCID: PMC10522378 DOI: 10.18632/aging.204994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023]
Abstract
Several studies have reported the role of CLCN4 in tumor progression. However, its mechanism remains to be thoroughly studied. The objective of this study was to explore the potential pathogenic role of CLCN4 in endometrial carcinoma (UCEC) with a better understanding of the pathological mechanisms involved. The potential roles of CLCN4 in different tumors were explored based on The Cancer Genome Atlas (TCGA), the expression difference, mutation, survival, pathological stage, Immunity subtypes, Immune infiltration, tumor microenvironment (TME), tumor mutation burden (TMB), microsatellite instability (MSI), mismatch repair (MMR) related to CLCN4 were analyzed. Then, the expression, prognosis, mutation, and functional enrichment of CLCN4 in UCEC were analyzed. Immunohistochemical experiment was used to verify the expression of CLCN4 in endometrial cancer tissues and normal tissues. In vitro, we knocked down of CLCN4 in HEC-1-A cells and performed CCK8, WB, RT-PCR, wound-healing, transwell assays to further validation of the molecular function. Results revealed that high expression of CLCN4 was observed in 20 cancer types of TCGA. CLCN4 expression correlates with poor survival in MESO, BLCA, THCA, especially UCEC tumors. CLCN4 expression was significantly associated with CD4+ T-cell infiltration, especially CD4+ Th1-cell. Immunohistochemical experiment reveals that CLCN4 is high expressed in endometrial tumors, in vitro experiment reveals that knockdown of CLCN4 inhibits the cells proliferation, migration and invasion. Our study is the first to offer a comprehensive understanding of the oncogenic roles of CLCN4 on different tumors. CLCN4 may become a potential biomarker in UCEC.
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Affiliation(s)
- Chenyang Wang
- Department of Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Jing Li
- Department of Gynecology, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, Shandong 266000, China
| | - Weina Liu
- Department of Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Shiya Li
- Department of Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
| | - Yi Zhang
- Department of Gynecology, The University of Auckland, Grafton, Auckland 1023, New Zealand
| | - Yanbin Jin
- Department of Gynecology, Hainan Affiliated Hospital of Hainan Medical University (Hainan General Hospital), Haikou 570311, China
| | - Jinquan Cui
- Department of Gynecology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou 450000, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450000, China
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23
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Hosur B, Sinha R, Jain NK, Muthanna BA, Bansal V, Singh S, Kamila G. A Novel Neuroimaging Phenotype in the X-Linked Intellectual Disability with a Missense Mutation of CNKSR2 Gene. Neurol India 2023; 71:980-983. [PMID: 37929438 DOI: 10.4103/0028-3886.388124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
Background Mental retardation, X-linked, syndromic, Houge type (MRXSHG) is a form of mental retardation characterized by intellectual disability, speech and language impairments, and early-onset seizures. It has been recently recorded in Online Mendelian Inheritance in Man (OMIM), and only 10 cases have been reported in the literature so far. Objective To highlight the novel neuroimaging findings in the pediatric X-linked intellectual disability with a missense mutation of connector enhancer of kinase suppressor of RAS2 (CNKSR2) gene. Material and Methods We present a case of intellectual disability, refractory epilepsy, speech and language delay with subtle dysmorphism, and behavioral issues in an 11-year-old boy with novel neuroimaging findings in a CNKSR2 gene with missense mutation. Results Brain MRI revealed involvement of the basal ganglia, predominantly the neostriatum, and along with the subependymal aspects with focal cavitations involving, especially the bilateral caudate heads. There was relative sparing of the globus pallidi and posterior putamina bilaterally. Whole-exome sequencing identified a hemizygous missense pathogenic variant in the CNKSR2 gene. The mother was found to be an asymptomatic carrier. Conclusion This case report highlights the rare missense mutation in the CNKSR2 gene and abnormal neuroimaging findings, which further provide information about the phenotypic characteristics of X-linked syndromic intellectual disability.
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Affiliation(s)
- Bharat Hosur
- Department of Radiodiagnosis, Command Hospital, Chandimandir, Panchkula, Haryana, India
| | - Rahul Sinha
- Department of Pediatrics and Pediatric Neurology, Command Hospital, Chandimandir, Panchkula, Haryana, India
| | - Narendra K Jain
- Department of Radiodiagnosis, Command Hospital, Chandimandir, Panchkula, Haryana, India
| | | | - Vandana Bansal
- Department of Pediatrics and Pediatric Neurology, Command Hospital, Chandimandir, Panchkula, Haryana, India
| | - Sonali Singh
- Department of Pediatrics, All India Institute of Medical Sciences, Delhi, India
| | - Gautam Kamila
- Department of Pediatrics, All India Institute of Medical Sciences, Delhi, India
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Lam Z, Wall E, Ryan G, Barber R, Kilby MD, Williams DK. Prenatal diagnosis of CLCN4-related neurodevelopmental disorder in fetuses with congenital brain anomalies. Prenat Diagn 2023; 43:1247-1250. [PMID: 37409888 DOI: 10.1002/pd.6404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/19/2023] [Accepted: 06/04/2023] [Indexed: 07/07/2023]
Abstract
We report two male fetuses born to a healthy unrelated couple, with agenesis of the corpus callosum identified on detailed 20-week ultrasound scans and confirmed by in-utero MRI. Whole-genome sequencing identified a likely pathogenic missense variant in the CLCN4 gene, establishing this as the causative gene in the family. Pathogenic variants in the CLCN4 gene cause a neurodevelopmental disorder (also called Raynaud-Claes syndrome) inherited in an X-linked pattern. The disorder is characterised by developmental delay, intellectual disability, autism spectrum disorder, epilepsy, mental health conditions, and significant feeding difficulties, predominantly, but not exclusively, affecting males. This is the first report of a prenatal phenotype associated with variants in the CLCN4 gene. The diagnosis of the CLCN4-related neurodevelopmental disorder in this family allowed accurate genetic counseling and discussion of reproductive choices. This leaves uncertainty about the possibility of a postnatal neurodevelopmental phenotype in heterozygous females, which we discuss.
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Affiliation(s)
- Zena Lam
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Elizabeth Wall
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Richard Barber
- West Midlands Regional Genetics Laboratory, Central and South Genomic Laboratory Hub, Birmingham, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
- Illumina, Granta Park, Great Abington, Cambridge, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Denise K Williams
- West Midlands Regional Clinical Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
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25
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Kido J, Egami K, Misumi Y, Sugawara K, Tsuchida N, Matsumoto N, Ueda M, Nakamura K. X-linked intellectual disability related to a novel variant of KLHL15. Hum Genome Var 2023; 10:21. [PMID: 37452054 PMCID: PMC10349042 DOI: 10.1038/s41439-023-00248-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/21/2023] [Indexed: 07/18/2023] Open
Abstract
Kelch-like (KLHL) 15, localized on chromosome Xp22.11, was recently identified as an X-linked intellectual disability gene. Herein, we report a case of a male patient with a novel nonsense variant, c.736 C > T p.(Arg246*), in KLHL15, who presented with impaired intelligence, short stature, frequent hypoglycemia, and periodic fever. Patients with nonsense variants in KLHL15 may develop intellectual disabilities, minor skeletal anomalies, and facial dysmorphisms.
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Affiliation(s)
- Jun Kido
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan.
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.
| | | | - Yohei Misumi
- Department of Neurology, Kumamoto University Hospital, Kumamoto, Japan
| | - Keishin Sugawara
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Mitsuharu Ueda
- Department of Neurology, Kumamoto University Hospital, Kumamoto, Japan
| | - Kimitoshi Nakamura
- Department of Pediatrics, Kumamoto University Hospital, Kumamoto, Japan
- Department of Pediatrics, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
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26
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Abdulkareem AA, Zaman Q, Khan H, Khan S, Rehman G, Tariq N, Ahmad M, Owais M, Najumuddin, Muthaffar OY, Bibi F, Khang R, Ryu SW, Naseer MI, Jelani M. Whole exome sequencing identified five novel variants in CNTN2, CARS2, ARSA, and CLCN4 leading to epilepsy in consanguineous families. Front Genet 2023; 14:1185065. [PMID: 37359369 PMCID: PMC10285458 DOI: 10.3389/fgene.2023.1185065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/26/2023] [Indexed: 11/20/2023] Open
Abstract
Introduction: Epilepsy is a group of neurological disorders characterized by recurring seizures and fits. The Epilepsy genes can be classified into four distinct groups, based on involvement of these genes in different pathways leading to Epilepsy as a phenotype. Genetically the disease has been associated with various pathways, leading to pure epilepsy-related disorders caused by CNTN2 variations, or involving physical or systemic issues along with epilepsy caused by CARS2 and ARSA, or developed by genes that are putatively involved in epilepsy lead by CLCN4 variations. Methods: In this study, five families of Pakistani origin (EP-01, EP-02, EP-04, EP-09, and EP-11) were included for molecular diagnosis. Results: Clinical presentations of these patients included neurological symptoms such as delayed development, seizures, regression, myoclonic epilepsy, progressive spastic tetraparesis, vision and hearing impairment, speech problems, muscle fibrillation, tremors, and cognitive decline. Whole exome sequencing in index patients and Sanger sequencing in all available individuals in each family identified four novel homozygous variants in genes CARS2: c.655G>A p.Ala219Thr (EP-01), ARSA: c.338T>C: p.Leu113Pro (EP-02), c.938G>T p.Arg313Leu (EP-11), CNTN2: c.1699G>T p.Glu567Ter (EP-04), and one novel hemizygous variant in gene CLCN4: c.2167C>T p.Arg723Trp (EP-09). Conclusion: To the best of our knowledge these variants were novel and had not been reported in familial epilepsy. These variants were absent in 200 ethnically matched healthy control chromosomes. Three dimensional protein analyses revealed drastic changes in the normal functions of the variant proteins. Furthermore, these variants were designated as "pathogenic" as per guidelines of American College of Medical Genetics 2015. Due to overlapping phenotypes, among the patients, clinical subtyping was not possible. However, whole exome sequencing successfully pinpointed the molecular diagnosis which could be helpful for better management of these patients. Therefore, we recommend that exome sequencing be performed as a first-line molecular diagnostic test in familial cases.
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Affiliation(s)
- Angham Abdulrhman Abdulkareem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Qaiser Zaman
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
- Higher Education Department, Peshawar, Khyber Pakhtunkhwa, Pakistan
- Department of Zoology, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Hamza Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Sabar Khan
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Gauhar Rehman
- Department of Zoology, Abdul Wali Khan University, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Nabeel Tariq
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Mashal Ahmad
- Department of Zoology, Government Postgraduate College Dargai, Malakand, Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Owais
- Mardan College of Medical Technologies, Mardan, Khyber Pakhtunkhwa, Pakistan
| | - Najumuddin
- Programme of Biotechnology, Department of Applied Sciences, Faculty of Engineering, Science and Technology (FEST), Hamdard University, Karachi, Pakistan
| | - Osama Yousef Muthaffar
- Department of Pediatrics, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Fehmida Bibi
- Special Infectious Agents Unit, King Fahd Medical Research Centre, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Rin Khang
- 3Billion Inc., Seoul, Republic of Korea
| | | | - Muhammad Imran Naseer
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Musharraf Jelani
- Rare Diseases Genetics and Genomics, Centre for Omic Sciences, Islamia College, Peshawar, Khyber Pakhtunkhwa, Pakistan
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Coppola MA, Tettey-Matey A, Imbrici P, Gavazzo P, Liantonio A, Pusch M. Biophysical Aspects of Neurodegenerative and Neurodevelopmental Disorders Involving Endo-/Lysosomal CLC Cl -/H + Antiporters. Life (Basel) 2023; 13:1317. [PMID: 37374100 DOI: 10.3390/life13061317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
Endosomes and lysosomes are intracellular vesicular organelles with important roles in cell functions such as protein homeostasis, clearance of extracellular material, and autophagy. Endolysosomes are characterized by an acidic luminal pH that is critical for proper function. Five members of the gene family of voltage-gated ChLoride Channels (CLC proteins) are localized to endolysosomal membranes, carrying out anion/proton exchange activity and thereby regulating pH and chloride concentration. Mutations in these vesicular CLCs cause global developmental delay, intellectual disability, various psychiatric conditions, lysosomal storage diseases, and neurodegeneration, resulting in severe pathologies or even death. Currently, there is no cure for any of these diseases. Here, we review the various diseases in which these proteins are involved and discuss the peculiar biophysical properties of the WT transporter and how these properties are altered in specific neurodegenerative and neurodevelopmental disorders.
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Affiliation(s)
- Maria Antonietta Coppola
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | | | - Paola Imbrici
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Paola Gavazzo
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy
| | - Antonella Liantonio
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", 70125 Bari, Italy
| | - Michael Pusch
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche, 16149 Genova, Italy
- RAISE Ecosystem, 16149 Genova, Italy
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28
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Caswell RC, Baptista J, Cairns LM, Wilson K, Stewart H. Clinical findings and structural analysis involving a patient with a novel KLHL15 variant. Eur J Med Genet 2023; 66:104768. [PMID: 37059329 DOI: 10.1016/j.ejmg.2023.104768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/30/2023] [Accepted: 04/12/2023] [Indexed: 04/16/2023]
Abstract
A de novo novel variant of uncertain significance p. (Arg532del) in the KLHL15 gene was identified by trio exome analysis in a child with global developmental delay, coarse facial features, repetitive behaviour, increased fatigability, poor feeding and gastro-oesophageal reflux. Comparative modelling and structural analysis were performed to gain insight into the effects of the variant on KLHL15 protein structure and function, with a view to aiding variant classification. The p. (Arg532del) variant affects a highly conserved residue within one of the Kelch repeats of the KLHL15 protein. This residue contributes to the stability of loop regions at the substrate binding surface of the protein; comparative modelling of the variant protein predicts altered topology at this surface, including at residue Tyr552, which is known to be important for substrate binding. We propose that it is highly probable that the p. (Arg532del) variant has a deleterious impact on KLHL15 structure, leading to a reduced level of protein function in vivo.
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Affiliation(s)
- Richard C Caswell
- Exeter Genomics Laboratory, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK
| | - Julia Baptista
- Peninsula Medical School, Faculty of Health, University of Plymouth, UK
| | - Lauren M Cairns
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK; Royal Berkshire Hospital, Royal Berkshire NHS Foundation Trust, Reading, RG1 5AN, UK
| | - Kate Wilson
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK; Genes Australia, 298 Gilchrist Ave, Herston QLD, 4006, Australia
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, OX3 7HE, UK.
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29
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Hu J, Xu X, Li J, Jiang Y, Hong X, Rexrode KM, Wang G, Hu FB, Zhang H, Karmaus WJ, Wang X, Liang L. Sex differences in the intergenerational link between maternal and neonatal whole blood DNA methylation: a genome-wide analysis in 2 birth cohorts. Clin Epigenetics 2023; 15:51. [PMID: 36966332 PMCID: PMC10040137 DOI: 10.1186/s13148-023-01442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 02/06/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND The mother-child inheritance of DNA methylation (DNAm) variations could contribute to the inheritance of disease susceptibility across generations. However, no study has investigated patterns of mother-child associations in DNAm at the genome-wide scale. It remains unknown whether there are sex differences in mother-child DNAm associations. RESULTS Using genome-wide DNAm profiling data (721,331 DNAm sites, including 704,552 on autosomes and 16,779 on the X chromosome) of 396 mother-newborn pairs (54.5% male) from the Boston Birth Cohort, we found significant sex differences in mother-newborn correlations in genome-wide DNAm patterns (Spearman's rho = 0.91-0.98; p = 4.0 × 10-8), with female newborns having stronger correlations. Sex differences in correlations were attenuated but remained significant after excluding X-chromosomal DNAm sites (Spearman's rho = 0.91-0.98; p = 0.035). Moreover, 89,267 DNAm sites (12.4% of all analyzed, including 88,051 [12.5% of analyzed] autosomal and 1,216 [7.2% of analyzed] X-chromosomal sites) showed significant mother-newborn associations in methylation levels, and the top autosomal DNAm sites had high heritability than the genome-wide background (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.92). Additionally, significant interactions between newborn sex and methylation levels were observed for 11 X-chromosomal and 4 autosomal DNAm sites that were mapped to genes that have been associated with sex-specific disease/traits or early development (e.g., EFHC2, NXY, ADCYAP1R1, and BMP4). Finally, 18,769 DNAm sites (14,482 [77.2%] on the X chromosome) showed mother-newborn differences in methylation levels that were significantly associated with newborn sex, and the top autosomal DNAm sites had relatively small heritability (e.g., the top 100 autosomal DNAm sites had a medium h2 of 0.23). These DNAm sites were mapped to 2,532 autosomal genes and 978 X-chromosomal genes with significant enrichment in pathways involved in neurodegenerative and psychological diseases, development, neurophysiological process, immune response, and sex-specific cancers. Replication analysis in the Isle of Wight birth cohort yielded consistent results. CONCLUSION In two independent birth cohorts, we demonstrated strong mother-newborn correlations in whole blood DNAm on both autosomes and ChrX, and such correlations vary substantially by sex. Future studies are needed to examine to what extent our findings contribute to developmental origins of pediatric and adult diseases with well-observed sex differences.
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Affiliation(s)
- Jie Hu
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Xin Xu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
| | - Jun Li
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Yu Jiang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiumei Hong
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Kathryn M Rexrode
- Division of Women's Health, Department of Medicine, Bigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Guoying Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Frank B Hu
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried J Karmaus
- Division of Epidemiology, Biostatistics, & Environmental Health, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Xiaobin Wang
- Center On the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, 655 Huntington Avenue, Building 2, Room 207, Boston, MA, 02115, USA.
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
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30
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Abstract
Although differential transcription drives the development of multicellular organisms, the ultimate readout of a protein-coding gene is ribosome-dependent mRNA translation. Ribosomes were once thought of as uniform molecular machines, but emerging evidence indicates that the complexity and diversity of ribosome biogenesis and function should be given a fresh look in the context of development. This Review begins with a discussion of different developmental disorders that have been linked with perturbations in ribosome production and function. We then highlight recent studies that reveal how different cells and tissues exhibit variable levels of ribosome production and protein synthesis, and how changes in protein synthesis capacity can influence specific cell fate decisions. We finish by touching upon ribosome heterogeneity in stress responses and development. These discussions highlight the importance of considering both ribosome levels and functional specialization in the context of development and disease.
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Affiliation(s)
- Chunyang Ni
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
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31
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Bustos F, Findlay GM. Therapeutic validation and targeting of signalling networks that are dysregulated in intellectual disability. FEBS J 2023; 290:1454-1460. [PMID: 35212144 PMCID: PMC10952735 DOI: 10.1111/febs.16411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/14/2022] [Accepted: 02/22/2022] [Indexed: 11/28/2022]
Abstract
Intellectual disability (ID) represents a major burden on healthcare systems in the developed world. However, there is a disconnect between our knowledge of genes that are mutated in ID and our understanding of the underpinning molecular mechanisms that cause these disorders. We argue that elucidating the signalling and transcriptional networks that are dysregulated in patients will afford new therapeutic opportunities.
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Affiliation(s)
- Francisco Bustos
- Pediatrics and Rare Diseases GroupSanford ResearchSioux FallsSDUSA
- Department of PediatricsSanford School of MedicineUniversity of South DakotaSioux FallsSDUSA
| | - Greg M. Findlay
- The MRC Protein Phosphorylation & Ubiquitylation UnitSchool of Life SciencesThe University of DundeeDundeeUK
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32
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Leonardi E, Aspromonte MC, Drongitis D, Bettella E, Verrillo L, Polli R, McEntagart M, Licchetta L, Dilena R, D'Arrigo S, Ciaccio C, Esposito S, Leuzzi V, Torella A, Baldo D, Lonardo F, Bonato G, Pellegrin S, Stanzial F, Posmyk R, Kaczorowska E, Carecchio M, Gos M, Rzońca-Niewczas S, Miano MG, Murgia A. Expanding the genetics and phenotypic spectrum of Lysine-specific demethylase 5C (KDM5C): a report of 13 novel variants. Eur J Hum Genet 2023; 31:202-215. [PMID: 36434256 PMCID: PMC9905063 DOI: 10.1038/s41431-022-01233-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 10/14/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022] Open
Abstract
Lysine-specific demethylase 5C (KDM5C) has been identified as an important chromatin remodeling gene, contributing to X-linked neurodevelopmental disorders (NDDs). The KDM5C gene, located in the Xp22 chromosomal region, encodes the H3K4me3-me2 eraser involved in neuronal plasticity and dendritic growth. Here we report 30 individuals carrying 13 novel and one previously identified KDM5C variants. Our cohort includes the first reported case of somatic mosaicism in a male carrying a KDM5C nucleotide substitution, and a dual molecular finding in a female carrying a homozygous truncating FUCA1 alteration together with a de novo KDM5C variant. With the use of next generation sequencing strategies, we detected 1 frameshift, 1 stop codon, 2 splice-site and 10 missense variants, which pathogenic role was carefully investigated by a thorough bioinformatic analysis. The pattern of X-chromosome inactivation was found to have an impact on KDM5C phenotypic expression in females of our cohort. The affected individuals of our case series manifested a neurodevelopmental condition characterized by psychomotor delay, intellectual disability with speech disorders, and behavioral features with particular disturbed sleep pattern; other observed clinical manifestations were short stature, obesity and hypertrichosis. Collectively, these findings expand the current knowledge about the pathogenic mechanisms leading to dysfunction of this important chromatin remodeling gene and contribute to a refinement of the KDM5C phenotypic spectrum.
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Affiliation(s)
- Emanuela Leonardi
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Maria Cristina Aspromonte
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Denise Drongitis
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Naples, Italy
| | - Elisa Bettella
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Lucia Verrillo
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", CNR, Naples, Italy
| | - Roberta Polli
- Department of Women's and Children's Health, University of Padova, Padova, Italy
- Pediatric Research Institute, Città della Speranza, Padova, Italy
| | - Meriel McEntagart
- Medical Genetics Unit, St. George's University Hospitals, London, UK
| | - Laura Licchetta
- IRCCS, Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Robertino Dilena
- Neurophysiopathology Unit, Foundation IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Stefano D'Arrigo
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudia Ciaccio
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Silvia Esposito
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Vincenzo Leuzzi
- Unit of Child Neurology and Psychiatry, Department of Human Neuroscience, Sapienza University of Rome, Rome, Italy
| | - Annalaura Torella
- University of Campania "Luigi Vanvitelli", Caserta, Italy
- Telethon Institute of Genetics and Medicine (TIGEM), Pozzuoli, Italy
| | - Demetrio Baldo
- Unit of medical genetics, ULSS 2 Treviso Hospital, Treviso, Italy
| | | | - Giulia Bonato
- Movement Disorders Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Serena Pellegrin
- Child Neurology and Neurorehabilitation Unit, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Renata Posmyk
- Department of Clinical Genetics, Medical University in Bialystok, Bialystok, Poland
| | - Ewa Kaczorowska
- Department of Biology and Medical Genetics, Medical University of Gdansk, Gdansk, Poland
| | - Miryam Carecchio
- Movement Disorders Unit, Department of Neuroscience, University of Padova, Padova, Italy
| | - Monika Gos
- Development Genetics Laboratory, Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Sylwia Rzońca-Niewczas
- Development Genetics Laboratory, Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | - Alessandra Murgia
- Department of Women's and Children's Health, University of Padova, Padova, Italy.
- Pediatric Research Institute, Città della Speranza, Padova, Italy.
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33
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Ramos AKS, Caldas-Rosa ECC, Ferreira BM, Versiani BR, Moretti PN, de Oliveira SF, Pic-Taylor A, Mazzeu JF. ZDHHC9 X-linked intellectual disability: Clinical and molecular characterization. Am J Med Genet A 2023; 191:599-604. [PMID: 36416207 DOI: 10.1002/ajmg.a.63052] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 10/28/2022] [Accepted: 11/08/2022] [Indexed: 11/24/2022]
Abstract
The ZDHHC9 gene encodes the Zinc Finger DHHC-Type Containing 9 protein that functions as a palmitoyltransferase. Variants in this gene have been reported as the cause of Raymond-type X-linked intellectual disability with only 16 families described in the literature. This study reviews molecular and clinical data from previously reported patients and reports the case of a 13-year-old patient with a splicing variant in ZDHHC9 presenting intellectual disability, developmental delay, facial dysmorphisms, and skeletal defects. Although intellectual disability and developmental delay with severe speech delay have been reported in all cases with available clinical data, the remaining clinical signs differ significantly between patients. Missense, nonsense, frameshift, and splicing variants, in addition to large exonic deletions, have been described suggesting a loss of function mechanism. Though variants are distributed in almost all exons, most missense and nonsense variants affect arginine residues located in the cytoplasmic domains of this transmembrane protein, suggesting possible mutational hotspots.
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Affiliation(s)
| | | | | | | | | | - Silviene Fabiana de Oliveira
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil
| | - Aline Pic-Taylor
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil.,Departamento de Genética e Morfologia, Instituto de Ciências Biológicas, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Biologia Animal, Universidade de Brasília, Brasília, Brazil
| | - Juliana F Mazzeu
- Programa de Pós-graduação em Ciências da Saúde, Universidade de Brasília, Brasília, Brazil.,Programa de Pós-graduação em Ciências Médicas, Universidade de Brasília, Brasília, Brazil.,Hospital Universitário, Universidade de Brasília, Brasília, Brazil.,Faculdade de Medicina, Universidade de Brasília, Brasília, Brazil
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34
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Younus M, Rasheed M, Lin Z, Asiri SA, Almazni IA, Alshehri MA, Shafiq S, Iqbal I, Khan A, Ullah H, Umair M, Waqas A. Homozygous Missense Variant in the N-Terminal Region of ANK3 Gene Is Associated with Developmental Delay, Seizures, Speech Abnormality, and Aggressive Behavior. Mol Syndromol 2023; 14:11-20. [PMID: 36777705 PMCID: PMC9912002 DOI: 10.1159/000526381] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 08/04/2022] [Indexed: 11/19/2022] Open
Abstract
Introduction Intellectual disability (ID) is a lifelong disability that affects an individual‧s learning capacity and adaptive behavior. Such individuals depend on their families for day-to-day survival and pose a significant challenge to the healthcare system, especially in developing countries. ID is a heterogeneous condition, and genetic studies are essential to unravel the underlying cellular pathway for brain development and functioning. Methods Here we studied a female index patient, born to a consanguineous Pakistani couple, showing clinical symptoms of ID, ataxia, hypotonia, developmental delay, seizures, speech abnormality, and aggressive behavior. Whole exome sequencing (WES) coupled with Sanger sequencing was performed for molecular diagnosis. Further, 3D protein modeling was performed to see the effect of variant on protein structure. Results WES identified a novel homozygous missense variant (c.178T>C; p.Tyr60His) in the ANK3 gene. In silico analysis and 3-dimensional (3D) protein modeling supports the deleterious impact of this variant on the encoding protein, which compromises the protein‧s overall structure and function. Conclusion Our finding supports the clinical and genetic diversity of the ANK3 gene as a plausible candidate gene for ID syndrome. Intelligence is a complex polygenic human trait, and understanding molecular and biological pathways involved in learning and memory can solve the complex puzzle of how cognition develops. Intellectual disability (ID) is defined as a deficit in an individual‧s learning and adaptive behavior at an early age of onset [American Psychiatric Association, 2013]. It is one of the major medical, and cognitive disorders with a prevalence of 1-3% in the population worldwide [Leonard and Wen, 2002]. ID often exists with other disabling mental conditions such as autism, attention deficit hyperactivity disorder, epilepsy, schizophrenia, bipolar disorder, or depression. Almost half of the cases appear to have a genetic explanation that ranges from cytogenetically visible abnormalities to monogenic defects [Flint, 2001; Ropers, 2010; Tucker-Drob et al., 2013]. Intellectual disability is a genetically heterogeneous condition, and more than 700 genes have been identified to cause ID alone or as a part of the syndrome. Research in X-linked ID has identified more than 100 disease-causing genes on the X chromosome that play a role in cognition; however, research into autosomal causes of ID is still ongoing [Vissers et al., 2016].
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Affiliation(s)
- Muhammad Younus
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Memoona Rasheed
- Department of Pathology, Islamabad Medical and Dental College, Islamabad, Pakistan
| | - Zhaohan Lin
- State Key Laboratory of Membrane Biology and Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology and Peking-Tsinghua Center for Life Sciences and PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing, China
| | - Saeed A. Asiri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Ibrahim A. Almazni
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed Ali Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Sarfraz Shafiq
- Department of Anatomy and Cell Biology, University of Western Ontario, London, Ontario, Canada
| | - Imran Iqbal
- Department of PLR, Institute of Active Polymers, Helmholtz-Zentrum Hereon, Teltow, Germany
| | - Amjad Khan
- Faculty of Science, Department of Biological Sciences (Zoology), University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Hanif Ullah
- Guangxi Key Laboratory for Genomic and Personalized Medicine, Guangxi Collaborative Innovation Center for Genomic and Personalized Medicine, Nanning, China
| | - Muhammad Umair
- Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs (MNGH), Riyadh, Saudi Arabia,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan,*Muhammad Umair,
| | - Ahmed Waqas
- Department of Zoology, Division of Science and Technology, University of Education Lahore, Lahore, Pakistan,**Ahmed Waqas,
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35
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Maia N, Ibarluzea N, Misra-Isrie M, Koboldt DC, Marques I, Soares G, Santos R, Marcelis CLM, Keski-Filppula R, Guitart M, Gabau Vila E, Lehman A, Hickey S, Mori M, Terhal P, Valenzuela I, Lasa-Aranzasti A, Cueto-González AM, Chhouk BH, Yeh RC, Neil JE, Abu-Libde B, Kleefstra T, Elting MW, Császár A, Kárteszi J, Bessenyei B, van Bokhoven H, Jorge P, van Hagen JM, de Brouwer APM. Missense MED12 variants in 22 males with intellectual disability: From nonspecific symptoms to complete syndromes. Am J Med Genet A 2023; 191:135-143. [PMID: 36271811 PMCID: PMC10092556 DOI: 10.1002/ajmg.a.63004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 07/26/2022] [Accepted: 08/13/2022] [Indexed: 12/14/2022]
Abstract
We describe the phenotype of 22 male patients (20 probands) carrying a hemizygous missense variant in MED12. The phenotypic spectrum is very broad ranging from nonspecific intellectual disability (ID) to the three well-known syndromes: Opitz-Kaveggia syndrome, Lujan-Fryns syndrome, or Ohdo syndrome. The identified variants were randomly distributed throughout the gene (p = 0.993, χ2 test), but mostly outside the functional domains (p = 0.004; χ2 test). Statistical analyses did not show a correlation between the MED12-related phenotypes and the locations of the variants (p = 0.295; Pearson correlation), nor the protein domain involved (p = 0.422; Pearson correlation). In conclusion, establishing a genotype-phenotype correlation in MED12-related diseases remains challenging. Therefore, we think that patients with a causative MED12 variant are currently underdiagnosed due to the broad patients' clinical presentations.
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Affiliation(s)
- Nuno Maia
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | | | - Mala Misra-Isrie
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Daniel C Koboldt
- Steve and Cindy Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Isabel Marques
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Gabriela Soares
- Unidade de Genética Médica, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto), Porto, Portugal
| | - Rosário Santos
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Carlo L M Marcelis
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Riikka Keski-Filppula
- Department of Clinical Genetics, Oulu University Hospital, Medical Research Center Oulu and PEDEGO Research Unit, University of Oulu, Oulu, Finland
| | - Miriam Guitart
- Paediatric Unit, ParcTaulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí, I3PTUniversitat Autònoma de Barcelona, Sabadell, Spain
| | - Elisabeth Gabau Vila
- Paediatric Unit, ParcTaulí Hospital Universitari, Institut d'Investigació i Innovació Parc Taulí, I3PTUniversitat Autònoma de Barcelona, Sabadell, Spain
| | - April Lehman
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Scott Hickey
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio, USA.,Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Mari Mori
- Division of Genetic & Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio, USA.,Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Paulien Terhal
- Division Laboratories, Pharmacy and Biomedical Genetics, Wilhelmina Children's Hospital, Utrecht, The Netherlands
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Anna Maria Cueto-González
- Department of Clinical and Molecular Genetics, Vall d'Hebron University Hospital and Medicine Genetics Group, Vall d'Hebron Research Institute, Barcelona, Spain
| | - Brian H Chhouk
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Rebecca C Yeh
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Jennifer E Neil
- Division of Genetics and Genomics and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA
| | | | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Andrea Császár
- Paediatric Ward, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Judit Kárteszi
- Genetic Counselling, Hospital of Zala County, Zalaegerszeg, Hungary
| | - Beáta Bessenyei
- Division of Clinical Genetics, Department of Laboratory Medicine, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Paula Jorge
- Unidade de Genética Molecular, Centro de Genética Médica Doutor Jacinto de Magalhães (CGM), Centro Hospitalar Universitário do Porto (CHUPorto); Unit for Multidisciplinary Research In Biomedicine (UMIB), Institute of Biomedical Sciences Abel Salazar (ICBAS), and ITR - Laboratory for Integrative and Translational Research in Population Health, University of Porto, Porto, Portugal
| | - Johanna M van Hagen
- Department of Human Genetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Arjan P M de Brouwer
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, The Netherlands
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Functional and clinical studies reveal pathophysiological complexity of CLCN4-related neurodevelopmental condition. Mol Psychiatry 2023; 28:668-697. [PMID: 36385166 PMCID: PMC9908558 DOI: 10.1038/s41380-022-01852-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 11/17/2022]
Abstract
Missense and truncating variants in the X-chromosome-linked CLCN4 gene, resulting in reduced or complete loss-of-function (LOF) of the encoded chloride/proton exchanger ClC-4, were recently demonstrated to cause a neurocognitive phenotype in both males and females. Through international clinical matchmaking and interrogation of public variant databases we assembled a database of 90 rare CLCN4 missense variants in 90 families: 41 unique and 18 recurrent variants in 49 families. For 43 families, including 22 males and 33 females, we collated detailed clinical and segregation data. To confirm causality of variants and to obtain insight into disease mechanisms, we investigated the effect on electrophysiological properties of 59 of the variants in Xenopus oocytes using extended voltage and pH ranges. Detailed analyses revealed new pathophysiological mechanisms: 25% (15/59) of variants demonstrated LOF, characterized by a "shift" of the voltage-dependent activation to more positive voltages, and nine variants resulted in a toxic gain-of-function, associated with a disrupted gate allowing inward transport at negative voltages. Functional results were not always in line with in silico pathogenicity scores, highlighting the complexity of pathogenicity assessment for accurate genetic counselling. The complex neurocognitive and psychiatric manifestations of this condition, and hitherto under-recognized impacts on growth, gastrointestinal function, and motor control are discussed. Including published cases, we summarize features in 122 individuals from 67 families with CLCN4-related neurodevelopmental condition and suggest future research directions with the aim of improving the integrated care for individuals with this diagnosis.
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Schwartz CE, Louie RJ, Toutain A, Skinner C, Friez MJ, Stevenson RE. X-Linked intellectual disability update 2022. Am J Med Genet A 2023; 191:144-159. [PMID: 36300573 DOI: 10.1002/ajmg.a.63008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 07/28/2022] [Accepted: 09/29/2022] [Indexed: 12/14/2022]
Abstract
Genes that are involved in the transcription process, mitochondrial function, glycoprotein metabolism, and ubiquitination dominate the list of 21 new genes associated with X-linked intellectual disability since the last update in 2017. The new genes were identified by sequencing of candidate genes (2), the entire X-chromosome (2), the whole exome (15), or the whole genome (2). With these additions, 42 (21%) of the 199 named XLID syndromes and 27 (25%) of the 108 numbered nonsyndromic XLID families remain to be resolved at the molecular level. Although the pace of discovery of new XLID genes has slowed during the past 5 years, the density of genes on the X chromosome that cause intellectual disability still appears to be twice the density of intellectual disability genes on the autosomes.
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Affiliation(s)
| | | | - Annick Toutain
- Department of Medical Genetics, Centre Hospitalier Universitaire, Tours, France
| | - Cindy Skinner
- Greenwood Genetic Center, Greenwood, South Carolina, USA
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Meziane H, Birling MC, Wendling O, Leblanc S, Dubos A, Selloum M, Pavlovic G, Sorg T, Kalscheuer VM, Billuart P, Laumonnier F, Chelly J, van Bokhoven H, Herault Y. Large-Scale Functional Assessment of Genes Involved in Rare Diseases with Intellectual Disabilities Unravels Unique Developmental and Behaviour Profiles in Mouse Models. Biomedicines 2022; 10:biomedicines10123148. [PMID: 36551904 PMCID: PMC9775489 DOI: 10.3390/biomedicines10123148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Major progress has been made over the last decade in identifying novel genes involved in neurodevelopmental disorders, although the task of elucidating their corresponding molecular and pathophysiological mechanisms, which are an essential prerequisite for developing therapies, has fallen far behind. We selected 45 genes for intellectual disabilities to generate and characterize mouse models. Thirty-nine of them were based on the frequency of pathogenic variants in patients and literature reports, with several corresponding to de novo variants, and six other candidate genes. We used an extensive screen covering the development and adult stages, focusing specifically on behaviour and cognition to assess a wide range of functions and their pathologies, ranging from basic neurological reflexes to cognitive abilities. A heatmap of behaviour phenotypes was established, together with the results of selected mutants. Overall, three main classes of mutant lines were identified based on activity phenotypes, with which other motor or cognitive deficits were associated. These data showed the heterogeneity of phenotypes between mutation types, recapitulating several human features, and emphasizing the importance of such systematic approaches for both deciphering genetic etiological causes of ID and autism spectrum disorders, and for building appropriate therapeutic strategies.
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Affiliation(s)
- Hamid Meziane
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Marie-Christine Birling
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Olivia Wendling
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Sophie Leblanc
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Aline Dubos
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Guillaume Pavlovic
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Vera M. Kalscheuer
- Max Planck Institute for Molecular Genetics, Research Group Development and Disease, Ihnestr. 63-73, 14195 Berlin, Germany
| | - Pierre Billuart
- Institute of Psychiatry and Neuroscience of Paris (IPNP), Université de Paris, INSERM U1266, “Genetic and Development of Cerebral Cortex”, 75014 Paris, France
- GHU Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, 75014 Paris, France
| | - Frédéric Laumonnier
- UMR1253, iBrain, University of Tours, Inserm, 37032 Tours, France
- Service de Génétique, Centre Hospitalier Régional Universitaire, 37044 Tours, France
| | - Jamel Chelly
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
| | - Hans van Bokhoven
- Department of Cognitive Neuroscience, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Department of Human Genetics, Radboudumc, 6500 HB Nijmegen, The Netherlands
- Donders Institute for Brain, Cognition, and Behaviour, Centre for Neuroscience, 6525 AJ Nijmegen, The Netherlands
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris (ICS), PHENOMIN, CELPHEDIA, 1 rue Laurent Fries, 67404 Illkirch, France
- Université de Strasbourg, CNRS, INSERM, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, 67404 Illkirch, France
- Correspondence: ; Tel.: +33-388-65-5715
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Hatch HAM, Secombe J. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J 2022; 289:7776-7787. [PMID: 34536985 PMCID: PMC8930784 DOI: 10.1111/febs.16204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
The widespread availability of genetic testing for those with neurodevelopmental disorders has highlighted the importance of many genes necessary for the proper development and function of the nervous system. One gene found to be genetically altered in the X-linked intellectual disability disorder Claes-Jensen syndrome is KDM5C, which encodes a histone demethylase that regulates transcription by altering chromatin. While the genetic link between KDM5C and cognitive (dys)function is clear, how KDM5C functions to control transcriptional programs within neurons to impact their growth and activity remains the subject of ongoing research. Here, we review our current knowledge of Claes-Jensen syndrome and discuss important new data using model organisms that have revealed the importance of KDM5C in regulating aspects of neuronal development and function. Continued research into the molecular and cellular activities regulated by KDM5C is expected to provide critical etiological insights into Claes-Jensen syndrome and highlight potential targets for developing therapies to improve the quality of life of those affected.
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Affiliation(s)
- Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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40
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Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X. Nat Commun 2022; 13:6570. [PMID: 36323681 PMCID: PMC9630267 DOI: 10.1038/s41467-022-34264-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression, and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using machine learning classifiers trained to distinguish disease-associated from dispensable genes, we classify 247 genes, including 115 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.
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Bustos F, Mathur S, Espejo-Serrano C, Toth R, Hastie CJ, Virdee S, Findlay GM. Activity-based probe profiling of RNF12 E3 ubiquitin ligase function in Tonne-Kalscheuer syndrome. Life Sci Alliance 2022; 5:5/11/e202101248. [PMID: 35764390 PMCID: PMC9240097 DOI: 10.26508/lsa.202101248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/24/2022] Open
Abstract
Ubiquitylation enzymes are involved in all aspects of eukaryotic biology and are frequently disrupted in disease. One example is the E3 ubiquitin ligase RNF12/RLIM, which is mutated in the developmental disorder Tønne-Kalscheuer syndrome (TOKAS). RNF12 TOKAS variants largely disrupt catalytic E3 ubiquitin ligase activity, which presents a pressing need to develop approaches to assess the impact of variants on RNF12 activity in patients. Here, we use photocrosslinking activity-based probes (photoABPs) to monitor RNF12 RING E3 ubiquitin ligase activity in normal and pathogenic contexts. We demonstrate that photoABPs undergo UV-induced labelling of RNF12 that is consistent with its RING E3 ligase activity. Furthermore, photoABPs robustly report the impact of RNF12 TOKAS variants on E3 activity, including variants within the RING domain and distal non-RING regulatory elements. Finally, we show that this technology can be rapidly deployed in human pluripotent stem cells. In summary, photoABPs are versatile tools that can directly identify disruptions to RING E3 ubiquitin ligase activity in human disease, thereby providing new insight into pathogenic mechanisms.
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Affiliation(s)
- Francisco Bustos
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Sunil Mathur
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Carmen Espejo-Serrano
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Rachel Toth
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - C James Hastie
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Satpal Virdee
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
| | - Greg M Findlay
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee, UK
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The emerging importance of METTL5-mediated ribosomal RNA methylation. Exp Mol Med 2022; 54:1617-1625. [PMID: 36266443 PMCID: PMC9636144 DOI: 10.1038/s12276-022-00869-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 07/21/2022] [Accepted: 08/11/2022] [Indexed: 01/19/2023] Open
Abstract
The study of the epitranscriptome has thus far focused largely on mRNA methylation. Recent human genetics studies suggest that methylation of ribosomal RNA also contributes to brain development and cognition. In particular, the m6A modification at the A-1832 position of the 18S rRNA is installed by METTL5. Mutations or deletions of Mettl5 in humans and mice, respectively, cause abnormal translation and gene expression that in turn mediates stem cell behaviors such as differentiation. In this review, we provide an overview of the current knowledge of the methyltransferase METTL5, as well as the molecular biology surrounding m6A on rRNA and how it regulates cell behavior.
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43
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Jolly LA, Kumar R, Penzes P, Piper M, Gecz J. The DUB Club: Deubiquitinating Enzymes and Neurodevelopmental Disorders. Biol Psychiatry 2022; 92:614-625. [PMID: 35662507 PMCID: PMC10084722 DOI: 10.1016/j.biopsych.2022.03.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 02/08/2023]
Abstract
Protein ubiquitination is a widespread, multifunctional, posttranslational protein modification, best known for its ability to direct protein degradation via the ubiquitin proteasome system (UPS). Ubiquitination is also reversible, and the human genome encodes over 90 deubiquitinating enzymes (DUBs), many of which appear to target specific subsets of ubiquitinated proteins. This review focuses on the roles of DUBs in neurodevelopmental disorders (NDDs). We present the current genetic evidence connecting 12 DUBs to a range of NDDs and the functional studies implicating at least 19 additional DUBs as candidate NDD genes. We highlight how the study of DUBs in NDDs offers critical insights into the role of protein degradation during brain development. Because one of the major known functions of a DUB is to antagonize the UPS, loss of function of DUB genes has been shown to culminate in loss of abundance of its protein substrates. The identification and study of NDD DUB substrates in the developing brain is revealing that they regulate networks of proteins that themselves are encoded by NDD genes. We describe the new technologies that are enabling the full resolution of DUB protein networks in the developing brain, with the view that this knowledge can direct the development of new therapeutic paradigms. The fact that the abundance of many NDD proteins is regulated by the UPS presents an exciting opportunity to combat NDDs caused by haploinsufficiency, because the loss of abundance of NDD proteins can be potentially rectified by antagonizing their UPS-based degradation.
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Affiliation(s)
- Lachlan A Jolly
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia.
| | - Raman Kumar
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael Piper
- School of Biomedical Sciences and Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Jozef Gecz
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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Ben-Mahmoud A, Jun KR, Gupta V, Shastri P, de la Fuente A, Park Y, Shin KC, Kim CA, da Cruz AD, Pinto IP, Minasi LB, Silva da Cruz A, Faivre L, Callier P, Racine C, Layman LC, Kong IK, Kim CH, Kim WY, Kim HG. A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders. Front Mol Neurosci 2022; 15:979061. [PMID: 36277487 PMCID: PMC9582330 DOI: 10.3389/fnmol.2022.979061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.
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Affiliation(s)
- Afif Ben-Mahmoud
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Ran Jun
- Department of Laboratory Medicine, Inje University Haeundae Paik Hospital, Busan, South Korea
| | - Vijay Gupta
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Pinang Shastri
- Department of Cardiovascular Medicine, Cape Fear Valley Medical Center, Fayetteville, NC, United States
| | - Alberto de la Fuente
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Yongsoo Park
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Kyung Chul Shin
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | - Chong Ae Kim
- Faculdade de Medicina, Unidade de Genética do Instituto da Criança – Hospital das Clínicas HCFMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Aparecido Divino da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Irene Plaza Pinto
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Lysa Bernardes Minasi
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Alex Silva da Cruz
- School of Medical and Life Sciences, Genetics Master Program, Replicon Research Group, Pontifical Catholic University of Goiás, Goiânia, Brazil
- Genetics Master Program, Replicon Research Nucleus, School of Agrarian and Biological Sciences, Pontifical Catholic University of Goias, Goiás, Brazil
| | - Laurence Faivre
- Inserm UMR 1231 GAD, Genetics of Developmental Disorders, Université de Bourgogne-Franche Comté, Dijon, France
- Centre de Référence Anomalies du Développement et Syndromes Malformatifs, Hôpital d’Enfants, Dijon, France
| | - Patrick Callier
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Caroline Racine
- UMR 1231 GAD, Inserm – Université Bourgogne-Franche Comté, Dijon, France
| | - Lawrence C. Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Augusta University, Augusta, GA, United States
- Department of Neuroscience and Regenerative Medicine, Augusta University, Augusta, GA, United States
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, South Korea
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Woo-Yang Kim
- Department of Biological Sciences, Kent State University, Kent, OH, United States
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
- *Correspondence: Hyung-Goo Kim,
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Sierra-Marquez J, Willuweit A, Schöneck M, Bungert-Plümke S, Gehlen J, Balduin C, Müller F, Lampert A, Fahlke C, Guzman RE. ClC-3 regulates the excitability of nociceptive neurons and is involved in inflammatory processes within the spinal sensory pathway. Front Cell Neurosci 2022; 16:920075. [PMID: 37124866 PMCID: PMC10134905 DOI: 10.3389/fncel.2022.920075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
ClC-3 Cl–/H+ exchangers are expressed in multiple endosomal compartments and likely modify intra-endosomal pH and [Cl–] via the stoichiometrically coupled exchange of two Cl– ions and one H+. We studied pain perception in Clcn3–/– mice and found that ClC-3 not only modifies the electrical activity of peripheral nociceptors but is also involved in inflammatory processes in the spinal cord. We demonstrate that ClC-3 regulates the number of Nav and Kv ion channels in the plasma membrane of dorsal root ganglion (DRG) neurons and that these changes impair the age-dependent decline in excitability of sensory neurons. To distinguish the role of ClC-3 in Cl–/H+ exchange from its other functions in pain perception, we used mice homozygous for the E281Q ClC-3 point mutation (Clcn3E281Q/E281Q), which completely eliminates transport activity. Since ClC-3 forms heterodimers with ClC-4, we crossed these animals with Clcn4–/– to obtain mice completely lacking in ClC-3-associated endosomal chloride–proton transport. The electrical properties of Clcn3E281Q/E281Q/Clcn4–/– DRG neurons were similar to those of wild-type cells, indicating that the age-dependent adjustment of neuronal excitability is independent of ClC-3 transport activity. Both Clcn3–/– and Clcn3E281Q/E281Q/Clcn4–/– animals exhibited microglial activation in the spinal cord, demonstrating that competent ClC-3 transport is needed to maintain glial cell homeostasis. Our findings illustrate how reduced Cl–/H+ exchange contributes to inflammatory responses and demonstrate a role for ClC-3 in the homeostatic regulation of neuronal excitability beyond its function in endosomal ion balance.
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Affiliation(s)
- Juan Sierra-Marquez
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Antje Willuweit
- Medical Imaging Physics, Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Michael Schöneck
- Medical Imaging Physics, Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Stefanie Bungert-Plümke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Jana Gehlen
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Carina Balduin
- Medical Imaging Physics, Institute of Neuroscience and Medicine (INM-4), Forschungszentrum Jülich, Jülich, Germany
| | - Frank Müller
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | | | - Christoph Fahlke
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
| | - Raul E. Guzman
- Institute of Biological Information Processing, Molecular and Cellular Physiology (IBI-1), Forschungszentrum Jülich, Jülich, Germany
- *Correspondence: Raul E. Guzman,
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Segarra-Fas A, Espejo-Serrano C, Bustos F, Zhou H, Wang F, Toth R, Macartney T, Bach I, Nardocci G, Findlay GM. An RNF12-USP26 amplification loop drives germ cell specification and is disrupted by disease-associated mutations. Sci Signal 2022; 15:eabm5995. [PMID: 35857630 PMCID: PMC7613676 DOI: 10.1126/scisignal.abm5995] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The E3 ubiquitin ligase RNF12 plays essential roles during development, and the gene encoding it, RLIM, is mutated in the X-linked human developmental disorder Tonne-Kalscheuer syndrome (TOKAS). Substrates of RNF12 include transcriptional regulators such as the pluripotency-associated transcriptional repressor REX1. Using global quantitative proteomics in male mouse embryonic stem cells, we identified the deubiquitylase USP26 as a putative downstream target of RNF12 activity. RNF12 relieved REX1-mediated repression of Usp26, leading to an increase in USP26 abundance and the formation of RNF12-USP26 complexes. Interaction with USP26 prevented RNF12 autoubiquitylation and proteasomal degradation, thereby establishing a transcriptional feed-forward loop that amplified RNF12-dependent derepression of REX1 targets. We showed that the RNF12-USP26 axis operated specifically in mouse testes and was required for the expression of gametogenesis genes and for germ cell differentiation in vitro. Furthermore, this RNF12-USP26 axis was disrupted by RLIM and USP26 variants found in TOKAS and infertility patients, respectively. This work reveals synergy within the ubiquitylation cycle that controls a key developmental process in gametogenesis and that is disrupted in human genetic disorders.
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Affiliation(s)
- Anna Segarra-Fas
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Carmen Espejo-Serrano
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Francisco Bustos
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Houjiang Zhou
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Feng Wang
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Rachel Toth
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Thomas Macartney
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
| | - Ingolf Bach
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Chan Medical School, Worcester, MA 01605, USA
| | - Gino Nardocci
- School of Medicine, Faculty of Medicine, Universidad de los Andes, Santiago, Chile
- Program in Molecular Biology and Bioinformatics, Center for Biomedical Research and Innovation (CIIB), Universidad de los Andes, Santiago, Chile
- IMPACT, Center of Interventional Medicine for Precision and Advanced Cellular Therapy, Santiago, Chile
| | - Greg M. Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, The University of Dundee, Dundee DD1 5EH, UK
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | | | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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48
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Yan S, Wang Y, Chen Y, Yuan H, Kuang X, Hou D, Li X, Pan L, Huang G, He J, Wang T, Peng X. A novel UBE2A splice site variant causing intellectual disability type Nascimento. Clin Case Rep 2022; 10:e5990. [PMID: 35846913 PMCID: PMC9272217 DOI: 10.1002/ccr3.5990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 04/12/2022] [Accepted: 04/22/2022] [Indexed: 11/11/2022] Open
Abstract
X-linked intellectual disability type Nascimento (XLID) is a rare disease caused by variants in the ubiquitin-conjugating enzyme E2A gene (UBE2A). Patients with XLID have similar phenotypes, including speech impairments, severe intellectual disability, hearing loss, wide facies, synophrys, generalized hirsutism, and urogenital abnormalities. Till date, only two splice-site variants of the UBE2A gene have been observed in patients with X-linked ID type Nascimento. Here, we report the case of a Chinese boy with a syndrome clinically similar to XLID with speech impairment, severe intellectual disability, and moderate hearing loss. However, different characteristics were also present in the patient, including an inability to maintain his head in an upright posture. Both of the patient's palms have a single transverse palmar crease. Subsequent whole-exome sequencing revealed a novel splice site variant in UBE2A (c.241 + 1 G > A). Our study not only expands the variant spectrum and clinical characteristics of UBE2A deficiency syndrome but also provides clinical evidence for genetic diagnoses.
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Affiliation(s)
- Shuyuan Yan
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Yanling Wang
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Ying Chen
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Hongxia Yuan
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Xiaoni Kuang
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Da Hou
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Xueyi Li
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Linglin Pan
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Guangwen Huang
- Hunan Provincial Maternal and Child Health Care Hospital Changsha China
| | - Jun He
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Tuanmei Wang
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
| | - Xiangwen Peng
- Changsha Maternal and Child Health Hospital Affiliated to Hunan Normal University Changsha China
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Guzman RE, Sierra-Marquez J, Bungert-Plümke S, Franzen A, Fahlke C. Functional Characterization of CLCN4 Variants Associated With X-Linked Intellectual Disability and Epilepsy. Front Mol Neurosci 2022; 15:872407. [PMID: 35721313 PMCID: PMC9198718 DOI: 10.3389/fnmol.2022.872407] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/27/2022] [Indexed: 11/13/2022] Open
Abstract
Early/late endosomes, recycling endosomes, and lysosomes together form the endo-lysosomal recycling pathway. This system plays a crucial role in cell differentiation and survival, and dysregulation of the endo-lysosomal system appears to be important in the pathogenesis of neurodevelopmental and neurodegenerative diseases. Each endo-lysosomal compartment fulfils a specific function, which is supported by ion transporters and channels that modify ion concentrations and electrical gradients across endo-lysosomal membranes. CLC-type Cl–/H+ exchangers are a group of endo-lysosomal transporters that are assumed to regulate luminal acidification and chloride concentration in multiple endosomal compartments. Heterodimers of ClC-3 and ClC-4 localize to various internal membranes, from the endoplasmic reticulum and Golgi to recycling endosomes and late endosomes/lysosomes. The importance of ClC-4-mediated ion transport is illustrated by the association of naturally occurring CLCN4 mutations with epileptic encephalopathy, intellectual disability, and behavioral disorders in human patients. However, how these mutations affect the expression, subcellular localization, and function of ClC-4 is insufficiently understood. We here studied 12 CLCN4 variants that were identified in patients with X-linked intellectual disability and epilepsy and were already characterized to some extent in earlier work. We analyzed the consequences of these mutations on ClC-4 ion transport, subcellular trafficking, and heterodimerization with ClC-3 using heterologous expression in mammalian cells, biochemistry, confocal imaging, and whole-cell patch-clamp recordings. The mutations led to a variety of changes in ClC-4 function, ranging from gain/loss of function and impaired heterodimerization with ClC-3 to subtle impairments in transport functions. Our results suggest that even slight functional changes to the endosomal Cl–/H+ exchangers can cause serious neurological symptoms.
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50
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Eigenhuis KN, Somsen HB, van den Berg DLC. Transcription Pause and Escape in Neurodevelopmental Disorders. Front Neurosci 2022; 16:846272. [PMID: 35615272 PMCID: PMC9125161 DOI: 10.3389/fnins.2022.846272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 04/11/2022] [Indexed: 11/17/2022] Open
Abstract
Transcription pause-release is an important, highly regulated step in the control of gene expression. Modulated by various factors, it enables signal integration and fine-tuning of transcriptional responses. Mutations in regulators of pause-release have been identified in a range of neurodevelopmental disorders that have several common features affecting multiple organ systems. This review summarizes current knowledge on this novel subclass of disorders, including an overview of clinical features, mechanistic details, and insight into the relevant neurodevelopmental processes.
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