1
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Pavinato L, Stanic J, Barzasi M, Gurgone A, Chiantia G, Cipriani V, Eberini I, Palazzolo L, Di Luca M, Costa A, Marcantoni A, Biamino E, Spada M, Hiatt SM, Kelley WV, Vestito L, Sisodiya SM, Efthymiou S, Chand P, Kaiyrzhanov R, Bruselles A, Cardaropoli S, Tartaglia M, De Rubeis S, Buxbaum JD, Smedley D, Ferrero GB, Giustetto M, Gardoni F, Brusco A. Missense variants in RPH3A cause defects in excitatory synaptic function and are associated with a clinically variable neurodevelopmental disorder. Genet Med 2023; 25:100922. [PMID: 37403762 DOI: 10.1016/j.gim.2023.100922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/22/2023] [Accepted: 06/25/2023] [Indexed: 07/06/2023] Open
Abstract
PURPOSE RPH3A encodes a protein involved in the stabilization of GluN2A subunit of N-methyl-D-aspartate (NMDA)-type glutamate receptors at the cell surface, forming a complex essential for synaptic plasticity and cognition. We investigated the effect of variants in RPH3A in patients with neurodevelopmental disorders. METHODS By using trio-based exome sequencing, GeneMatcher, and screening of 100,000 Genomes Project data, we identified 6 heterozygous variants in RPH3A. In silico and in vitro models, including rat hippocampal neuronal cultures, have been used to characterize the effect of the variants. RESULTS Four cases had a neurodevelopmental disorder with untreatable epileptic seizures [p.(Gln73His)dn; p.(Arg209Lys); p.(Thr450Ser)dn; p.(Gln508His)], and 2 cases [p.(Arg235Ser); p.(Asn618Ser)dn] showed high-functioning autism spectrum disorder. Using neuronal cultures, we demonstrated that p.(Thr450Ser) and p.(Asn618Ser) reduce the synaptic localization of GluN2A; p.(Thr450Ser) also increased the surface levels of GluN2A. Electrophysiological recordings showed increased GluN2A-dependent NMDA ionotropic glutamate receptor currents for both variants and alteration of postsynaptic calcium levels. Finally, expression of the Rph3AThr450Ser variant in neurons affected dendritic spine morphology. CONCLUSION Overall, we provide evidence that missense gain-of-function variants in RPH3A increase GluN2A-containing NMDA ionotropic glutamate receptors at extrasynaptic sites, altering synaptic function and leading to a clinically variable neurodevelopmental presentation ranging from untreatable epilepsy to autism spectrum disorder.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Turin, Italy; Institute of Oncology Research (IOR), Bellinzona, Switzerland; Università della Svizzera Italiana, Lugano, Switzerland
| | - Jennifer Stanic
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Marta Barzasi
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Antonia Gurgone
- Department of Neuroscience, University of Turin, Turin, Italy
| | | | - Valentina Cipriani
- William Harvey Research Institute, Clinical Pharmacology Precision Medicine, Queen Mary University of London, Charterhouse Square, United Kingdom
| | - Ivano Eberini
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Luca Palazzolo
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Monica Di Luca
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Alex Costa
- Department of Biosciences, University of the Studies of Milan, Milan, Italy; Institute of Biophysics, Consiglio Nazionale delle Ricerche (CNR), Milan, Italy
| | - Andrea Marcantoni
- Department of Drug Science and Technology, University of Turin, Turin, Italy
| | - Elisa Biamino
- Department of Pediatrics, Regina Margherita Children Hospital, Turin, Italy
| | - Marco Spada
- Department of Pediatrics, Regina Margherita Children Hospital, Turin, Italy
| | - Susan M Hiatt
- HudsonAlpha Institute for Biotechnology, Huntsville, AL
| | | | - Letizia Vestito
- William Harvey Research Institute, Clinical Pharmacology Precision Medicine, Queen Mary University of London, Charterhouse Square, United Kingdom
| | - Sanjay M Sisodiya
- Department of Clinical and Experimental Epilepsy, UCL Queen Square Institute of Neurology, London, United Kingdom; Chalfont Centre for Epilepsy Bucks, Chalfont St Peter, United Kingdom
| | - Stephanie Efthymiou
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Prem Chand
- Department of Paediatric and Child Health, Aga Khan University Hospital, Karachi, Pakistan
| | - Rauan Kaiyrzhanov
- University College London, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Torino, Torino, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Damian Smedley
- William Harvey Research Institute, Clinical Pharmacology Precision Medicine, Queen Mary University of London, Charterhouse Square, United Kingdom
| | | | | | - Fabrizio Gardoni
- Department of Pharmacological and Biomolecular Sciences, DiSFeB, University of the Studies of Milan, Milan, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.
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2
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Giovenino C, Trajkova S, Pavinato L, Cardaropoli S, Pullano V, Ferrero E, Sukarova-Angelovska E, Carestiato S, Salmin P, Rinninella A, Battaglia A, Bertoli L, Fadda A, Palermo F, Carli D, Mussa A, Dimartino P, Bruselles A, Froukh T, Mandrile G, Pasini B, De Rubeis S, Buxbaum JD, Pippucci T, Tartaglia M, Rossato M, Delledonne M, Ferrero GB, Brusco A. Skewed X-chromosome inactivation in unsolved neurodevelopmental disease cases can guide re-evaluation For X-linked genes. Eur J Hum Genet 2023; 31:1228-1236. [PMID: 36879111 PMCID: PMC10620389 DOI: 10.1038/s41431-023-01324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/24/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023] Open
Abstract
Despite major advances in genome technology and analysis, >50% of patients with a neurodevelopmental disorder (NDD) remain undiagnosed after extensive evaluation. A point in case is our clinically heterogeneous cohort of NDD patients that remained undiagnosed after FRAXA testing, chromosomal microarray analysis and trio exome sequencing (ES). In this study, we explored the frequency of non-random X chromosome inactivation (XCI) in the mothers of male patients and affected females, the rationale being that skewed XCI might be masking previously discarded genetic variants found on the X chromosome. A multiplex fluorescent PCR-based assay was used to analyse the pattern of XCI after digestion with HhaI methylation-sensitive restriction enzyme. In families with skewed XCI, we re-evaluated trio-based ES and identified pathogenic variants and a deletion on the X chromosome. Linkage analysis and RT-PCR were used to further study the inactive X chromosome allele, and Xdrop long-DNA technology was used to define chromosome deletion boundaries. We found skewed XCI (>90%) in 16/186 (8.6%) mothers of NDD males and in 12/90 (13.3%) NDD females, far beyond the expected rate of XCI in the normal population (3.6%, OR = 4.10; OR = 2.51). By re-analyzing ES and clinical data, we solved 7/28 cases (25%) with skewed XCI, identifying variants in KDM5C, PDZD4, PHF6, TAF1, OTUD5 and ZMYM3, and a deletion in ATRX. We conclude that XCI profiling is a simple assay that targets a subgroup of patients that can benefit from re-evaluation of X-linked variants, thus improving the diagnostic yield in NDD patients and identifying new X-linked disorders.
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Affiliation(s)
- Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Verdiana Pullano
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Pediatric Diseases, Faculty of Medicine, Ss. Cyril and Methodius University in Skopje, 1000, Skopje, Republic of North Macedonia
| | - Silvia Carestiato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Paola Salmin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Antonina Rinninella
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124, Catania, Italy
| | - Anthony Battaglia
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Luca Bertoli
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Antonio Fadda
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Flavia Palermo
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Alessandro Mussa
- Department of Public Health and Pediatrics, University of Turin, 10126, Turin, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Alessandro Bruselles
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Tawfiq Froukh
- Department of Biotechnology and Genetic Engineering, Philadelphia University, Amman, Jordan
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, University of Torino, Orbassano, TO, Italy
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Tommaso Pippucci
- U.O. Genetica Medica, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italia
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00146, Rome, Italy
| | - Marzia Rossato
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | - Massimo Delledonne
- Functional Genomics Lab, Department of Biotechnology, University of Verona, 37134, Verona, Italy
| | | | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126, Turin, Italy.
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3
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Ferrero E, Di Gregorio E, Ferrero M, Ortolan E, Moon YA, Di Campli A, Pavinato L, Mancini C, Tripathy D, Manes M, Hoxha E, Costanzi C, Pozzi E, Rossi Sebastiano M, Mitro N, Tempia F, Caruso D, Borroni B, Basso M, Sallese M, Brusco A. Spinocerebellar ataxia 38: structure-function analysis shows ELOVL5 G230V is proteotoxic, conformationally altered and a mutational hotspot. Hum Genet 2023; 142:1055-1076. [PMID: 37199746 PMCID: PMC10449689 DOI: 10.1007/s00439-023-02572-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 05/10/2023] [Indexed: 05/19/2023]
Abstract
Fatty acid elongase ELOVL5 is part of a protein family of multipass transmembrane proteins that reside in the endoplasmic reticulum where they regulate long-chain fatty acid elongation. A missense variant (c.689G>T p.Gly230Val) in ELOVL5 causes Spinocerebellar Ataxia subtype 38 (SCA38), a neurodegenerative disorder characterized by autosomal dominant inheritance, cerebellar Purkinje cell demise and adult-onset ataxia. Having previously showed aberrant accumulation of p.G230V in the Golgi complex, here we further investigated the pathogenic mechanisms triggered by p.G230V, integrating functional studies with bioinformatic analyses of protein sequence and structure. Biochemical analysis showed that p.G230V enzymatic activity was normal. In contrast, SCA38-derived fibroblasts showed reduced expression of ELOVL5, Golgi complex enlargement and increased proteasomal degradation with respect to controls. By heterologous overexpression, p.G230V was significantly more active than wild-type ELOVL5 in triggering the unfolded protein response and in decreasing viability in mouse cortical neurons. By homology modelling, we generated native and p.G230V protein structures whose superposition revealed a shift in Loop 6 in p.G230V that altered a highly conserved intramolecular disulphide bond. The conformation of this bond, connecting Loop 2 and Loop 6, appears to be elongase-specific. Alteration of this intramolecular interaction was also observed when comparing wild-type ELOVL4 and the p.W246G variant which causes SCA34. We demonstrate by sequence and structure analyses that ELOVL5 p.G230V and ELOVL4 p.W246G are position-equivalent missense variants. We conclude that SCA38 is a conformational disease and propose combined loss of function by mislocalization and gain of toxic function by ER/Golgi stress as early events in SCA38 pathogenesis.
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Affiliation(s)
- Enza Ferrero
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Eleonora Di Gregorio
- Unit of Medical Genetics, Città della Salute e Della Scienza Hospital, Turin, Italy
| | - Marta Ferrero
- Experimental Zooprophylactic Institute of Piedmont, Liguria and Aosta Valley, Turin, Italy
| | - Erika Ortolan
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Young-Ah Moon
- Department of Molecular Medicine, Inha University College of Medicine, Incheon, South Korea
| | - Antonella Di Campli
- Institute of Protein Biochemistry, Italian National Research Council, Naples, Italy
- Department of Innovative Technologies in Medicine and Dentistry, G. d'Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Cecilia Mancini
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
- Genetics and Rare Diseases Research Division, Bambino Gesù Children's Hospital, Rome, Italy
| | - Debasmita Tripathy
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Marta Manes
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Eriola Hoxha
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano and Department of Neuroscience, University of Torino, Turin, Italy
| | | | - Elisa Pozzi
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy
| | - Matteo Rossi Sebastiano
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - Nico Mitro
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Filippo Tempia
- Neuroscience Institute Cavalieri Ottolenghi, Orbassano and Department of Neuroscience, University of Torino, Turin, Italy
| | - Donatella Caruso
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Barbara Borroni
- Department of Clinical and Experimental Sciences, University of Brescia, Brescia, Italy
| | - Manuela Basso
- Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Michele Sallese
- Centre for Advanced Studies and Technology, G. d'Annunzio University of Chieti-Pescara, Chieti, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Via Santena 19, 10126, Turin, Italy.
- Unit of Medical Genetics, Città della Salute e Della Scienza Hospital, Turin, Italy.
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4
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Pavinato L, Delle Vedove A, Carli D, Ferrero M, Carestiato S, Howe JL, Agolini E, Coviello DA, van de Laar I, Au PYB, Di Gregorio E, Fabbiani A, Croci S, Mencarelli MA, Bruno LP, Renieri A, Veltra D, Sofocleous C, Faivre L, Mazel B, Safraou H, Denommé-Pichon AS, van Slegtenhorst MA, Giesbertz N, van Jaarsveld RH, Childers A, Rogers RC, Novelli A, De Rubeis S, Buxbaum JD, Scherer SW, Ferrero GB, Wirth B, Brusco A. CAPRIN1 haploinsufficiency causes a neurodevelopmental disorder with language impairment, ADHD and ASD. Brain 2023; 146:534-548. [PMID: 35979925 PMCID: PMC10169411 DOI: 10.1093/brain/awac278] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/04/2022] [Accepted: 07/11/2022] [Indexed: 11/12/2022] Open
Abstract
We describe an autosomal dominant disorder associated with loss-of-function variants in the Cell cycle associated protein 1 (CAPRIN1; MIM*601178). CAPRIN1 encodes a ubiquitous protein that regulates the transport and translation of neuronal mRNAs critical for synaptic plasticity, as well as mRNAs encoding proteins important for cell proliferation and migration in multiple cell types. We identified 12 cases with loss-of-function CAPRIN1 variants, and a neurodevelopmental phenotype characterized by language impairment/speech delay (100%), intellectual disability (83%), attention deficit hyperactivity disorder (82%) and autism spectrum disorder (67%). Affected individuals also had respiratory problems (50%), limb/skeletal anomalies (50%), developmental delay (42%) feeding difficulties (33%), seizures (33%) and ophthalmologic problems (33%). In patient-derived lymphoblasts and fibroblasts, we showed a monoallelic expression of the wild-type allele, and a reduction of the transcript and protein compatible with a half dose. To further study pathogenic mechanisms, we generated sCAPRIN1+/- human induced pluripotent stem cells via CRISPR-Cas9 mutagenesis and differentiated them into neuronal progenitor cells and cortical neurons. CAPRIN1 loss caused reduced neuronal processes, overall disruption of the neuronal organization and an increased neuronal degeneration. We also observed an alteration of mRNA translation in CAPRIN1+/- neurons, compatible with its suggested function as translational inhibitor. CAPRIN1+/- neurons also showed an impaired calcium signalling and increased oxidative stress, two mechanisms that may directly affect neuronal networks development, maintenance and function. According to what was previously observed in the mouse model, measurements of activity in CAPRIN1+/- neurons via micro-electrode arrays indicated lower spike rates and bursts, with an overall reduced activity. In conclusion, we demonstrate that CAPRIN1 haploinsufficiency causes a novel autosomal dominant neurodevelopmental disorder and identify morphological and functional alterations associated with this disorder in human neuronal models.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.,Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Andrea Delle Vedove
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Turin, 10126 Turin, Italy.,Pediatric Onco-Hematology, Stem Cell Transplantation and Cell Therapy Division, Regina Margherita Children's Hospital, Città Della Salute e Della Scienza di Torino, 10126 Turin, Italy
| | - Marta Ferrero
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.,Experimental Zooprophylactic Institute of Piedmont, Liguria e Valle d'Aosta, 10154 Turin, Italy
| | - Silvia Carestiato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Jennifer L Howe
- The Centre for Applied Genomics, Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - Emanuele Agolini
- Laboratory of Medical Genetics, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Domenico A Coviello
- Laboratory of Human Genetics, IRCCS Istituto Giannina Gaslini, 16147 Genoa, Italy
| | - Ingrid van de Laar
- Clinical Genetics, Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Ping Yee Billie Au
- Department of Medical Genetics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Alessandra Fabbiani
- Medical Genetics Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy.,Medical Genetics, University of Siena, 53100 Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Susanna Croci
- Medical Genetics, University of Siena, 53100 Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | | | - Lucia P Bruno
- Medical Genetics, University of Siena, 53100 Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Alessandra Renieri
- Medical Genetics Unit, Azienda Ospedaliera Universitaria Senese, 53100 Siena, Italy.,Medical Genetics, University of Siena, 53100 Siena, Italy.,Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy
| | - Danai Veltra
- Laboratory of Medical Genetics, School of Medicine, National & Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
| | - Christalena Sofocleous
- Laboratory of Medical Genetics, School of Medicine, National & Kapodistrian University of Athens, 'Aghia Sophia' Children's Hospital, 11527 Athens, Greece
| | - Laurence Faivre
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD, CHU Dijon, 21079 Dijon, France.,UMR1231 GAD, Inserm-Université Bourgogne-Franche Comté, 21078 Dijon, France
| | - Benoit Mazel
- Centre de référence Anomalies du Développement et Syndromes Malformatifs, Fédération Hospitalo-Universitaire TRANSLAD, CHU Dijon, 21079 Dijon, France
| | - Hana Safraou
- UMR1231 GAD, Inserm-Université Bourgogne-Franche Comté, 21078 Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Anne-Sophie Denommé-Pichon
- UMR1231 GAD, Inserm-Université Bourgogne-Franche Comté, 21078 Dijon, France.,Unité Fonctionnelle Innovation en Diagnostic génomique des maladies rares, FHU TRANSLAD, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Marjon A van Slegtenhorst
- Clinical Genetics, Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Noor Giesbertz
- Department of Genetics, University Medical Centre Utrecht, 3584 CX, Utrecht, The Netherlands
| | - Richard H van Jaarsveld
- Department of Genetics, University Medical Centre Utrecht, 3584 CX, Utrecht, The Netherlands
| | | | | | - Antonio Novelli
- Laboratory of Medical Genetics, IRCCS, Ospedale Pediatrico Bambino Gesù, Rome, Italy
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON M5S 1A1, Canada
| | | | - Brunhilde Wirth
- Institute of Human Genetics, Center for Molecular Medicine Cologne, Center for Rare Diseases Cologne, University Hospital Cologne, University of Cologne, 50931 Cologne, Germany.,Institute for Genetics, University of Cologne, 50674 Cologne, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
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5
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Angelini C, Morellato A, Alfieri A, Pavinato L, Cravero T, Bianciotto OT, Salemme V, Natalini D, Centonze G, Raspanti A, Garofalo T, Valdembri D, Serini G, Marcantoni A, Becchetti A, Giustetto M, Turco E, Defilippi P. p140Cap Regulates the Composition and Localization of the NMDAR Complex in Synaptic Lipid Rafts. J Neurosci 2022; 42:7183-7200. [PMID: 35953295 PMCID: PMC9512579 DOI: 10.1523/jneurosci.1775-21.2022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 11/21/2022] Open
Abstract
The NMDARs are key players in both physiological and pathologic synaptic plasticity because of their involvement in many aspects of neuronal transmission as well as learning and memory. The contribution in these events of different types of GluN2A-interacting proteins is still unclear. The p140Cap scaffold protein acts as a hub for postsynaptic complexes relevant to psychiatric and neurologic disorders and regulates synaptic functions, such as the stabilization of mature dendritic spine, memory consolidation, LTP, and LTD. Here we demonstrate that p140Cap directly binds the GluN2A subunit of NMDAR and modulates GluN2A-associated molecular network. Indeed, in p140Cap KO male mice, GluN2A is less associated with PSD95 both in ex vivo synaptosomes and in cultured hippocampal neurons, and p140Cap expression in KO neurons can rescue GluN2A and PSD95 colocalization. p140Cap is crucial in the recruitment of GluN2A-containing NMDARs and, consequently, in regulating NMDARs' intrinsic properties. p140Cap is associated to synaptic lipid-raft (LR) and to soluble postsynaptic membranes, and GluN2A and PSD95 are less recruited into synaptic LR of p140Cap KO male mice. Gated-stimulated emission depletion microscopy on hippocampal neurons confirmed that p140Cap is required for embedding GluN2A clusters in LR in an activity-dependent fashion. In the synaptic compartment, p140Cap influences the association between GluN2A and PSD95 and modulates GluN2A enrichment into LR. Overall, such increase in these membrane domains rich in signaling molecules results in improved signal transduction efficiency.SIGNIFICANCE STATEMENT Here we originally show that the adaptor protein p140Cap directly binds the GluN2A subunit of NMDAR and modulates the GluN2A-associated molecular network. Moreover, we show, for the first time, that p140Cap also associates to synaptic lipid rafts and controls the selective recruitment of GluN2A and PSD95 to this specific compartment. Finally, gated-stimulated emission depletion microscopy on hippocampal neurons confirmed that p140Cap is required for embedding GluN2A clusters in lipid rafts in an activity-dependent fashion. Overall, our findings provide the molecular and functional dissection of p140Cap as a new active member of a highly dynamic synaptic network involved in memory consolidation, LTP, and LTD, which are known to be altered in neurologic and psychiatric disorders.
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Affiliation(s)
- Costanza Angelini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Alessandro Morellato
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Annalisa Alfieri
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, Medical Genetics Unit, University of Torino, Torino, 10126, Italy
| | - Tiziana Cravero
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Olga Teresa Bianciotto
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Vincenzo Salemme
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Dora Natalini
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Giorgia Centonze
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Alessandra Raspanti
- Neuroscience Department "Rita Levi Montalcini," University of Torino, Torino, 10125, Italy
| | - Tina Garofalo
- Department of Experimental Medicine, Sapienza University, Roma, 00161, Italy
| | - Donatella Valdembri
- Department of Oncology, University of Torino School of Medicine, Regione Gonzole, 10, 10043, Orbassano, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, 10060, Italy
| | - Guido Serini
- Department of Oncology, University of Torino School of Medicine, Regione Gonzole, 10, 10043, Orbassano, TO, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, 10060, Italy
| | - Andrea Marcantoni
- Department of Drug Science, Laboratory of Cellular and Molecular Neuroscience, University of Torino, Torino, 10126, Italy
- Department of Biotechnology and Biosciences and NeuroMI, University of Milano-Bicocca, Milano, 20126, Italy
| | - Andrea Becchetti
- Department of Biotechnology and Biosciences and NeuroMI, University of Milano-Bicocca, Milano, 20126, Italy
| | - Maurizio Giustetto
- Neuroscience Department "Rita Levi Montalcini," University of Torino, Torino, 10125, Italy
| | - Emilia Turco
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
| | - Paola Defilippi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy
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6
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Fu JM, Satterstrom FK, Peng M, Brand H, Collins RL, Dong S, Wamsley B, Klei L, Wang L, Hao SP, Stevens CR, Cusick C, Babadi M, Banks E, Collins B, Dodge S, Gabriel SB, Gauthier L, Lee SK, Liang L, Ljungdahl A, Mahjani B, Sloofman L, Smirnov AN, Barbosa M, Betancur C, Brusco A, Chung BHY, Cook EH, Cuccaro ML, Domenici E, Ferrero GB, Gargus JJ, Herman GE, Hertz-Picciotto I, Maciel P, Manoach DS, Passos-Bueno MR, Persico AM, Renieri A, Sutcliffe JS, Tassone F, Trabetti E, Campos G, Cardaropoli S, Carli D, Chan MCY, Fallerini C, Giorgio E, Girardi AC, Hansen-Kiss E, Lee SL, Lintas C, Ludena Y, Nguyen R, Pavinato L, Pericak-Vance M, Pessah IN, Schmidt RJ, Smith M, Costa CIS, Trajkova S, Wang JYT, Yu MHC, Cutler DJ, De Rubeis S, Buxbaum JD, Daly MJ, Devlin B, Roeder K, Sanders SJ, Talkowski ME. Rare coding variation provides insight into the genetic architecture and phenotypic context of autism. Nat Genet 2022; 54:1320-1331. [PMID: 35982160 PMCID: PMC9653013 DOI: 10.1038/s41588-022-01104-0] [Citation(s) in RCA: 137] [Impact Index Per Article: 68.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 05/24/2022] [Indexed: 01/11/2023]
Abstract
Some individuals with autism spectrum disorder (ASD) carry functional mutations rarely observed in the general population. We explored the genes disrupted by these variants from joint analysis of protein-truncating variants (PTVs), missense variants and copy number variants (CNVs) in a cohort of 63,237 individuals. We discovered 72 genes associated with ASD at false discovery rate (FDR) ≤ 0.001 (185 at FDR ≤ 0.05). De novo PTVs, damaging missense variants and CNVs represented 57.5%, 21.1% and 8.44% of association evidence, while CNVs conferred greatest relative risk. Meta-analysis with cohorts ascertained for developmental delay (DD) (n = 91,605) yielded 373 genes associated with ASD/DD at FDR ≤ 0.001 (664 at FDR ≤ 0.05), some of which differed in relative frequency of mutation between ASD and DD cohorts. The DD-associated genes were enriched in transcriptomes of progenitor and immature neuronal cells, whereas genes showing stronger evidence in ASD were more enriched in maturing neurons and overlapped with schizophrenia-associated genes, emphasizing that these neuropsychiatric disorders may share common pathways to risk.
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Affiliation(s)
- Jack M Fu
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - F Kyle Satterstrom
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Minshi Peng
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Harrison Brand
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Ryan L Collins
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Shan Dong
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Brie Wamsley
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Lambertus Klei
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Lily Wang
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA
| | - Stephanie P Hao
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Pediatric Surgical Research Laboratories, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Christine R Stevens
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Caroline Cusick
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mehrtash Babadi
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric Banks
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Brett Collins
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sheila Dodge
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stacey B Gabriel
- Genomics Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Laura Gauthier
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Samuel K Lee
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lindsay Liang
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Alicia Ljungdahl
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA
| | - Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Laura Sloofman
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Andrey N Smirnov
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Mafalda Barbosa
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
- Medical Genetics Unit, 'Città della Salute e della Scienza' University Hospital, Turin, Italy
| | - Brian H Y Chung
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Edwin H Cook
- Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA
| | - Michael L Cuccaro
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Enrico Domenici
- Department of Cellular, Computational and Integrative Biology, , University of Trento, Trento, Italy
| | | | - J Jay Gargus
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Gail E Herman
- The Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Irva Hertz-Picciotto
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute, School of Medicine, University of Minho, Braga, Portugal
| | - Dara S Manoach
- Department of Psychiatry, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Maria Rita Passos-Bueno
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Antonio M Persico
- Interdepartmental Program 'Autism 0-90', 'Gaetano Martino' University Hospital, University of Messina, Messina, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena, Italy
| | - James S Sutcliffe
- Department of Molecular Physiology & Biophysics and Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt Genetics Institute, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Flora Tassone
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Biochemistry and Molecular Medicine, University of California Davis, School of Medicine, Sacramento, CA, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, Section of Biology and Genetics, University of Verona, Verona, Italy
| | - Gabriele Campos
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Simona Cardaropoli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Diana Carli
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Marcus C Y Chan
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena, Italy
- Medical Genetics, , University of Siena, Siena, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Ana Cristina Girardi
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Emily Hansen-Kiss
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center at Houston, School of Dentistry, Houston, TX, USA
| | - So Lun Lee
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Carla Lintas
- Service for Neurodevelopmental Disorders, University Campus Bio-medico of Rome, Rome, Italy
| | - Yunin Ludena
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Rachel Nguyen
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Margaret Pericak-Vance
- The John P Hussman Institute for Human Genomics, The University of Miami Miller School of Medicine, Miami, FL, USA
| | - Isaac N Pessah
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
- Department of Molecular Biosciences, University of California Davis, School of Veterinary Medicine, Davis, CA, USA
| | - Rebecca J Schmidt
- MIND (Medical Investigation of Neurodevelopmental Disorders) Institute, University of California Davis, Davis, CA, USA
| | - Moyra Smith
- Center for Autism Research and Translation, University of California Irvine, Irvine, CA, USA
| | - Claudia I S Costa
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Jaqueline Y T Wang
- Centro de Pesquisas sobre o Genoma Humano e Células tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Mullin H C Yu
- Department of Pediatrics and Adolescent Medicine, Duchess of Kent Children's Hospital, The University of Hong Kong, Hong Kong Special Administrative Region, China
| | - David J Cutler
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Mark J Daly
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Kathryn Roeder
- Department of Statistics and Data Science, Carnegie Mellon University, Pittsburgh, PA, USA.
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Stephan J Sanders
- Department of Psychiatry, UCSF Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
| | - Michael E Talkowski
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Program in Bioinformatics and Integrative Genomics, Harvard Medical School, Boston, MA, USA.
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7
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Scala M, Drouot N, MacLennan SC, Wessels MW, Krygier M, Pavinato L, Telegrafi A, de Man SA, van Slegtenhorst M, Iacomino M, Madia F, Scudieri P, Uva P, Giacomini T, Nobile G, Mancardi MM, Balagura G, Galloni GB, Verrotti A, Umair M, Khan A, Liebelt J, Schmidts M, Langer T, Brusco A, Lipska-Ziętkiewicz BS, Saris JJ, Charlet-Berguerand N, Zara F, Striano P, Piton A. De novo truncating NOVA2 variants affect alternative splicing and lead to heterogeneous neurodevelopmental phenotypes. Hum Mutat 2022; 43:1299-1313. [PMID: 35607920 PMCID: PMC9543825 DOI: 10.1002/humu.24414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 05/02/2022] [Accepted: 05/22/2022] [Indexed: 11/10/2022]
Abstract
Alternative splicing (AS) is crucial for cell-type specific gene transcription and plays a critical role in neuronal differentiation and synaptic plasticity. De novo frameshift variants in NOVA2, encoding a neuron-specific key splicing factor, have been recently associated with a new neurodevelopmental disorder (NDD) with hypotonia, neurological features, and brain abnormalities. We investigated eight unrelated individuals by exome sequencing (ES) and identified seven novel pathogenic NOVA2 variants, including two with a novel localization at the KH1 and KH3 domains. In addition to a severe NDD phenotype, novel clinical features included psychomotor regression, attention deficit-hyperactivity disorder (ADHD), dyspraxia, and urogenital and endocrinological manifestations. To test the effect of the variants on splicing regulation, we transfected HeLa cells with wildtype and mutant NOVA2 cDNA. The novel variants NM_002516.4: c.754_756delCTGinsTT p.(Leu252Phefs*144) and c.1329dup p.(Lys444Glnfs*82) all negatively affected AS events. The distal p.(Lys444Glnfs*82) variant, causing a partial removal of the KH3 domain, had a milder functional effect leading to an intermediate phenotype. Our findings expand the molecular and phenotypic spectrum of NOVA2-related NDD, supporting the pathogenic role of AS disruption by truncating variants and suggesting that this is a heterogeneous condition with variable clinical course. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Marcello Scala
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Nathalie Drouot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Suzanna C MacLennan
- Department of Paediatric Neurology, Women's and Children's Hospital, Adelaide, South Australia, Australia
| | - Marja W Wessels
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Magdalena Krygier
- Department of Developmental Neurology, Medical University of Gdańsk, ul. Dębinki 7 80-952, Gdańsk, Poland
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Center for Molecular Medicine Cologne, Institute of Human Genetics, University of Cologne, 50931, Cologne, Germany
| | - Aida Telegrafi
- Clinical Genomics Program, GeneDx, Gaithersburg, MD, USA
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | | | - Michele Iacomino
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Francesca Madia
- Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Scudieri
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Paolo Uva
- Clinical Bioinformatics Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Thea Giacomini
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Giulia Nobile
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Maria Margherita Mancardi
- Unit of Child Neuropsychiatry, IRCCS Istituto Giannina Gaslini, Genoa, Italy, DINOGMI, University of Genoa, Genoa, Italy
| | - Ganna Balagura
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Giovanni Battista Galloni
- Struttura Complessa Neuropsichiatria Infantile Sud, Azienda Sanitaria Locale Città di Torino, Torino, Italy
| | | | - 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, Riyadh, Saudi Arabia.,Department of Life Sciences, School of Science, University of Management and Technology (UMT), Lahore, Pakistan
| | - Amjad Khan
- Faculty of Biological Science, Department of Zoology, University of Lakki Marwat, Lakki Marwat, Pakistan
| | - Jan Liebelt
- South Australian Clinical Genetics Service, Women's and Children's Hospital, Adelaide, SA, Australia
| | - Miriam Schmidts
- Department of General Pediatrics and Adolescent Medicine, Medical Center and Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thorsten Langer
- Department of Neuropediatrics and Muscle Disorders, Center for Pediatrics, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126, Turin, Italy.,Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, 10126, Turin, Italy
| | - Beata S Lipska-Ziętkiewicz
- Clinical Genetics Unit, Department of Biology and Medical Genetics, Medical University of Gdańsk, Gdańsk, Poland.,27Centre for Rare Diseases, Medical University of Gdańsk, Gdańsk, Poland
| | - Jasper J Saris
- Department of Clinical Genetics, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France
| | - Federico Zara
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Unit of Medical Genetics, IRCCS Giannina Gaslini Institute, Via Gerolamo Gaslini 5, 16147, Genoa, Italy
| | - Pasquale Striano
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa, Italy.,Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa, Italy
| | - Amélie Piton
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, 67400, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, 67400, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, 67400, France.,Université de Strasbourg, Illkirch, 67400, France.,Laboratory of Genetic Diagnostic, Hôpitaux Universitaires de Strasbourg, Strasbourg, 67000, France.,Institut Universitaire de France, Paris, Île-de-France, France
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8
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Marcogliese PC, Deal SL, Andrews J, Harnish JM, Bhavana VH, Graves HK, Jangam S, Luo X, Liu N, Bei D, Chao YH, Hull B, Lee PT, Pan H, Bhadane P, Huang MC, Longley CM, Chao HT, Chung HL, Haelterman NA, Kanca O, Manivannan SN, Rossetti LZ, German RJ, Gerard A, Schwaibold EMC, Fehr S, Guerrini R, Vetro A, England E, Murali CN, Barakat TS, van Dooren MF, Wilke M, van Slegtenhorst M, Lesca G, Sabatier I, Chatron N, Brownstein CA, Madden JA, Agrawal PB, Keren B, Courtin T, Perrin L, Brugger M, Roser T, Leiz S, Mau-Them FT, Delanne J, Sukarova-Angelovska E, Trajkova S, Rosenhahn E, Strehlow V, Platzer K, Keller R, Pavinato L, Brusco A, Rosenfeld JA, Marom R, Wangler MF, Yamamoto S. Drosophila functional screening of de novo variants in autism uncovers damaging variants and facilitates discovery of rare neurodevelopmental diseases. Cell Rep 2022; 38:110517. [PMID: 35294868 PMCID: PMC8983390 DOI: 10.1016/j.celrep.2022.110517] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 09/23/2021] [Accepted: 02/18/2022] [Indexed: 12/30/2022] Open
Abstract
Individuals with autism spectrum disorder (ASD) exhibit an increased burden of de novo mutations (DNMs) in a broadening range of genes. While these studies have implicated hundreds of genes in ASD pathogenesis, which DNMs cause functional consequences in vivo remains unclear. We functionally test the effects of ASD missense DNMs using Drosophila through "humanization" rescue and overexpression-based strategies. We examine 79 ASD variants in 74 genes identified in the Simons Simplex Collection and find 38% of them to cause functional alterations. Moreover, we identify GLRA2 as the cause of a spectrum of neurodevelopmental phenotypes beyond ASD in 13 previously undiagnosed subjects. Functional characterization of variants in ASD candidate genes points to conserved neurobiological mechanisms and facilitates gene discovery for rare neurodevelopmental diseases.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Samantha L Deal
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Jonathan Andrews
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - J Michael Harnish
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - V Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sharayu Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Hematology/Oncology, BCM, Houston, TX 77030, USA
| | - Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Danqing Bei
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Yu-Hsin Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Brooke Hull
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Hongling Pan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Pradnya Bhadane
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Mei-Chu Huang
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Colleen M Longley
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA
| | - Hsiao-Tuan Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Department of Pediatrics, Division of Neurology and Developmental Neuroscience, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; McNair Medical Institute, The Robert and Janice McNair Foundation, Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Nele A Haelterman
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Sathiya N Manivannan
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Linda Z Rossetti
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
| | - Ryan J German
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA
| | - Amanda Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | | | - Sarah Fehr
- Praxis für Humangenetik Tübingen, Tübingen, Germany
| | - Renzo Guerrini
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Annalisa Vetro
- Neuroscience Department, Children's Hospital Meyer-University of Florence, Florence, Italy
| | - Eleina England
- The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Chaya N Murali
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Tahsin Stefan Barakat
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marieke F van Dooren
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Martina Wilke
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gaetan Lesca
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Isabelle Sabatier
- Department of Pediatric Neurology, Lyon University Hospitals, Lyon, France
| | - Nicolas Chatron
- Department of Medical Genetics, Lyon University Hospital, Université Claude Bernard Lyon 1, Lyon, France; Institut NeuroMyoGène, CNRS UMR 5310 - INSERM U1217, Université Claude Bernard Lyon 1, Lyon, France
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Jill A Madden
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Boris Keren
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Thomas Courtin
- Genetic Department, Pitié-Salpêtrière Hospital, APHP.Sorbonne Université, Paris 75013, France
| | - Laurence Perrin
- Genetic Department, Robert Debré Hospital, APHP.Nord-Université de Paris, Paris 75019, France
| | - Melanie Brugger
- Institute of Human Genetics, Technical University Munich, Munich, Germany
| | - Timo Roser
- Division of Pediatric Neurology, Developmental Medicine and Social Pediatrics, Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University, Lindwurmstraße 4, 80337 Munich, Germany
| | - Steffen Leiz
- Department of Pediatrics and Adolescent Medicine, Hospital Dritter Orden, Munich, Germany
| | - Frederic Tran Mau-Them
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France; Laboratoire de Génétique, Innovation en Diagnostic Génomique des Maladies Rares UF6254, Plateau Technique de Biologie, CHU Dijon, 14 Rue Paul Gaffarel, BP 77908, 21079 Dijon, France
| | - Julian Delanne
- INSERM U1231, LNC UMR1231 GAD, Burgundy University, 21000 Dijon, France
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, University Clinic for Children's Diseases, Medical Faculty, University Sv. Kiril i Metodij, Skopje, Republic of Macedonia
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Erik Rosenhahn
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Vincent Strehlow
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Roberto Keller
- Adult Autism Center, Mental Health Department, Health Unit ASL Città di Torino, Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, Turin, Italy; Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, Turin, Italy
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Baylor Genetics Laboratories, Houston, TX 77021, USA
| | - Ronit Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; TCH, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital (TCH), Houston, TX 77030, USA; Program in Developmental Biology, BCM, Houston, TX 77030, USA; Department of Neuroscience, BCM, Houston, TX 77030, USA; Development, Disease Models & Therapeutics Graduate Program, BCM, Houston, TX 77030, USA.
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9
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Pavinato L, Villamor-Payà M, Sanchiz-Calvo M, Andreoli C, Gay M, Vilaseca M, Arauz-Garofalo G, Ciolfi A, Bruselles A, Pippucci T, Prota V, Carli D, Giorgio E, Radio FC, Antona V, Giuffrè M, Ranguin K, Colson C, De Rubeis S, Dimartino P, Buxbaum JD, Ferrero GB, Tartaglia M, Martinelli S, Stracker TH, Brusco A. Functional analysis of TLK2 variants and their proximal interactomes implicates impaired kinase activity and chromatin maintenance defects in their pathogenesis. J Med Genet 2022; 59:170-179. [PMID: 33323470 PMCID: PMC10631451 DOI: 10.1136/jmedgenet-2020-107281] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 10/19/2020] [Accepted: 11/14/2020] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The Tousled-like kinases 1 and 2 (TLK1 and TLK2) are involved in many fundamental processes, including DNA replication, cell cycle checkpoint recovery and chromatin remodelling. Mutations in TLK2 were recently associated with 'Mental Retardation Autosomal Dominant 57' (MRD57, MIM# 618050), a neurodevelopmental disorder characterised by a highly variable phenotype, including mild-to-moderate intellectual disability, behavioural abnormalities, facial dysmorphisms, microcephaly, epilepsy and skeletal anomalies. METHODS We re-evaluate whole exome sequencing and array-CGH data from a large cohort of patients affected by neurodevelopmental disorders. Using spatial proteomics (BioID) and single-cell gel electrophoresis, we investigated the proximity interaction landscape of TLK2 and analysed the effects of p.(Asp551Gly) and a previously reported missense variant (c.1850C>T; p.(Ser617Leu)) on TLK2 interactions, localisation and activity. RESULTS We identified three new unrelated MRD57 families. Two were sporadic and caused by a missense change (c.1652A>G; p.(Asp551Gly)) or a 39 kb deletion encompassing TLK2, and one was familial with three affected siblings who inherited a nonsense change from an affected mother (c.1423G>T; p.(Glu475Ter)). The clinical phenotypes were consistent with those of previously reported cases. The tested mutations strongly impaired TLK2 kinase activity. Proximal interactions between TLK2 and other factors implicated in neurological disorders, including CHD7, CHD8, BRD4 and NACC1, were identified. Finally, we demonstrated a more relaxed chromatin state in lymphoblastoid cells harbouring the p.(Asp551Gly) variant compared with control cells, conferring susceptibility to DNA damage. CONCLUSION Our study identified novel TLK2 pathogenic variants, confirming and further expanding the MRD57-related phenotype. The molecular characterisation of missense variants increases our knowledge about TLK2 function and provides new insights into its role in neurodevelopmental disorders.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Torino, Italy
- Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Marina Villamor-Payà
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Maria Sanchiz-Calvo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Cristina Andreoli
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Marina Gay
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Marta Vilaseca
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Gianluca Arauz-Garofalo
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
| | - Andrea Ciolfi
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | - Tommaso Pippucci
- Medical Genetics Unity, Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Valentina Prota
- Department of Environment and Health, Istituto Superiore di Sanità, Roma, Italy
| | - Diana Carli
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Elisa Giorgio
- Department of Medical Sciences, University of Turin, Torino, Italy
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | | | - Vincenzo Antona
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Mario Giuffrè
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Kara Ranguin
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Cindy Colson
- Department of Genetics, Reference center for Rare Diseases and Developmental Anomalies, Caen, France
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Joseph D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York City, New York, USA
| | - Giovanni Battista Ferrero
- Department of Pediatrics and Public Health and Pediatric Sciences, University of Turin, Torino, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù IRCCS, Roma, Italy
| | - Simone Martinelli
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Roma, Italy
| | - Travis H Stracker
- The Barcelona Institute of Science and Technology, Institute for Research in Biomedicine, Barcelona, Spain
- Radiation Oncology Branch, National Cancer Institute, Bethesda, Maryland, USA
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Torino, Italy
- Unit of Medical Genetics, "Città della Salute e della Scienza" University Hospital, Torino, Italy
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10
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Verdura E, Rodríguez-Palmero A, Vélez-Santamaria V, Planas-Serra L, de la Calle I, Raspall-Chaure M, Roubertie A, Benkirane M, Saettini F, Pavinato L, Mandrile G, O'Leary M, O'Heir E, Barredo E, Chacón A, Michaud V, Goizet C, Ruiz M, Schlüter A, Rouvet I, Sala-Coromina J, Fossati C, Iascone M, Canonico F, Marcé-Grau A, de Souza P, Adams DR, Casasnovas C, Rehm HL, Mefford HC, González Gutierrez-Solana L, Brusco A, Koenig M, Macaya A, Pujol A. Biallelic PI4KA variants cause a novel neurodevelopmental syndrome with hypomyelinating leukodystrophy. Brain 2021; 144:2659-2669. [PMID: 34415322 PMCID: PMC8557332 DOI: 10.1093/brain/awab124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/10/2021] [Accepted: 02/15/2021] [Indexed: 11/14/2022] Open
Abstract
Phosphoinositides are lipids that play a critical role in processes such as cellular signalling, ion channel activity and membrane trafficking. When mutated, several genes that encode proteins that participate in the metabolism of these lipids give rise to neurological or developmental phenotypes. PI4KA is a phosphoinositide kinase that is highly expressed in the brain and is essential for life. Here we used whole exome or genome sequencing to identify 10 unrelated patients harbouring biallelic variants in PI4KA that caused a spectrum of conditions ranging from severe global neurodevelopmental delay with hypomyelination and developmental brain abnormalities to pure spastic paraplegia. Some patients presented immunological deficits or genito-urinary abnormalities. Functional analyses by western blotting and immunofluorescence showed decreased PI4KA levels in the patients’ fibroblasts. Immunofluorescence and targeted lipidomics indicated that PI4KA activity was diminished in fibroblasts and peripheral blood mononuclear cells. In conclusion, we report a novel severe metabolic disorder caused by PI4KA malfunction, highlighting the importance of phosphoinositide signalling in human brain development and the myelin sheath.
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Affiliation(s)
- Edgard Verdura
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Pediatric Neurology Unit, Department of Pediatrics, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Catalonia, Spain
| | - Valentina Vélez-Santamaria
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Irene de la Calle
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain
| | - Miquel Raspall-Chaure
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Agathe Roubertie
- Département de Neuropédiatrie, Hôpital Gui de Chauliac Pôle Neurosciences Tête et Cou, Montpellier, France.,INSERM U1051, Institut des Neurosciences de Montpellier, Montpellier, France
| | - Mehdi Benkirane
- Laboratoire de Génétique de Maladies Rares EA7402, Institut Universitaire de Recherche Clinique, Université de Montpellier, CHU Montpellier, CEDEX 5, 34295 Montpellier, France
| | - Francesco Saettini
- Paediatric Hematology Department, Fondazione MBBM, University of Milano Bicocca, Monza, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy
| | - Giorgia Mandrile
- Thalassemia Centre and Medical Genetics Unit, San Luigi Gonzaga University Hospital, Orbassano, Italy
| | - Melanie O'Leary
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Emily O'Heir
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Estibaliz Barredo
- Neuropediatric Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Almudena Chacón
- Neuropediatric Department, Hospital Universitario Gregorio Marañón, Madrid, Spain
| | - Vincent Michaud
- Molecular Genetics Laboratory, Bordeaux University Hospital, Bordeaux, Aquitaine, France.,INSERM U1211, Rare Diseases Laboratory: Genetics and Metabolism, University of Bordeaux, Talence, Aquitaine, France
| | - Cyril Goizet
- INSERM U1211, Rare Diseases Laboratory: Genetics and Metabolism, University of Bordeaux, Talence, Aquitaine, France.,Reference Center for Rare Neurogenetic Diseases, Department of Medical Genetics, University Hospital Centre Bordeaux Pellegrin Hospital Group, Bordeaux, Aquitaine, France
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Agatha Schlüter
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain
| | - Isabelle Rouvet
- Cellular Biotechnology Department and Biobank, Hospices Civils de Lyon, CHU de Lyon, Lyon, France
| | - Julia Sala-Coromina
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Chiara Fossati
- Department of Paediatrics, Fondazione MBBM, Monza, Italy
| | - Maria Iascone
- Molecular Genetics Laboratory, USSD LGM, Papa Giovanni XXIII Hospital, Bergamo, Italy
| | - Francesco Canonico
- Department of Neuroradiology, University of Milan-Bicocca, San Gerardo Hospital, ASST di Monza, Monza, Italy
| | - Anna Marcé-Grau
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Precilla de Souza
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - David R Adams
- Office of the Clinical Director, National Human Genome Research Institute, NIH, Bethesda, MD, USA.,Undiagnosed Diseases Program, The Common Fund, NIH, Bethesda, MD, USA
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Neuromuscular Unit, Neurology Department, Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Heidi L Rehm
- Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Heather C Mefford
- Division of Genetic Medicine, Department of Paediatrics, University of Washington, Seattle, WA 98195, USA
| | - Luis González Gutierrez-Solana
- Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Pediatric Neurology, Hospital Infantil Universitario Niño Jesús, Madrid, Spain
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126 Torino, Italy.,Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy
| | - Michel Koenig
- Laboratoire de Génétique de Maladies Rares EA7402, Institut Universitaire de Recherche Clinique, Université de Montpellier, CHU Montpellier, CEDEX 5, 34295 Montpellier, France
| | - Alfons Macaya
- Neurology Research Group, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Paediatric Neurology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Catalonia, Spain.,Centre for Biomedical Research in Network on Rare Diseases (CIBERER), Instituto de Salud Carlos III, 28029, Madrid, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Catalonia, Spain
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11
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Pavinato L, Nematian-Ardestani E, Zonta A, De Rubeis S, Buxbaum J, Mancini C, Bruselles A, Tartaglia M, Pessia M, Tucker SJ, D’Adamo MC, Brusco A. KCNK18 Biallelic Variants Associated with Intellectual Disability and Neurodevelopmental Disorders Alter TRESK Channel Activity. Int J Mol Sci 2021; 22:ijms22116064. [PMID: 34199759 PMCID: PMC8200030 DOI: 10.3390/ijms22116064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/19/2022] Open
Abstract
The TWIK-related spinal cord potassium channel (TRESK) is encoded by KCNK18, and variants in this gene have previously been associated with susceptibility to familial migraine with aura (MIM #613656). A single amino acid substitution in the same protein, p.Trp101Arg, has also been associated with intellectual disability (ID), opening the possibility that variants in this gene might be involved in different disorders. Here, we report the identification of KCNK18 biallelic missense variants (p.Tyr163Asp and p.Ser252Leu) in a family characterized by three siblings affected by mild-to-moderate ID, autism spectrum disorder (ASD) and other neurodevelopment-related features. Functional characterization of the variants alone or in combination showed impaired channel activity. Interestingly, Ser252 is an important regulatory site of TRESK, suggesting that alteration of this residue could lead to additive downstream effects. The functional relevance of these mutations and the observed co-segregation in all the affected members of the family expand the clinical variability associated with altered TRESK function and provide further insight into the relationship between altered function of this ion channel and human disease.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Center for Molecular Medicine Cologne, Institute of Human Genetics, University of Cologne, 50931 Cologne, Germany
| | - Ehsan Nematian-Ardestani
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
| | - Andrea Zonta
- Unit of Medical Genetics, “Città della Salute e della Scienza” University Hospital, 10126 Turin, Italy;
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.D.R.); (J.B.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joseph Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (S.D.R.); (J.B.)
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Cecilia Mancini
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (C.M.); (M.T.)
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, 00165 Rome, Italy; (C.M.); (M.T.)
| | - Mauro Pessia
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Stephen J. Tucker
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 4BH, UK;
| | - Maria Cristina D’Adamo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, MSD-2080 Msida, Malta; (E.N.-A.); (M.P.)
- Correspondence: (M.C.D.); (A.B.)
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy;
- Unit of Medical Genetics, “Città della Salute e della Scienza” University Hospital, 10126 Turin, Italy;
- Correspondence: (M.C.D.); (A.B.)
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12
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Pavinato L, Trajkova S, Grosso E, Giorgio E, Bruselles A, Radio FC, Pippucci T, Dimartino P, Tartaglia M, Petlichkovski A, De Rubeis S, Buxbaum J, Ferrero GB, Keller R, Brusco A. Expanding the clinical phenotype of the ultra-rare Skraban-Deardorff syndrome: Two novel individuals with WDR26 loss-of-function variants and a literature review. Am J Med Genet A 2021; 185:1712-1720. [PMID: 33675273 DOI: 10.1002/ajmg.a.62157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 12/23/2022]
Abstract
De novo variants in the WDR26 gene leading to haploinsufficiency have recently been associated with Skraban-Deardorff syndrome. This condition is an ultra-rare autosomal dominant neurodevelopmental disorder characterized by a broad range of clinical signs, including intellectual disability (ID), developmental delay (DD), seizures, abnormal facial features, feeding difficulties, and minor skeletal anomalies. Currently, 18 cases have been reported in the literature and for only 15 of them a clinical description is available. Here, we describe a child with Skraban-Deardorff syndrome associated with the WDR26 pathogenic de novo variant NM_025160.6:c.69dupC, p.(Gly24ArgfsTer48), and an adult associated with the pathogenic de novo variant c.1076G > A, p.(Trp359Ter). The adult patient was a 29-year-old female with detailed information on clinical history and pharmacological treatments since birth, providing an opportunity to map disease progression and patient management. By comparing our cases with published reports of Skraban-Deardorff syndrome, we provide a genetic and clinical summary of this ultrarare condition, describe the clinical management from childhood to adult age, and further expand on the clinical phenotype.
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Affiliation(s)
- Lisa Pavinato
- Department of Medical Sciences, University of Turin, Turin, Italy.,Institute of Human Genetics and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Slavica Trajkova
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Enrico Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Alessandro Bruselles
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, Rome, Italy
| | | | - Tommaso Pippucci
- Medical Genetics Unit, Polyclinic Sant'Orsola-Malpighi University Hospital, Bologna, Italy
| | - Paola Dimartino
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Marco Tartaglia
- Genetics and Rare Diseases Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Aleksandar Petlichkovski
- Institute for Immunobiology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje, Macedonia
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joseph Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Giovanni Battista Ferrero
- Department of Clinical and Biological Sciences, School of Medicine, University of Turin, Orbassano, Torino, Italy
| | - Roberto Keller
- Adult autism center, Mental Health Department, Local Health Unit ASL Città di Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Turin, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
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13
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Trajkova S, Di Gregorio E, Ferrero GB, Carli D, Pavinato L, Delplancq G, Kuentz P, Brusco A. New Insights into Potocki-Shaffer Syndrome: Report of Two Novel Cases and Literature Review. Brain Sci 2020; 10:brainsci10110788. [PMID: 33126574 PMCID: PMC7693731 DOI: 10.3390/brainsci10110788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/16/2020] [Accepted: 10/27/2020] [Indexed: 12/24/2022] Open
Abstract
Potocki-Shaffer syndrome (PSS) is a rare non-recurrent contiguous gene deletion syndrome involving chromosome 11p11.2. Current literature implies a minimal region with haploinsufficiency of three genes, ALX4 (parietal foramina), EXT2 (multiple exostoses), and PHF21A (craniofacial anomalies, and intellectual disability). The rest of the PSS phenotype is still not associated with a specific gene. We report a systematic review of the literature and included two novel cases. Because deletions are highly variable in size, we defined three groups of patients considering the PSS-genes involved. We found 23 full PSS cases (ALX4, EXT2, and PHF21A), 14 cases with EXT2-ALX4, and three with PHF21A only. Among the latter, we describe a novel male child showing developmental delay, café-au-lait spots, liner postnatal overgrowth and West-like epileptic encephalopathy. We suggest PSS cases may have epileptic spasms early in life, and PHF21A is likely to be the causative gene. Given their subtle presentation these may be overlooked and if left untreated could lead to a severe type or deterioration in the developmental plateau. If our hypothesis is correct, a timely therapy may ameliorate PSS phenotype and improve patients’ outcomes. Our analysis also shows PHF21A is a candidate for the overgrowth phenotype.
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Affiliation(s)
- Slavica Trajkova
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy; (E.D.)
| | - Giovanni Battista Ferrero
- Department of Public Health and Paediatrics, University of Torino, 10126 Turin, Italy; (G.B.F.); (D.C.)
| | - Diana Carli
- Department of Public Health and Paediatrics, University of Torino, 10126 Turin, Italy; (G.B.F.); (D.C.)
| | - Lisa Pavinato
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
| | - Geoffroy Delplancq
- Centre de Génétique Humaine, Université de Franche-Comté, 25000 Besançon, France; (G.D.)
- Service de Pédiatrie, CHU, 25000 Besançon, France
| | - Paul Kuentz
- Oncobiologie Génétique Bioinformatique, PCBio, Centre Hospitalier Universitaire de Besançon, 25000 Besançon, France; (P.K.)
- UMR-Inserm 1231 GAD, Génétique des Anomalies du développement, Université de Bourgogne Franche-Comté, 21000 Dijon, France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (FHU TRANSLAD), Centre Hospitalier Universitaire de Dijon et Université de Bourgogne Franche-Comté, 21000 Dijon, France
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, 10126 Turin, Italy; (S.T.); (L.P.)
- Medical Genetics Unit, Città della Salute e della Scienza, University Hospital, 10126 Turin, Italy; (E.D.)
- Correspondence: (A.B.)
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