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van der Westhuizen ET. Single nucleotide variations encoding missense mutations in G protein-coupled receptors may contribute to autism. Br J Pharmacol 2024; 181:2158-2181. [PMID: 36787962 DOI: 10.1111/bph.16057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/21/2022] [Accepted: 02/04/2023] [Indexed: 02/16/2023] Open
Abstract
Autism is a neurodevelopmental condition with a range of symptoms that vary in intensity and severity from person to person. Genetic sequencing has identified thousands of genes containing mutations in autistic individuals, which may contribute to the development of autistic symptoms. Several of these genes encode G protein-coupled receptors (GPCRs), which are cell surface expressed proteins that transduce extracellular messages to the intracellular space. Mutations in GPCRs can impact their function, resulting in aberrant signalling within cells and across neurotransmitter systems in the brain. This review summarises the current knowledge on autism-associated single nucleotide variations encoding missense mutations in GPCRs and the impact of these genetic mutations on GPCR function. For some autism-associated mutations, changes in GPCR expression levels, ligand affinity, potency and efficacy have been observed. However, for many the functional consequences remain unknown. Thus, further work to characterise the functional impacts of the genetically identified mutations is required. LINKED ARTICLES: This article is part of a themed issue Therapeutic Targeting of G Protein-Coupled Receptors: hot topics from the Australasian Society of Clinical and Experimental Pharmacologists and Toxicologists 2021 Virtual Annual Scientific Meeting. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v181.14/issuetoc.
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Sivera R, Pelayo-Negro AL, Jericó I, Domínguez-González C, Horga A, Rodriguez De Rivera FJ, Gallardo E, Tembl JI, Bermejo-Guerrero L, Pagola Lorz MI, Azorín I, Cordoba M, Fenollar-Cortés MDM, Millet E, Vilchez JJ, Espinós C, Apellániz-Ruiz M, Sevilla T. Expanding the Clinical Spectrum of DRP2-Associated Charcot-Marie-Tooth Disease. Neurology 2024; 102:e209174. [PMID: 38513194 DOI: 10.1212/wnl.0000000000209174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 12/11/2023] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND AND OBJECTIVES Germline truncating variants in the DRP2 gene (encoding dystrophin-related protein 2) cause the disruption of the periaxin-DRP2-dystroglycan complex and have been linked to Charcot-Marie-Tooth disease. However, the causality and the underlying phenotype of the genetic alterations are not clearly defined. METHODS This cross-sectional retrospective observational study includes 9 patients with Charcot-Marie-Tooth disease (CMT) with DRP2 germline variants evaluated at 6 centers throughout Spain. RESULTS We identified 7 Spanish families with 4 different DRP2 likely pathogenic germline variants. In agreement with an X-linked inheritance, men harboring hemizygous DRP2 variants presented with an intermediate form of CMT, whereas heterozygous women were asymptomatic. Symptom onset was variable (36.6 ± 16 years), with lower limb weakness and multimodal sensory loss producing a mild-to-moderate functional impairment. Nerve echography revealed an increase in the cross-sectional area of nerve roots and proximal nerves. Lower limb muscle magnetic resonance imaging confirmed the presence of a length-dependent fatty infiltration. Immunostaining in intradermal nerve fibers demonstrated the absence of DRP2 and electron microscopy revealed abnormal myelin thickness that was also detectable in the sural nerve sections. DISCUSSION Our findings support the causality of DRP2 pathogenic germline variants in CMT and further define the phenotype as a late-onset sensory and motor length-dependent neuropathy, with intermediate velocities and thickening of proximal nerve segments.
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Affiliation(s)
- Rafael Sivera
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Ana L Pelayo-Negro
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Ivonne Jericó
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Cristina Domínguez-González
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Alejandro Horga
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Francisco J Rodriguez De Rivera
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Elena Gallardo
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Jose Ignacio Tembl
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Laura Bermejo-Guerrero
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Maria Inmaculada Pagola Lorz
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Inmaculada Azorín
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Marta Cordoba
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - María Del Mar Fenollar-Cortés
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Elvira Millet
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Juan J Vilchez
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Carmen Espinós
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - María Apellániz-Ruiz
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
| | - Teresa Sevilla
- From the Servicio de Neurología (R.S., J.I.T., T.S.) and Servicio de Neurofisiología (E.M.), Unidad de Enfermedades Neuromusculares, Hospital Universitari i Politècnic La Fe, Grupo de Investigación en enfermedades neuromusculares y ataxias, Instituto de Investigación Sanitaria La Fe, Valencia; CIBER de enfermedades raras (CIBERER) (R.S., C.D.-G., I.A., J.J.V., C.E., T.S.) and Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED) (A.L.P.-N., E.G.), Instituto de Salud Carlos III, Madrid; Servicio de Neurología (A.L.P.-N.), Hospital Universitario Marqués de Valdecilla (IDIVAL), Santander; Departamento de Neurología (I.J., M.I.P.L.), Hospital Universitario de Navarra, Instituto de Investigación Sanitaria de Navarra-IdiSNA, Pamplona; Servicio de Neurología (C.D.-G., L.B.-G.), Unidad de Enfermedades Neuromusculares, Hospital Universitario 12 de Octubre, Grupo de Investigación en Enfermedades mitocondriales y neuromusculares, Instituto de Investigación imas12; Servicio de Neurología (A.H.) and Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Servicio de Neurología (F.J.R.D.R.), Instituto de Investigación Sanitaria del Hospital Universitario La Paz - IDIPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid; Servicio de Radiodiagnóstico (E.G.), Hospital Universitario Marqués de Valdecilla, Santander; Grupo de Investigación en enfermedades neuromusculares y ataxias (I.A., J.J.V.), Instituto de Investigación Sanitaria La Fe, Valencia; Área de Neurología (M.C.), Health in code; Unidad de Genética Clínica (M.M.F.-C.), Servicio de Análisis Clínicos, Instituto de Medicina de Laboratorio, Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos de Madrid-IdISSC; Lab of Rare Neurodegenerative Diseases (C.E.), Centro de Investigación Príncipe Felipe (CIPF), Valencia; Unidad de Medicina Genómica (M.A.-R.), Instituto de Investigación Sanitaria de Navarra-IdiSNA, Universidad Pública de Navarra (UPNA), Navarrabiomed, Hospital Universitario de Navarra (HUN), Pamplona; and Departamento de Medicina (T.S.), Universitat de Valencia, Spain
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Borreca A, Mantovani C, Desiato G, Corradini I, Filipello F, Elia CA, D'Autilia F, Santamaria G, Garlanda C, Morini R, Pozzi D, Matteoli M. Loss of interleukin 1 signaling causes impairment of microglia- mediated synapse elimination and autistic-like behaviour in mice. Brain Behav Immun 2024; 117:493-509. [PMID: 38307446 DOI: 10.1016/j.bbi.2024.01.221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 01/11/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024] Open
Abstract
In the last years, the hypothesis that elevated levels of proinflammatory cytokines contribute to the pathogenesis of neurodevelopmental diseases has gained popularity. IL-1 is one of the main cytokines found to be elevated in Autism spectrum disorder (ASD), a complex neurodevelopmental condition characterized by defects in social communication and cognitive impairments. In this study, we demonstrate that mice lacking IL-1 signaling display autistic-like defects associated with an excessive number of synapses. We also show that microglia lacking IL-1 signaling at early neurodevelopmental stages are unable to properly perform the process of synapse engulfment and display excessive activation of mammalian target of rapamycin (mTOR) signaling. Notably, even the acute inhibition of IL-1R1 by IL-1Ra is sufficient to enhance mTOR signaling and reduce synaptosome phagocytosis in WT microglia. Finally, we demonstrate that rapamycin treatment rescues the defects in IL-1R deficient mice. These data unveil an exclusive role of microglial IL-1 in synapse refinement via mTOR signaling and indicate a novel mechanism possibly involved in neurodevelopmental disorders associated with defects in the IL-1 pathway.
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Affiliation(s)
- Antonella Borreca
- Institute of Neuroscience (IN-CNR), Consiglio Nazionale delle Ricerche, Milan, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Cristina Mantovani
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy
| | - Genni Desiato
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Irene Corradini
- Institute of Neuroscience (IN-CNR), Consiglio Nazionale delle Ricerche, Milan, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Fabia Filipello
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Chiara Adriana Elia
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Francesca D'Autilia
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Giulia Santamaria
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Cecilia Garlanda
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy
| | - Raffaella Morini
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy
| | - Davide Pozzi
- IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy; Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini 4, 20072 Pieve Emanuele, Milan, Italy.
| | - Michela Matteoli
- Institute of Neuroscience (IN-CNR), Consiglio Nazionale delle Ricerche, Milan, Italy; IRCCS Humanitas Research Hospital, Via Manzoni 56, 20089 Rozzano, Milan, Italy.
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4
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Geller E, Noble MA, Morales M, Gockley J, Emera D, Uebbing S, Cotney JL, Noonan JP. Massively parallel disruption of enhancers active in human neural stem cells. Cell Rep 2024; 43:113693. [PMID: 38271204 PMCID: PMC11078116 DOI: 10.1016/j.celrep.2024.113693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 11/02/2023] [Accepted: 01/05/2024] [Indexed: 01/27/2024] Open
Abstract
Changes in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders, potentially by altering neural progenitor proliferation. However, the effects of genetic variation within regulatory elements on neural progenitors remain obscure. We use sgRNA-Cas9 screens in human neural stem cells (hNSCs) to disrupt 10,674 genes and 26,385 conserved regions in 2,227 enhancers active in the developing human cortex and determine effects on proliferation. Genes with proliferation phenotypes are associated with neurodevelopmental disorders and show biased expression in specific fetal human brain neural progenitor populations. Although enhancer disruptions overall have weaker effects than gene disruptions, we identify enhancer disruptions that severely alter hNSC self-renewal. Disruptions in human accelerated regions, implicated in human brain evolution, also alter proliferation. Integrating proliferation phenotypes with chromatin interactions reveals regulatory relationships between enhancers and their target genes contributing to neurogenesis and potentially to human cortical evolution.
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Affiliation(s)
- Evan Geller
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mark A Noble
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Matheo Morales
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Jake Gockley
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Deena Emera
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Severin Uebbing
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Justin L Cotney
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - James P Noonan
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA; Department of Neuroscience, Yale School of Medicine, New Haven, CT 06510, USA; Wu Tsai Institute, Yale University, New Haven, CT 06510, USA.
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5
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Kitazawa M. Evolution of the nervous system by acquisition of retrovirus-derived genes in mammals. Genes Genet Syst 2024; 98:321-336. [PMID: 38220159 DOI: 10.1266/ggs.23-00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024] Open
Abstract
In the course of evolution, the most highly developed organ is likely the brain, which has become more complex over time and acquired diverse forms and functions in different species. In particular, mammals have developed complex and high-functioning brains, and it has been reported that several genes derived from retroviruses were involved in mammalian brain evolution, that is, generating the complexity of the nervous system. Especially, the sushi-ichi-related retrotransposon homolog (SIRH)/retrotransposon gag-like (RTL) genes have been suggested to play a role in the evolutionary processes shaping brain morphology and function in mammals. Genetic mutation and altered expression of genes are linked to neurological disorders, highlighting how the acquisition of virus-derived genes in mammals has both driven brain evolution and imposed a susceptibility to diseases. This review provides an overview of the functions, diversity, evolution and diseases associated with SIRH/RTL genes in the nervous system. The contribution of retroviruses to brain evolution is an important research topic in evolutionary biology and neuroscience, and further insights are expected to be gained through future studies.
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Affiliation(s)
- Moe Kitazawa
- School of BioSciences, Faculty of Science, The University of Melbourne
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6
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Mariano V, Kanellopoulos AK, Ricci C, Di Marino D, Borrie SC, Dupraz S, Bradke F, Achsel T, Legius E, Odent S, Billuart P, Bienvenu T, Bagni C. Intellectual Disability and Behavioral Deficits Linked to CYFIP1 Missense Variants Disrupting Actin Polymerization. Biol Psychiatry 2024; 95:161-174. [PMID: 37704042 DOI: 10.1016/j.biopsych.2023.08.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/27/2023] [Accepted: 08/31/2023] [Indexed: 09/15/2023]
Abstract
BACKGROUND 15q11.2 deletions and duplications have been linked to autism spectrum disorder, schizophrenia, and intellectual disability. Recent evidence suggests that dysfunctional CYFIP1 (cytoplasmic FMR1 interacting protein 1) contributes to the clinical phenotypes observed in individuals with 15q11.2 deletion/duplication syndrome. CYFIP1 plays crucial roles in neuronal development and brain connectivity, promoting actin polymerization and regulating local protein synthesis. However, information about the impact of single nucleotide variants in CYFIP1 on neurodevelopmental disorders is limited. METHODS Here, we report a family with 2 probands exhibiting intellectual disability, autism spectrum disorder, spastic tetraparesis, and brain morphology defects and who carry biallelic missense point mutations in the CYFIP1 gene. We used skin fibroblasts from one of the probands, the parents, and typically developing individuals to investigate the effect of the variants on the functionality of CYFIP1. In addition, we generated Drosophila knockin mutants to address the effect of the variants in vivo and gain insight into the molecular mechanism that underlies the clinical phenotype. RESULTS Our study revealed that the 2 missense variants are in protein domains responsible for maintaining the interaction within the wave regulatory complex. Molecular and cellular analyses in skin fibroblasts from one proband showed deficits in actin polymerization. The fly model for these mutations exhibited abnormal brain morphology and F-actin loss and recapitulated the core behavioral symptoms, such as deficits in social interaction and motor coordination. CONCLUSIONS Our findings suggest that the 2 CYFIP1 variants contribute to the clinical phenotype in the probands that reflects deficits in actin-mediated brain development processes.
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Affiliation(s)
- Vittoria Mariano
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Human Genetics, KU Leuven, Belgium
| | | | - Carlotta Ricci
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, New York-Marche Structural Biology Center, Polytechnic University of Marche, Ancona, Italy; Department of Neuroscience, Neuronal Death and Neuroprotection Unit, Mario Negri Institute for Pharmacological Research-IRCCS, Milan, Italy
| | | | - Sebastian Dupraz
- Axonal Growth and Regeneration Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Frank Bradke
- Axonal Growth and Regeneration Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Tilmann Achsel
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Eric Legius
- Department of Human Genetics, KU Leuven, Belgium
| | - Sylvie Odent
- Service de Génétique Clinique, Centre Labellisé pour les Anomalies du Développement Ouest, Centre Hospitalier Universitaire de Rennes, Rennes, France; Institut de Génétique et Développement de Rennes, CNRS, UMR 6290, Université de Rennes, ERN-ITHACA, France
| | - Pierre Billuart
- Institut de Psychiatrie et de Neurosciences de Paris, Institut National de la Santé et de la Recherche Médicale U1266, Université de Paris Cité (UPC), Paris, France
| | - Thierry Bienvenu
- Institut de Psychiatrie et de Neurosciences de Paris, Institut National de la Santé et de la Recherche Médicale U1266, Université de Paris Cité (UPC), Paris, France
| | - Claudia Bagni
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland; Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.
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7
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Wang S, Wang B, Drury V, Drake S, Sun N, Alkhairo H, Arbelaez J, Duhn C, Bal VH, Langley K, Martin J, Hoekstra PJ, Dietrich A, Xing J, Heiman GA, Tischfield JA, Fernandez TV, Owen MJ, O'Donovan MC, Thapar A, State MW, Willsey AJ. Rare X-linked variants carry predominantly male risk in autism, Tourette syndrome, and ADHD. Nat Commun 2023; 14:8077. [PMID: 38057346 PMCID: PMC10700338 DOI: 10.1038/s41467-023-43776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/18/2023] [Indexed: 12/08/2023] Open
Abstract
Autism spectrum disorder (ASD), Tourette syndrome (TS), and attention-deficit/hyperactivity disorder (ADHD) display strong male sex bias, due to a combination of genetic and biological factors, as well as selective ascertainment. While the hemizygous nature of chromosome X (Chr X) in males has long been postulated as a key point of "male vulnerability", rare genetic variation on this chromosome has not been systematically characterized in large-scale whole exome sequencing studies of "idiopathic" ASD, TS, and ADHD. Here, we take advantage of informative recombinations in simplex ASD families to pinpoint risk-enriched regions on Chr X, within which rare maternally-inherited damaging variants carry substantial risk in males with ASD. We then apply a modified transmission disequilibrium test to 13,052 ASD probands and identify a novel high confidence ASD risk gene at exome-wide significance (MAGEC3). Finally, we observe that rare damaging variants within these risk regions carry similar effect sizes in males with TS or ADHD, further clarifying genetic mechanisms underlying male vulnerability in multiple neurodevelopmental disorders that can be exploited for systematic gene discovery.
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Affiliation(s)
- Sheng Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa Drury
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Sam Drake
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Nawei Sun
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Hasan Alkhairo
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Juan Arbelaez
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Clif Duhn
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Vanessa H Bal
- Graduate School of Applied and Professional Psychology, Rutgers University, New Brunswick, NJ, USA
| | - Kate Langley
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
- School of Psychology, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Pieter J Hoekstra
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Andrea Dietrich
- University of Groningen, University Medical Center Groningen, Department of Child and Adolescent Psychiatry, Groningen, The Netherlands
- Accare Child Study Center, Groningen, The Netherlands
| | - Jinchuan Xing
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Gary A Heiman
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Jay A Tischfield
- Department of Genetics and the Human Genetics Institute of New Jersey, Rutgers, the State University of New Jersey, Piscataway, NJ, USA
| | - Thomas V Fernandez
- Yale Child Study Center and Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA
| | - Michael J Owen
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Michael C O'Donovan
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Anita Thapar
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University School of Medicine, Cardiff, Wales, UK
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, 94143, USA.
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, 94143, USA.
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8
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Kereszturi É. Diversity and Classification of Genetic Variations in Autism Spectrum Disorder. Int J Mol Sci 2023; 24:16768. [PMID: 38069091 PMCID: PMC10706722 DOI: 10.3390/ijms242316768] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/19/2023] [Accepted: 11/25/2023] [Indexed: 12/18/2023] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental condition with symptoms that affect the whole personality and all aspects of life. Although there is a high degree of heterogeneity in both its etiology and its characteristic behavioral patterns, the disorder is well-captured along the autistic triad. Currently, ASD status can be confirmed following an assessment of behavioral features, but there is a growing emphasis on conceptualizing autism as a spectrum, which allows for establishing a diagnosis based on the level of support need, free of discrete categories. Since ASD has a high genetic predominance, the number of genetic variations identified in the background of the condition is increasing exponentially as genetic testing methods are rapidly evolving. However, due to the huge amount of data to be analyzed, grouping the different DNA variations is still challenging. Therefore, in the present review, a multidimensional classification scheme was developed to accommodate most of the currently known genetic variants associated with autism. Genetic variations have been grouped according to six criteria (extent, time of onset, information content, frequency, number of genes involved, inheritance pattern), which are themselves not discrete categories, but form a coherent continuum in line with the autism spectrum approach.
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Affiliation(s)
- Éva Kereszturi
- Department of Molecular Biology, Semmelweis University, H-1085 Budapest, Hungary
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9
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Mount RA, Athif M, O’Connor M, Saligrama A, Tseng HA, Sridhar S, Zhou C, Bortz E, San Antonio E, Kramer MA, Man HY, Han X. The autism spectrum disorder risk gene NEXMIF over-synchronizes hippocampal CA1 network and alters neuronal coding. Front Neurosci 2023; 17:1277501. [PMID: 37965217 PMCID: PMC10641898 DOI: 10.3389/fnins.2023.1277501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/10/2023] [Indexed: 11/16/2023] Open
Abstract
Mutations in autism spectrum disorder (ASD) risk genes disrupt neural network dynamics that ultimately lead to abnormal behavior. To understand how ASD-risk genes influence neural circuit computation during behavior, we analyzed the hippocampal network by performing large-scale cellular calcium imaging from hundreds of individual CA1 neurons simultaneously in transgenic mice with total knockout of the X-linked ASD-risk gene NEXMIF (neurite extension and migration factor). As NEXMIF knockout in mice led to profound learning and memory deficits, we examined the CA1 network during voluntary locomotion, a fundamental component of spatial memory. We found that NEXMIF knockout does not alter the overall excitability of individual neurons but exaggerates movement-related neuronal responses. To quantify network functional connectivity changes, we applied closeness centrality analysis from graph theory to our large-scale calcium imaging datasets, in addition to using the conventional pairwise correlation analysis. Closeness centrality analysis considers both the number of connections and the connection strength between neurons within a network. We found that in wild-type mice the CA1 network desynchronizes during locomotion, consistent with increased network information coding during active behavior. Upon NEXMIF knockout, CA1 network is over-synchronized regardless of behavioral state and fails to desynchronize during locomotion, highlighting how perturbations in ASD-implicated genes create abnormal network synchronization that could contribute to ASD-related behaviors.
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Affiliation(s)
- Rebecca A. Mount
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Mohamed Athif
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | | | - Amith Saligrama
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
- Commonwealth School, Boston, MA, United States
| | - Hua-an Tseng
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Sudiksha Sridhar
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Chengqian Zhou
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Emma Bortz
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Erynne San Antonio
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
| | - Mark A. Kramer
- Department of Mathematics, Boston University, Boston, MA, United States
| | - Heng-Ye Man
- Department of Biology, Boston University, Boston, MA, United States
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, MA, United States
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10
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Murphy KE, Duncan B, Sperringer JE, Zhang E, Haberman V, Wyatt EV, Maness P. Ankyrin B promotes developmental spine regulation in the mouse prefrontal cortex. Cereb Cortex 2023; 33:10634-10648. [PMID: 37642601 PMCID: PMC10560577 DOI: 10.1093/cercor/bhad311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023] Open
Abstract
Postnatal regulation of dendritic spine formation and refinement in cortical pyramidal neurons is critical for excitatory/inhibitory balance in neocortical networks. Recent studies have identified a selective spine pruning mechanism in the mouse prefrontal cortex mediated by class 3 Semaphorins and the L1 cell adhesion molecules, neuron-glia related cell adhesion molecule, Close Homolog of L1, and L1. L1 cell adhesion molecules bind Ankyrin B, an actin-spectrin adaptor encoded by Ankyrin2, a high-confidence gene for autism spectrum disorder. In a new inducible mouse model (Nex1Cre-ERT2: Ank2flox: RCE), Ankyrin2 deletion in early postnatal pyramidal neurons increased spine density on apical dendrites in prefrontal cortex layer 2/3 of homozygous and heterozygous Ankyrin2-deficient mice. In contrast, Ankyrin2 deletion in adulthood had no effect on spine density. Sema3F-induced spine pruning was impaired in cortical neuron cultures from Ankyrin B-null mice and was rescued by re-expression of the 220 kDa Ankyrin B isoform but not 440 kDa Ankyrin B. Ankyrin B bound to neuron-glia related CAM at a cytoplasmic domain motif (FIGQY1231), and mutation to FIGQH inhibited binding, impairing Sema3F-induced spine pruning in neuronal cultures. Identification of a novel function for Ankyrin B in dendritic spine regulation provides insight into cortical circuit development, as well as potential molecular deficiencies in autism spectrum disorder.
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Affiliation(s)
- Kelsey E Murphy
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Bryce Duncan
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Justin E Sperringer
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Erin Zhang
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Victoria Haberman
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Elliott V Wyatt
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
| | - Patricia Maness
- Department of Biochemistry and Biophysics, University of North Carolina School of Medicine at Chapel Hill, Campus Box 7260, Chapel Hill, NC, 27599, United States
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11
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Abdi M, Aliyev E, Trost B, Kohailan M, Aamer W, Syed N, Shaath R, Gandhi GD, Engchuan W, Howe J, Thiruvahindrapuram B, Geng M, Whitney J, Syed A, Lakshmi J, Hussein S, Albashir N, Hussein A, Poggiolini I, Elhag SF, Palaniswamy S, Kambouris M, de Fatima Janjua M, Tahir MOE, Nazeer A, Shahwar D, Azeem MW, Mokrab Y, Aati NA, Akil A, Scherer SW, Kamal M, Fakhro KA. Genomic architecture of autism spectrum disorder in Qatar: The BARAKA-Qatar Study. Genome Med 2023; 15:81. [PMID: 37805537 PMCID: PMC10560429 DOI: 10.1186/s13073-023-01228-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/04/2023] [Indexed: 10/09/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a neurodevelopmental condition characterized by impaired social and communication skills, restricted interests, and repetitive behaviors. The prevalence of ASD among children in Qatar was recently estimated to be 1.1%, though the genetic architecture underlying ASD both in Qatar and the greater Middle East has been largely unexplored. Here, we describe the first genomic data release from the BARAKA-Qatar Study-a nationwide program building a broadly consented biorepository of individuals with ASD and their families available for sample and data sharing and multi-omics research. METHODS In this first release, we present a comprehensive analysis of whole-genome sequencing (WGS) data of the first 100 families (372 individuals), investigating the genetic architecture, including single-nucleotide variants (SNVs), copy number variants (CNVs), tandem repeat expansions (TREs), as well as mitochondrial DNA variants (mtDNA) segregating with ASD in local families. RESULTS Overall, we identify potentially pathogenic variants in known genes or regions in 27 out of 100 families (27%), of which 11 variants (40.7%) were classified as pathogenic or likely-pathogenic based on American College of Medical Genetics (ACMG) guidelines. Dominant variants, including de novo and inherited, contributed to 15 (55.6%) of these families, consisting of SNVs/indels (66.7%), CNVs (13.3%), TREs (13.3%), and mtDNA variants (6.7%). Moreover, homozygous variants were found in 7 families (25.9%), with a sixfold increase in homozygous burden in consanguineous versus non-consanguineous families (13.6% and 1.8%, respectively). Furthermore, 28 novel ASD candidate genes were identified in 20 families, 23 of which had recurrent hits in MSSNG and SSC cohorts. CONCLUSIONS This study illustrates the value of ASD studies in under-represented populations and the importance of WGS as a comprehensive tool for establishing a molecular diagnosis for families with ASD. Moreover, it uncovers a significant role for recessive variation in ASD architecture in consanguineous settings and provides a unique resource of Middle Eastern genomes for future research to the global ASD community.
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Affiliation(s)
- Mona Abdi
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Brett Trost
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | | | - Waleed Aamer
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Najeeb Syed
- Genomics Data Science Core, Sidra Medicine, Doha, Qatar
| | - Rulan Shaath
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Worrawat Engchuan
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Melissa Geng
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Joe Whitney
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Amira Syed
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Sura Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Amal Hussein
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | | | - Saba F Elhag
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Hamad Medical Corporation, Doha, Qatar
| | | | - Marios Kambouris
- Pathology and Laboratory Medicine Department, Genetics Division, Sidra Medicine, Doha, Qatar
| | | | | | - Ahsan Nazeer
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Durre Shahwar
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Muhammad Waqar Azeem
- Department of Psychiatry, Sidra Medicine, Doha, Qatar
- Weill Cornell Medicine, Doha, Qatar
| | - Younes Mokrab
- Department of Genetics, Sidra Medicine, Doha, Qatar
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar
- Qatar University, Doha, Qatar
| | | | - Ammira Akil
- Department of Genetics, Sidra Medicine, Doha, Qatar
| | - Stephen W Scherer
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Madeeha Kamal
- Department of Pediatrics, Sidra Medicine, Doha, Qatar
| | - Khalid A Fakhro
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
- Department of Genetics, Sidra Medicine, Doha, Qatar.
- Department of Genetic Medicine, Weill Cornell Medicine, Doha, Qatar.
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12
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Ishino F, Itoh J, Irie M, Matsuzawa A, Naruse M, Suzuki T, Hiraoka Y, Kaneko-Ishino T. Retrovirus-Derived RTL9 Plays an Important Role in Innate Antifungal Immunity in the Eutherian Brain. Int J Mol Sci 2023; 24:14884. [PMID: 37834332 PMCID: PMC10573853 DOI: 10.3390/ijms241914884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/25/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Retrotransposon Gag-like (RTL) genes play a variety of essential and important roles in the eutherian placenta and brain. It has recently been demonstrated that RTL5 and RTL6 (also known as sushi-ichi retrotransposon homolog 8 (SIRH8) and SIRH3) are microglial genes that play important roles in the brain's innate immunity against viruses and bacteria through their removal of double-stranded RNA and lipopolysaccharide, respectively. In this work, we addressed the function of RTL9 (also known as SIRH10). Using knock-in mice that produce RTL9-mCherry fusion protein, we examined RTL9 expression in the brain and its reaction to fungal zymosan. Here, we demonstrate that RTL9 plays an important role, degrading zymosan in the brain. The RTL9 protein is localized in the microglial lysosomes where incorporated zymosan is digested. Furthermore, in Rtl9 knockout mice expressing RTL9ΔC protein lacking the C-terminus retroviral GAG-like region, the zymosan degrading activity was lost. Thus, RTL9 is essentially engaged in this reaction, presumably via its GAG-like region. Together with our previous study, this result highlights the importance of three retrovirus-derived microglial RTL genes as eutherian-specific constituents of the current brain innate immune system: RTL9, RTL5 and RTL6, responding to fungi, viruses and bacteria, respectively.
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Affiliation(s)
- Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.I.); (A.M.); (M.N.)
| | - Johbu Itoh
- Department of Pathology, School of Medicine, Tokai University, Isehara 259-1193, Japan;
| | - Masahito Irie
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.I.); (A.M.); (M.N.)
- Faculty of Nursing, School of Medicine, Tokai University, Isehara 259-1193, Japan
| | - Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.I.); (A.M.); (M.N.)
- Department of Genomic Function and Diversity, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Mie Naruse
- Department of Epigenetics, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.I.); (A.M.); (M.N.)
| | - Toru Suzuki
- Laboratory of Genome Editing for Biomedical Research, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (T.S.); (Y.H.)
| | - Yuichi Hiraoka
- Laboratory of Genome Editing for Biomedical Research, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (T.S.); (Y.H.)
- Laboratory of Molecular Neuroscience, Medical Research Institute (MRI), Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Isehara 259-1193, Japan
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13
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Shiura H, Kitazawa M, Ishino F, Kaneko-Ishino T. Roles of retrovirus-derived PEG10 and PEG11/RTL1 in mammalian development and evolution and their involvement in human disease. Front Cell Dev Biol 2023; 11:1273638. [PMID: 37842090 PMCID: PMC10570562 DOI: 10.3389/fcell.2023.1273638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/14/2023] [Indexed: 10/17/2023] Open
Abstract
PEG10 and PEG11/RTL1 are paternally expressed, imprinted genes that play essential roles in the current eutherian developmental system and are therefore associated with developmental abnormalities caused by aberrant genomic imprinting. They are also presumed to be retrovirus-derived genes with homology to the sushi-ichi retrotransposon GAG and POL, further expanding our comprehension of mammalian evolution via the domestication (exaptation) of retrovirus-derived acquired genes. In this manuscript, we review the importance of PEG10 and PEG11/RTL1 in genomic imprinting research via their functional roles in development and human disease, including neurodevelopmental disorders of genomic imprinting, Angelman, Kagami-Ogata and Temple syndromes, and the impact of newly inserted DNA on the emergence of newly imprinted regions. We also discuss their possible roles as ancestors of other retrovirus-derived RTL/SIRH genes that likewise play important roles in the current mammalian developmental system, such as in the placenta, brain and innate immune system.
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Affiliation(s)
- Hirosuke Shiura
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi, Japan
| | - Moe Kitazawa
- School of BioSciences, Faculty of Science, The University of Melbourne, Melbourne, VIC, Australia
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo, Japan
| | - Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Isehara, Kanagawa, Japan
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14
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Kaneko-Ishino T, Ishino F. Retrovirus-Derived RTL/SIRH: Their Diverse Roles in the Current Eutherian Developmental System and Contribution to Eutherian Evolution. Biomolecules 2023; 13:1436. [PMID: 37892118 PMCID: PMC10604271 DOI: 10.3390/biom13101436] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 10/29/2023] Open
Abstract
Eutherians have 11 retrotransposon Gag-like (RTL)/sushi-ichi retrotransposon homolog (SIRH) genes presumably derived from a certain retrovirus. Accumulating evidence indicates that the RTL/SIRH genes play a variety of roles in the current mammalian developmental system, such as in the placenta, brain, and innate immune system, in a eutherian-specific manner. It has been shown that the functional role of Paternally Expressed 10 (PEG10) in placental formation is unique to the therian mammals, as are the eutherian-specific roles of PEG10 and PEG11/RTL1 in maintaining the fetal capillary network and the endocrine regulation of RTL7/SIRH7 (aka Leucine Zipper Down-Regulated in Cancer 1 (LDOCK1)) in the placenta. In the brain, PEG11/RTL1 is expressed in the corticospinal tract and hippocampal commissure, mammalian-specific structures, and in the corpus callosum, a eutherian-specific structure. Unexpectedly, at least three RTL/SIRH genes, RTL5/SIRH8, RTL6/SIRH3, and RTL9/SIRH10, play important roles in combating a variety of pathogens, namely viruses, bacteria, and fungi, respectively, suggesting that the innate immunity system of the brain in eutherians has been enhanced by the emergence of these new components. In this review, we will summarize the function of 10 out of the 11 RTL/SIRH genes and discuss their roles in eutherian development and evolution.
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Affiliation(s)
- Tomoko Kaneko-Ishino
- Faculty of Nursing, School of Medicine, Tokai University, Kanagawa 259-1193, Japan
| | - Fumitoshi Ishino
- Center for Experimental Animals, Institute of Research, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
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15
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Holling T, Brylka L, Scholz T, Bierhals T, Herget T, Meinecke P, Schinke T, Oheim R, Kutsche K. TMCO3, a Putative K + :Proton Antiporter at the Golgi Apparatus, Is Important for Longitudinal Growth in Mice and Humans. J Bone Miner Res 2023; 38:1334-1349. [PMID: 37554015 DOI: 10.1002/jbmr.4827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 04/27/2023] [Accepted: 05/07/2023] [Indexed: 08/10/2023]
Abstract
Isolated short stature, defined as short stature without any other abnormalities, is a common heterogeneous condition in children. Exome sequencing identified the homozygous nonsense variant c.1832G>A/p.(Trp611*) in TMCO3 in two sisters with isolated short stature. Radiological studies, biochemical measurements, assessment of the skeletal status, and three-dimensional bone microarchitecture revealed no relevant skeletal and bone abnormalities in both sisters. The homozygous TMCO3 variant segregated with short stature in the family. TMCO3 transcript levels were reduced by ~50% in leukocyte-derived RNA of both sisters compared with controls, likely due to nonsense-mediated mRNA decay. In primary urinary cells of heterozygous family members, we detected significantly reduced TMCO3 protein levels. TMCO3 is functionally uncharacterized. We ectopically expressed wild-type TMCO3 in HeLa and ATDC5 chondrogenic cells and detected TMCO3 predominantly at the Golgi apparatus, whereas the TMCO3W611* mutant did not reach the Golgi. Coordinated co-expression of TMCO3W611* -HA and EGFP in HeLa cells confirmed intrinsic instability and/or degradation of the mutant. Tmco3 is expressed in all relevant mouse skeletal cell types. Highest abundance of Tmco3 was found in chondrocytes of the prehypertrophic zone in mouse and minipig growth plates where it co-localizes with a Golgi marker. Knockdown of Tmco3 in differentiated ATDC5 cells caused reduced and increased expression of Pthlh and Ihh, respectively. Measurement of long bones in Tmco3tm1b(KOMP)Wtsi knockout mice revealed significant shortening of forelimbs and hindlimbs. TMCO3 is a potential member of the monovalent cation:proton antiporter 2 (CPA2) family. By in silico tools and homology modeling, TMCO3 is predicted to have an N-terminal secretory signal peptide, forms a dimer localized to the membrane, and is organized in a dimerization and a core domain. The core domain contains the CPA2 motif essential for K+ binding and selectivity. Collectively, our data demonstrate that loss of TMCO3 causes growth defects in both humans and mice. © 2023 American Society for Bone and Mineral Research (ASBMR).
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Affiliation(s)
- Tess Holling
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Laura Brylka
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tasja Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Theresia Herget
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thorsten Schinke
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ralf Oheim
- Department of Osteology and Biomechanics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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16
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Murphy KE, Duncan BW, Sperringer JE, Zhang EY, Haberman VA, Wyatt EV, Maness PF. Ankyrin B Promotes Developmental Spine Regulation in the Mouse Prefrontal Cortex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548527. [PMID: 37503187 PMCID: PMC10369899 DOI: 10.1101/2023.07.11.548527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Postnatal regulation of dendritic spine formation and refinement in cortical pyramidal neurons is critical for excitatory/inhibitory balance in neocortical networks. Recent studies have identified a selective spine pruning mechanism in the mouse prefrontal cortex (PFC) mediated by class 3 Semaphorins and the L1-CAM cell adhesion molecules Neuron-glia related CAM (NrCAM), Close Homolog of L1 (CHL1), and L1. L1-CAMs bind Ankyrin B (AnkB), an actin-spectrin adaptor encoded by Ankyrin2 ( ANK2 ), a high confidence gene for autism spectrum disorder (ASD). In a new inducible mouse model (Nex1Cre-ERT2: Ank2 flox : RCE), Ank2 deletion in early postnatal pyramidal neurons increased spine density on apical dendrites in PFC layer 2/3 of homozygous and heterozygous Ank2 -deficient mice. In contrast, Ank2 deletion in adulthood had no effect on spine density. Sema3F-induced spine pruning was impaired in cortical neuron cultures from AnkB-null mice and was rescued by re-expression of the 220 kDa AnkB isoform but not 440 kDa AnkB. AnkB bound to NrCAM at a cytoplasmic domain motif (FIGQY 1231 ), and mutation to FIGQH inhibited binding, impairing Sema3F-induced spine pruning in neuronal cultures. Identification of a novel function for AnkB in dendritic spine regulation provides insight into cortical circuit development, as well as potential molecular deficiencies in ASD.
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17
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Miyake N, Tsurusaki Y, Fukai R, Kushima I, Okamoto N, Ohashi K, Nakamura K, Hashimoto R, Hiraki Y, Son S, Kato M, Sakai Y, Osaka H, Deguchi K, Matsuishi T, Takeshita S, Fattal-Valevski A, Ekhilevitch N, Tohyama J, Yap P, Keng WT, Kobayashi H, Takubo K, Okada T, Saitoh S, Yasuda Y, Murai T, Nakamura K, Ohga S, Matsumoto A, Inoue K, Saikusa T, Hershkovitz T, Kobayashi Y, Morikawa M, Ito A, Hara T, Uno Y, Seiwa C, Ishizuka K, Shirahata E, Fujita A, Koshimizu E, Miyatake S, Takata A, Mizuguchi T, Ozaki N, Matsumoto N. Molecular diagnosis of 405 individuals with autism spectrum disorder. Eur J Hum Genet 2023:10.1038/s41431-023-01335-7. [PMID: 36973392 DOI: 10.1038/s41431-023-01335-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 02/08/2023] [Accepted: 03/07/2023] [Indexed: 03/29/2023] Open
Abstract
Autism spectrum disorder (ASD) is caused by combined genetic and environmental factors. Genetic heritability in ASD is estimated as 60-90%, and genetic investigations have revealed many monogenic factors. We analyzed 405 patients with ASD using family-based exome sequencing to detect disease-causing single-nucleotide variants (SNVs), small insertions and deletions (indels), and copy number variations (CNVs) for molecular diagnoses. All candidate variants were validated by Sanger sequencing or quantitative polymerase chain reaction and were evaluated using the American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines for molecular diagnosis. We identified 55 disease-causing SNVs/indels in 53 affected individuals and 13 disease-causing CNVs in 13 affected individuals, achieving a molecular diagnosis in 66 of 405 affected individuals (16.3%). Among the 55 disease-causing SNVs/indels, 51 occurred de novo, 2 were compound heterozygous (in one patient), and 2 were X-linked hemizygous variants inherited from unaffected mothers. The molecular diagnosis rate in females was significantly higher than that in males. We analyzed affected sibling cases of 24 quads and 2 quintets, but only one pair of siblings shared an identical pathogenic variant. Notably, there was a higher molecular diagnostic rate in simplex cases than in multiplex families. Our simulation indicated that the diagnostic yield is increasing by 0.63% (range 0-2.5%) per year. Based on our simple simulation, diagnostic yield is improving over time. Thus, periodical reevaluation of ES data should be strongly encouraged in undiagnosed ASD patients.
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Affiliation(s)
- Noriko Miyake
- Department of Human Genetics, National Center for Global Health and Medicine, Tokyo, Japan.
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Ryoko Fukai
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Kei Ohashi
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Kazuhiko Nakamura
- Department of Neuropsychiatry, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | - Shuraku Son
- Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | | | - Toyojiro Matsuishi
- Departments of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
- Department of Pediatrics, St. Mary's Hospital, Kurume, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, Yokohama, Japan
| | - Aviva Fattal-Valevski
- Pediatric Neurology Institute, Dana-Dwek Children's Hospital, Tel Aviv Medical Center & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nina Ekhilevitch
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Jun Tohyama
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Patrick Yap
- Genetic Health Service New Zealand, Auckland, New Zealand
- Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Wee Teik Keng
- Genetic Department, Hospital Kuala Lumpur, Kuala Lumpur, Malaysia
| | - Hiroshi Kobayashi
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Keiyo Takubo
- Department of Stem Cell Biology, Research Institute, National Center for Global Health and Medicine, Tokyo, Japan
| | - Takashi Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Department of Developmental Disorders, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Shinji Saitoh
- Department of Pediatrics and Neonatology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Yuka Yasuda
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Toshiya Murai
- Department of Psychiatry, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, Yamagata, Japan
| | - Shouichi Ohga
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ayumi Matsumoto
- Department of Pediatrics, Jichi Medical University, Shimotsuke, Japan
| | - Ken Inoue
- Deguchi Pediatric Clinic, Omura, Japan
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Japan
| | - Tomoko Saikusa
- Departments of Pediatrics and Child Health, Kurume University School of Medicine, Kurume, Japan
- Department of Pediatrics, St. Mary's Hospital, Kurume, Japan
| | - Tova Hershkovitz
- The Genetics Institute, Rambam Health Care Campus, Haifa, Israel
| | - Yu Kobayashi
- Department of Child Neurology, National Hospital Organization Nishiniigata Chuo Hospital, Niigata, Japan
| | - Mako Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Aiko Ito
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | | | - Yota Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Chizuru Seiwa
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | - Kanako Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Emi Shirahata
- Department of Pediatrics, Yamagata Prefectural Rehabilitation Center for Children with Disabilities, Yamagata, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
- Department of Clinical Genetics, Yokohama City University Hospital, Yokohama, Japan
| | - Atsushi Takata
- Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Institute for Glyco-core Research (iGCORE), Nagoya University, Nagoya, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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18
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Ribonuclease inhibitor 1 (RNH1) deficiency cause congenital cataracts and global developmental delay with infection-induced psychomotor regression and anemia. Eur J Hum Genet 2023:10.1038/s41431-023-01327-7. [PMID: 36935417 PMCID: PMC10400601 DOI: 10.1038/s41431-023-01327-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/21/2023] Open
Abstract
Ribonuclease inhibitor 1, also known as angiogenin inhibitor 1, encoded by RNH1, is a ubiquitously expressed leucine-rich repeat protein, which is highly conserved in mammalian species. Inactivation of rnh1 in mice causes an embryonically lethal anemia, but the exact biological function of RNH1 in humans remains unknown and no human genetic disease has so far been associated with RNH1. Here, we describe a family with two out of seven siblings affected by a disease characterized by congenital cataract, global developmental delay, myopathy and psychomotor deterioration, seizures and periodic anemia associated with upper respiratory tract infections. A homozygous splice-site variant (c.615-2A > C) in RNH1 segregated with the disease. Sequencing of RNA derived from patient fibroblasts and cDNA analysis of skeletal muscle mRNA showed aberrant splicing with skipping of exon 7. Western blot analysis revealed a total lack of the RNH1 protein. Functional analysis revealed that patient fibroblasts were more sensitive to RNase A exposure, and this phenotype was reversed by transduction with a lentivirus expressing RNH1 to complement patient cells. Our results demonstrate that loss-of-function of RNH1 in humans is associated with a multiorgan developmental disease with recessive inheritance. It may be speculated that the infection-induced deterioration resulted from an increased susceptibility toward extracellular RNases and/or other inflammatory responses normally kept in place by the RNase inhibitor RNH1.
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19
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Alasiri A, Karczewski KJ, Cole B, Loza BL, Moore JH, van der Laan SW, Asselbergs FW, Keating BJ, van Setten J. LoFTK: a framework for fully automated calculation of predicted Loss-of-Function variants and genes. BioData Min 2023; 16:3. [PMID: 36732776 PMCID: PMC9893534 DOI: 10.1186/s13040-023-00321-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 01/04/2023] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Loss-of-Function (LoF) variants in human genes are important due to their impact on clinical phenotypes and frequent occurrence in the genomes of healthy individuals. The association of LoF variants with complex diseases and traits may lead to the discovery and validation of novel therapeutic targets. Current approaches predict high-confidence LoF variants without identifying the specific genes or the number of copies they affect. Moreover, there is a lack of methods for detecting knockout genes caused by compound heterozygous (CH) LoF variants. RESULTS We have developed the Loss-of-Function ToolKit (LoFTK), which allows efficient and automated prediction of LoF variants from genotyped, imputed and sequenced genomes. LoFTK enables the identification of genes that are inactive in one or two copies and provides summary statistics for downstream analyses. LoFTK can identify CH LoF variants, which result in LoF genes with two copies lost. Using data from parents and offspring we show that 96% of CH LoF genes predicted by LoFTK in the offspring have the respective alleles donated by each parent. CONCLUSIONS LoFTK is a command-line based tool that provides a reliable computational workflow for predicting LoF variants from genotyped and sequenced genomes, identifying genes that are inactive in 1 or 2 copies. LoFTK is an open software and is freely available to non-commercial users at https://github.com/CirculatoryHealth/LoFTK .
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Affiliation(s)
- Abdulrahman Alasiri
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands
- Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Brian Cole
- Bioinformatics Core, Harvard Medical School, Boston, MA, USA
| | - Bao-Li Loza
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason H Moore
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Sander W van der Laan
- Central Diagnostic Laboratory, Division Laboratories, Pharmacy, and Biomedical Genetics, University Medical Center Utrecht, University of Utrecht, Utrecht, Netherlands
| | - Folkert W Asselbergs
- Department of Cardiology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
- Health Data Research UK and Institute of Health Informatics, University College London, London, UK
| | - Brendan J Keating
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jessica van Setten
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, University of Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, Netherlands.
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20
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Santoso AD, De Ridder D. Fatty Acid Amide Hydrolase: An Integrative Clinical Perspective. Cannabis Cannabinoid Res 2023; 8:56-76. [PMID: 35900294 DOI: 10.1089/can.2021.0237] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Introduction: Fatty acid amide hydrolase (FAAH) is one of the main terminating enzymes of the endocannabinoid system (ECS). Since being discovered in 1996, the modulation of FAAH has been viewed as a compelling alternative strategy to obtain the beneficial effect of the ECS. With a considerable amount of FAAH-related publication over time, the next step would be to comprehend the proximity of this evidence for clinical application. Objective: This review intends to highlight the rationale of FAAH modulation and provide the latest evidence from clinical studies. Methods: Publication searches were conducted to gather information focused on FAAH-related clinical evidence with an extension to the experimental research to understand the biological plausibility. The subtopics were selected to be multidisciplinary to offer more perspective on the current state of the arts. Discussion: Experimental and clinical studies have demonstrated that FAAH was highly expressed not only in the central nervous system but also in the peripheral tissues. As the key regulator of endocannabinoid signaling, it would appear that FAAH plays a role in the modulation of mood and emotional response, reward system, pain perception, energy metabolism and appetite regulation, inflammation, and other biological processes. Genetic variants may be associated with some conditions such as substance/alcohol use disorders, obesity, and eating disorder. The advancement of functional neuroimaging has enabled the evaluation of the neurochemistry of FAAH in brain tissues and this can be incorporated into clinical trials. Intriguingly, the application of FAAH inhibitors in clinical trials seems to provide less striking results in comparison with the animal models, although some potential still can be seen. Conclusion: Modulation of FAAH has an immense potential to be a new therapeutic candidate for several disorders. Further exploration, however, is still needed to ensure who is the best candidate for the treatment strategy.
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Affiliation(s)
- Anugrah D Santoso
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
- Department of Urology, Faculty of Medicine Universitas Airlangga, Dr. Soetomo General Academic Hospital, Surabaya, Indonesia
| | - Dirk De Ridder
- Laboratory of Experimental Urology, Department of Development and Regeneration, KU Leuven, Leuven, Belgium
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21
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Vashisth S, Chahrour MH. Genomic strategies to untangle the etiology of autism: A primer. Autism Res 2023; 16:31-39. [PMID: 36415077 PMCID: PMC10615252 DOI: 10.1002/aur.2844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in communication, diminished social skills, and restrictive and repetitive behaviors and interests. ASD affects approximately 2.3% of the population and is highly heterogeneous, both phenotypically and genetically. As genomic technologies advance, our understanding of the genetic architecture of ASD is becoming clearer, encompassing spontaneous and inherited alterations throughout the genome, and delineating alterations that are either rare or common in the population. This commentary provides an overview of the genomic strategies and resulting major findings of genetic alterations associated with ASD.
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Affiliation(s)
- Shayal Vashisth
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Maria H. Chahrour
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Peter O’Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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22
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Nagirnaja L, Lopes AM, Charng WL, Miller B, Stakaitis R, Golubickaite I, Stendahl A, Luan T, Friedrich C, Mahyari E, Fadial E, Kasak L, Vigh-Conrad K, Oud MS, Xavier MJ, Cheers SR, James ER, Guo J, Jenkins TG, Riera-Escamilla A, Barros A, Carvalho F, Fernandes S, Gonçalves J, Gurnett CA, Jørgensen N, Jezek D, Jungheim ES, Kliesch S, McLachlan RI, Omurtag KR, Pilatz A, Sandlow JI, Smith J, Eisenberg ML, Hotaling JM, Jarvi KA, Punab M, Rajpert-De Meyts E, Carrell DT, Krausz C, Laan M, O’Bryan MK, Schlegel PN, Tüttelmann F, Veltman JA, Almstrup K, Aston KI, Conrad DF. Diverse monogenic subforms of human spermatogenic failure. Nat Commun 2022; 13:7953. [PMID: 36572685 PMCID: PMC9792524 DOI: 10.1038/s41467-022-35661-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 12/16/2022] [Indexed: 12/27/2022] Open
Abstract
Non-obstructive azoospermia (NOA) is the most severe form of male infertility and typically incurable. Defining the genetic basis of NOA has proven challenging, and the most advanced classification of NOA subforms is not based on genetics, but simple description of testis histology. In this study, we exome-sequenced over 1000 clinically diagnosed NOA cases and identified a plausible recessive Mendelian cause in 20%. We find further support for 21 genes in a 2-stage burden test with 2072 cases and 11,587 fertile controls. The disrupted genes are primarily on the autosomes, enriched for undescribed human "knockouts", and, for the most part, have yet to be linked to a Mendelian trait. Integration with single-cell RNA sequencing data shows that azoospermia genes can be grouped into molecular subforms with synchronized expression patterns, and analogs of these subforms exist in mice. This analysis framework identifies groups of genes with known roles in spermatogenesis but also reveals unrecognized subforms, such as a set of genes expressed across mitotic divisions of differentiating spermatogonia. Our findings highlight NOA as an understudied Mendelian disorder and provide a conceptual structure for organizing the complex genetics of male infertility, which may provide a rational basis for disease classification.
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Affiliation(s)
- Liina Nagirnaja
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Alexandra M. Lopes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226IPATIMUP - Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Porto, Portugal
| | - Wu-Lin Charng
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Brian Miller
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Rytis Stakaitis
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Laboratory of Molecular Neurooncology, Neuroscience Institute, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Ieva Golubickaite
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.45083.3a0000 0004 0432 6841Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alexandra Stendahl
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Tianpengcheng Luan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Corinna Friedrich
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Eisa Mahyari
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Eloise Fadial
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Laura Kasak
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Katinka Vigh-Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
| | - Manon S. Oud
- grid.10417.330000 0004 0444 9382Department of Human Genetics, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Miguel J. Xavier
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Samuel R. Cheers
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia
| | - Emma R. James
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA ,grid.223827.e0000 0001 2193 0096Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT USA
| | - Jingtao Guo
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Timothy G. Jenkins
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Antoni Riera-Escamilla
- grid.418813.70000 0004 1767 1951Andrology Department, Fundació Puigvert, Universitat Autònoma de Barcelona, Instituto de Investigaciones Biomédicas Sant Pau (IIB-Sant Pau), Barcelona, Catalonia Spain ,grid.7080.f0000 0001 2296 0625Molecular Biology Laboratory, Fundació Puigvert, Instituto de Investigaciones Biomédicas Sant Pau (IIB Sant Pau), Universitat Autònoma de Barcelona, Barcelona, Catalonia 08025 Spain
| | - Alberto Barros
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Filipa Carvalho
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - Susana Fernandes
- grid.5808.50000 0001 1503 7226i3S - Instituto de Investigação e Inovação em Saúde, University of Porto, Porto, Portugal ,grid.5808.50000 0001 1503 7226Serviço de Genética, Departamento de Patologia, Faculdade de Medicina da Universidade do Porto, Porto, Portugal
| | - João Gonçalves
- grid.422270.10000 0001 2287 695XDepartamento de Genética Humana, Instituto Nacional de Saúde Dr. Ricardo Jorge, Lisboa, Portugal ,grid.10772.330000000121511713Centre for Toxicogenomics and Human Health, Nova Medical School, Lisbon, Portugal
| | - Christina A. Gurnett
- grid.4367.60000 0001 2355 7002Department of Neurology, Washington University, St. Louis, MO USA
| | - Niels Jørgensen
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Davor Jezek
- grid.4808.40000 0001 0657 4636Department of Histology and Embryology, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Emily S. Jungheim
- grid.16753.360000 0001 2299 3507Department of Obstetrics and Gynecology at Northwestern University, Division of Reproductive Endocrinology, Chicago, IL USA
| | - Sabine Kliesch
- grid.16149.3b0000 0004 0551 4246Department of Clinical and Surgical Andrology, Centre of Reproductive Medicine and Andrology, University Hospital Münster, Münster, Germany
| | - Robert I. McLachlan
- grid.1002.30000 0004 1936 7857Hudson Institute of Medical Research and the Department of Obstetrics and Gynecology, Monash University, Clayton, VIC Australia
| | - Kenan R. Omurtag
- grid.34477.330000000122986657Department of Obstetrics and Gynecology at Washington University, Division of Reproductive Endocrinology, St. Louis, MO USA
| | - Adrian Pilatz
- grid.8664.c0000 0001 2165 8627Clinic for Urology, Pediatric Urology and Andrology, Justus Liebig University, Giessen, Germany
| | - Jay I. Sandlow
- grid.30760.320000 0001 2111 8460Department of Urology, Medical College of Wisconsin, Milwaukee, WI USA
| | - James Smith
- grid.266102.10000 0001 2297 6811Department of Urology, University California San Francisco, San Francisco, CA USA
| | - Michael L. Eisenberg
- grid.168010.e0000000419368956Department of Urology, Stanford University School of Medicine, Stanford, CA USA
| | - James M. Hotaling
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Keith A. Jarvi
- grid.17063.330000 0001 2157 2938Division of Urology, Department of Surgery, Mount Sinai Hospital, University of Toronto, Toronto, ON Canada
| | - Margus Punab
- grid.412269.a0000 0001 0585 7044Andrology Center, Tartu University Hospital, Tartu, Estonia ,grid.10939.320000 0001 0943 7661Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ewa Rajpert-De Meyts
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Douglas T. Carrell
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Csilla Krausz
- grid.8404.80000 0004 1757 2304Department of Experimental and Clinical Biomedical Sciences, University of Florence, Florence, Italy
| | - Maris Laan
- grid.10939.320000 0001 0943 7661Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Moira K. O’Bryan
- grid.1008.90000 0001 2179 088XSchool of BioSciences, Faculty of Science, The University of Melbourne, Parkville, VIC Australia ,grid.1002.30000 0004 1936 7857School of Biological Sciences, Monash University, Clayton, VIC Australia
| | - Peter N. Schlegel
- grid.5386.8000000041936877XDepartment of Urology, Weill Cornell Medicine, New York, NY USA
| | - Frank Tüttelmann
- grid.5949.10000 0001 2172 9288Institute of Reproductive Genetics, University of Münster, Münster, Germany
| | - Joris A. Veltman
- grid.1006.70000 0001 0462 7212Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle-upon-Tyne, UK
| | - Kristian Almstrup
- grid.475435.4Department of Growth and Reproduction, Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark ,grid.475435.4International Center for Research and Research Training in Endocrine Disruption of Male Reproduction and Child Health (EDMaRC), Copenhagen University Hospital - Rigshospitalet, Copenhagen, Denmark
| | - Kenneth I. Aston
- grid.223827.e0000 0001 2193 0096Andrology and IVF Laboratory, Department of Surgery (Urology), University of Utah School of Medicine, Salt Lake City, UT USA
| | - Donald F. Conrad
- grid.5288.70000 0000 9758 5690Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR USA
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23
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Dougherty JD, Marrus N, Maloney SE, Yip B, Sandin S, Turner TN, Selmanovic D, Kroll KL, Gutmann DH, Constantino JN, Weiss LA. Can the "female protective effect" liability threshold model explain sex differences in autism spectrum disorder? Neuron 2022; 110:3243-3262. [PMID: 35868305 PMCID: PMC9588569 DOI: 10.1016/j.neuron.2022.06.020] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/09/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
Male sex is a strong risk factor for autism spectrum disorder (ASD). The leading theory for a "female protective effect" (FPE) envisions males and females have "differing thresholds" under a "liability threshold model" (DT-LTM). Specifically, this model posits that females require either a greater number or larger magnitude of risk factors (i.e., greater liability) to manifest ASD, which is supported by the finding that a greater proportion of females with ASD have highly penetrant genetic mutations. Herein, we derive testable hypotheses from the DT-LTM for ASD, investigating heritability, familial recurrence, correlation between ASD penetrance and sex ratio, population traits, clinical features, the stability of the sex ratio across diagnostic changes, and highlight other key prerequisites. Our findings reveal that several key predictions of the DT-LTM are not supported by current data, requiring us to establish a different conceptual framework for evaluating alternate models that explain sex differences in ASD.
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Affiliation(s)
- Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA.
| | - Natasha Marrus
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Susan E Maloney
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Benjamin Yip
- JC School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong, China
| | - Sven Sandin
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Seaver Autism Center for Research and Treatment at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Tychele N Turner
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Din Selmanovic
- Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA; Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Kristen L Kroll
- Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA; Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO, USA
| | - John N Constantino
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA; Intellectual and Developmental Disabilities Research Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Lauren A Weiss
- Institute for Human Genetics, Department of Psychiatry and Behavioral Sciences, Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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24
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The people behind the papers - Masahito Irie, Fumitoshi Ishino and Tomoko Kaneko-Ishino. Development 2022; 149:dev201295. [PMID: 36162815 DOI: 10.1242/dev.201295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Viral-derived genes have had a huge impact during mammalian evolution, with many of the exapted genes being expressed in the placenta. Now, new research published in Development describes the importance of two genes with retroviral origins in microglia, the innate immune cells of the brain, which are derived from another extra-embryonic tissue, the yolk sac. We caught up with the first author, Masahito Irie, and the corresponding authors, Fumitoshi Ishino, Professor at Tokyo Medical and Dental University, and Tomoko Kaneko-Ishino, Professor at Tokai University, to hear about more about their research.
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25
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Antaki D, Guevara J, Maihofer AX, Klein M, Gujral M, Grove J, Carey CE, Hong O, Arranz MJ, Hervas A, Corsello C, Vaux KK, Muotri AR, Iakoucheva LM, Courchesne E, Pierce K, Gleeson JG, Robinson EB, Nievergelt CM, Sebat J. A phenotypic spectrum of autism is attributable to the combined effects of rare variants, polygenic risk and sex. Nat Genet 2022; 54:1284-1292. [PMID: 35654974 PMCID: PMC9474668 DOI: 10.1038/s41588-022-01064-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 03/28/2022] [Indexed: 01/21/2023]
Abstract
The genetic etiology of autism spectrum disorder (ASD) is multifactorial, but how combinations of genetic factors determine risk is unclear. In a large family sample, we show that genetic loads of rare and polygenic risk are inversely correlated in cases and greater in females than in males, consistent with a liability threshold that differs by sex. De novo mutations (DNMs), rare inherited variants and polygenic scores were associated with various dimensions of symptom severity in children and parents. Parental age effects on risk for ASD in offspring were attributable to a combination of genetic mechanisms, including DNMs that accumulate in the paternal germline and inherited risk that influences behavior in parents. Genes implicated by rare variants were enriched in excitatory and inhibitory neurons compared with genes implicated by common variants. Our results suggest that a phenotypic spectrum of ASD is attributable to a spectrum of genetic factors that impact different neurodevelopmental processes.
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Affiliation(s)
- Danny Antaki
- Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - James Guevara
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Marieke Klein
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Madhusudan Gujral
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Aarhus, Denmark
- Center for Genomics and Personalized Medicine and Center for Integrative Sequencing, iSEQ, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Caitlin E Carey
- Harvard T.H. Chan School of Public Health, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Oanh Hong
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
| | - Maria J Arranz
- Research Laboratory Unit, Fundacio Docencia i Recerca Mutua, Terrassa, Spain
| | - Amaia Hervas
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Christina Corsello
- TEACCH Autism Program, University of North Carolina, Chapel Hill, NC, USA
| | | | - Alysson R Muotri
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Pediatrics and Department of Cellular & Molecular Medicine, University of California San Diego, School of Medicine, Center for Academic Research and Training in Anthropogeny, Archealization Center, Kavli Institute for Brain and Mind, La Jolla, CA, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Autism Center of Excellence, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
- Autism Center of Excellence, University of California San Diego, La Jolla, CA, USA
| | - Joseph G Gleeson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
- Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Elise B Robinson
- Harvard T.H. Chan School of Public Health, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Jonathan Sebat
- Beyster Center for Psychiatric Genomics, University of California San Diego, La Jolla, CA, USA.
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA.
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26
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Willsey HR, Willsey AJ, Wang B, State MW. Genomics, convergent neuroscience and progress in understanding autism spectrum disorder. Nat Rev Neurosci 2022; 23:323-341. [PMID: 35440779 PMCID: PMC10693992 DOI: 10.1038/s41583-022-00576-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2022] [Indexed: 12/31/2022]
Abstract
More than a hundred genes have been identified that, when disrupted, impart large risk for autism spectrum disorder (ASD). Current knowledge about the encoded proteins - although incomplete - points to a very wide range of developmentally dynamic and diverse biological processes. Moreover, the core symptoms of ASD involve distinctly human characteristics, presenting challenges to interpreting evolutionarily distant model systems. Indeed, despite a decade of striking progress in gene discovery, an actionable understanding of pathobiology remains elusive. Increasingly, convergent neuroscience approaches have been recognized as an important complement to traditional uses of genetics to illuminate the biology of human disorders. These methods seek to identify intersection among molecular-level, cellular-level and circuit-level functions across multiple risk genes and have highlighted developing excitatory neurons in the human mid-gestational prefrontal cortex as an important pathobiological nexus in ASD. In addition, neurogenesis, chromatin modification and synaptic function have emerged as key potential mediators of genetic vulnerability. The continued expansion of foundational 'omics' data sets, the application of higher-throughput model systems and incorporating developmental trajectories and sex differences into future analyses will refine and extend these results. Ultimately, a systems-level understanding of ASD genetic risk holds promise for clarifying pathobiology and advancing therapeutics.
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Affiliation(s)
- Helen Rankin Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - A Jeremy Willsey
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
| | - Belinda Wang
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA
| | - Matthew W State
- Department of Psychiatry and Behavioral Sciences, UCSF Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
- Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA, USA.
- Langley Porter Psychiatric Institute, University of California, San Francisco, San Francisco, CA, USA.
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Protasova MS, Gusev FE, Andreeva TV, Klyushnikov SA, Illarioshkin SN, Rogaev EI. Novel genes bearing mutations in rare cases of early-onset ataxia with cerebellar hypoplasia. Eur J Hum Genet 2022; 30:703-711. [PMID: 35351988 DOI: 10.1038/s41431-022-01088-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/09/2022] [Accepted: 03/10/2022] [Indexed: 12/13/2022] Open
Abstract
We propose an approach for the identification of mutant genes for rare diseases in single cases of unknown etiology. All genes with rare biologically significant variants sorted from individual exome data are tested further for profiling of their spatial-temporal and cell/tissue specific expression compared to that of their paralogs. We developed a simple bioinformatics tool ("Essential Paralogue by Expression" (EPbE)) for such analysis. Here, we present rare clinical forms of early ataxia with cerebellar hypoplasia. Using whole-exome sequencing and the EPbE tool, we identified two novel mutant genes previously not associated with congenital human diseases. In Family I, the unique missense mutation (p.Lys258Glu) was found in the LRCH2 gene inherited in an X-linked manner. p.Lys258Glu occurs in the evolutionarily invariant site of the leucine-rich repeat domain of LRCH2. In Family II and Family III, the identical genetic variant was found in the CSMD1 gene inherited as an autosomal-recessive trait. The variant leads to amino acid substitution p.Gly2979Ser in a highly conserved region of the complement-interacting domain of CSMD1. The LRCH2 gene for Family I patients (in which congenital cerebellar hypoplasia was associated with demyelinating polyneuropathy) is expressed in Schwann and precursor Schwann cells and predominantly over its paralogous genes in the developing cerebellar cortex. The CSMD1 gene is predominantly expressed over its paralogous genes in the cerebellum, specifically in the period of late childhood. Thus, the comparative spatial-temporal expression of the selected genes corresponds to the neurological manifestations of the disease.
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Affiliation(s)
- Maria S Protasova
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Fedor E Gusev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia
| | - Tatiana V Andreeva
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Sergey A Klyushnikov
- Department of Neurogenetics, Research Center of Neurology, 123367, Moscow, Russia
| | | | - Evgeny I Rogaev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics Russian Academy of Sciences, 119333, Moscow, Russia. .,Center for Genetics and Life Science, Sirius University of Science and Technology, 354340, Sochi, Russia. .,Department of Psychiatry, UMass Chan Medical School, Shrewsbury, MA, 01545, USA.
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28
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Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat 2022; 43:16-29. [PMID: 34633740 PMCID: PMC8720068 DOI: 10.1002/humu.24289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 11/06/2022]
Abstract
Autism spectrum disorders (ASD) are neurodevelopmental disorders with an estimated heritability of >60%. Family-based genetic studies of ASD have generally focused on multiple small kindreds, searching for de novo variants of major effect. We hypothesized that molecular genetic analysis of large multiplex families would enable the identification of variants of milder effects. We studied a large multigenerational family of European ancestry with multiple family members affected with ASD or the broader autism phenotype (BAP). We identified a rare heterozygous variant in the gene encoding 1,4-ɑ-glucan branching enzyme 1 (GBE1) that was present in seven of seven individuals with ASD, nine of ten individuals with the BAP, and none of four tested unaffected individuals. We genotyped a community-acquired cohort of 389 individuals with ASD and identified three additional probands. Cascade analysis demonstrated that the variant was present in 11 of 13 individuals with familial ASD/BAP and neither of the two tested unaffected individuals in these three families, also of European ancestry. The variant was not enriched in the combined UK10K ASD cohorts of European ancestry but heterozygous GBE1 deletion was overrepresented in large ASD cohorts, collectively suggesting an association between GBE1 and ASD.
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Affiliation(s)
- Miriam Fanjul-Fernández
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Natasha J Brown
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute Victoria, Parkville, Victoria, Australia
- Royal Children’s Hospital Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Barwon Health, Geelong, Victoria, Australia
| | - Peter Hickey
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Peter Diakumis
- University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer, Melbourne, Victoria, Australia
| | - Haloom Rafehi
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Kiymet Bozaoglu
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cherie C Green
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Department of Psychology and Counselling, School of Psychology and Public Health, La Trobe University, Melbourne, Victoria, Australia
| | - Audrey Rattray
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
| | - Savannah Young
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Dana Alhuzaimi
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Hayley S Mountford
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, UK
| | - Greta Gillies
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Vesna Lukic
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
| | - Tanya Vick
- Barwon Health, Geelong, Victoria, Australia
| | | | - Bradley P Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- Howard Hughes Medical Institute, University of Washington School of Medicine, Seattle, Washington, USA
| | - Martin B Delatycki
- Victorian Clinical Genetics Services, Parkville, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Sarah J Wilson
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Melbourne School of Psychological Sciences, The University of Melbourne, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
| | - Melanie Bahlo
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia
- Department of Medical Biology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ingrid E Scheffer
- Department of Medicine, University of Melbourne, Austin Health, Melbourne, Victoria, Australia
- Florey Institute, Melbourne, Victoria, Australia
- Department of Paediatrics, The University of Melbourne, Royal Children’s Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul J Lockhart
- Department of Paediatrics, The University of Melbourne, Melbourne, Victoria, Australia
- Bruce Lefroy Centre for Genetic Health Research, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
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Somatic Mosaicism and Autism Spectrum Disorder. Genes (Basel) 2021; 12:genes12111699. [PMID: 34828306 PMCID: PMC8619103 DOI: 10.3390/genes12111699] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/23/2021] [Accepted: 10/23/2021] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a genetically heterogenous neurodevelopmental disorder. In the early years of next-generation sequencing, de novo germline variants were shown to contribute to ASD risk. These germline mutations are present in all of the cells of an affected individual and can be detected in any tissue, including clinically accessible DNA sources such as blood or saliva. In recent years, studies have also implicated de novo somatic variants in ASD risk. These somatic mutations arise postzygotically and are present in only a subset of the cells of an affected individual. Depending on the developmental time and progenitor cell in which a somatic mutation occurs, it may be detectable in some tissues and not in others. Somatic mutations detectable at relatively low sequencing coverage in clinically accessible tissues are suggested to contribute to 3-5% of simplex ASD diagnoses, and "brain limited" somatic mutations have been identified in postmortem ASD brain tissue. Somatic mutations likely represent the genetic diagnosis in a proportion of otherwise unexplained individuals with ASD, and brain limited somatic mutations can be used as markers to discover risk genes, cell types, brain regions, and cellular pathways important for ASD pathogenesis and to potentially target for therapeutics.
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Shamseldin HE, AlAbdi L, Maddirevula S, Alsaif HS, Alzahrani F, Ewida N, Hashem M, Abdulwahab F, Abuyousef O, Kuwahara H, Gao X, Alkuraya FS. Lethal variants in humans: lessons learned from a large molecular autopsy cohort. Genome Med 2021; 13:161. [PMID: 34645488 PMCID: PMC8511862 DOI: 10.1186/s13073-021-00973-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Molecular autopsy refers to DNA-based identification of the cause of death. Despite recent attempts to broaden its scope, the term remains typically reserved to sudden unexplained death in young adults. In this study, we aim to showcase the utility of molecular autopsy in defining lethal variants in humans. METHODS We describe our experience with a cohort of 481 cases in whom the cause of premature death was investigated using DNA from the index or relatives (molecular autopsy by proxy). Molecular autopsy tool was typically exome sequencing although some were investigated using targeted approaches in the earlier stages of the study; these include positional mapping, targeted gene sequencing, chromosomal microarray, and gene panels. RESULTS The study includes 449 cases from consanguineous families and 141 lacked family history (simplex). The age range was embryos to 18 years. A likely causal variant (pathogenic/likely pathogenic) was identified in 63.8% (307/481), a much higher yield compared to the general diagnostic yield (43%) from the same population. The predominance of recessive lethal alleles allowed us to implement molecular autopsy by proxy in 55 couples, and the yield was similarly high (63.6%). We also note the occurrence of biallelic lethal forms of typically non-lethal dominant disorders, sometimes representing a novel bona fide biallelic recessive disease trait. Forty-six disease genes with no OMIM phenotype were identified in the course of this study. The presented data support the candidacy of two other previously reported novel disease genes (FAAH2 and MSN). The focus on lethal phenotypes revealed many examples of interesting phenotypic expansion as well as remarkable variability in clinical presentation. Furthermore, important insights into population genetics and variant interpretation are highlighted based on the results. CONCLUSIONS Molecular autopsy, broadly defined, proved to be a helpful clinical approach that provides unique insights into lethal variants and the clinical annotation of the human genome.
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Affiliation(s)
- Hanan E Shamseldin
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Lama AlAbdi
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Sateesh Maddirevula
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hessa S Alsaif
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
- Center of Excellence for Biomedicine, King Abdulaziz City for Science and Technology, Riyadh, 12354, Saudi Arabia
| | - Fatema Alzahrani
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Nour Ewida
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Mais Hashem
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Firdous Abdulwahab
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Omar Abuyousef
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Hiroyuki Kuwahara
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xin Gao
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia.
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Simone M, Margari L, Pompamea F, De Giacomo A, Gabellone A, Marzulli L, Palumbi R. Autism Spectrum Disorder and Duchenne Muscular Dystrophy: A Clinical Case on the Potential Role of the Dystrophin in Autism Neurobiology. J Clin Med 2021; 10:4370. [PMID: 34640386 PMCID: PMC8509154 DOI: 10.3390/jcm10194370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 02/03/2023] Open
Abstract
A diagnosis of autism spectrum disorder is reported in up to 19% of dystrophinopathies. However, over the last ten years, only a few papers have been published on this topic. Therefore, further studies are required to analyze this association in depth and ultimately to understand the role of the brain dystrophin isoform in the pathogenesis of ASD and other neurodevelopmental disorders. In this paper, we report a clinical case of a patient affected by ASD and Duchenne muscular dystrophy, who carries a large deletion of the dystrophin gene. Then we present a brief overview of the literature about similar cases and about the potential role of the dystrophin protein in the neurobiology of autism spectrum disorder.
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Affiliation(s)
- Marta Simone
- Biomedical Sciences and Human Oncology Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.S.); (F.P.); (A.G.); (L.M.)
| | - Lucia Margari
- Biomedical Sciences and Human Oncology Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.S.); (F.P.); (A.G.); (L.M.)
| | - Francesco Pompamea
- Biomedical Sciences and Human Oncology Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.S.); (F.P.); (A.G.); (L.M.)
| | - Andrea De Giacomo
- Basic Medical Sciences, Neurosciences, and Sensory Organs Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.G.); (R.P.)
| | - Alessandra Gabellone
- Biomedical Sciences and Human Oncology Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.S.); (F.P.); (A.G.); (L.M.)
| | - Lucia Marzulli
- Biomedical Sciences and Human Oncology Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (M.S.); (F.P.); (A.G.); (L.M.)
| | - Roberto Palumbi
- Basic Medical Sciences, Neurosciences, and Sensory Organs Department, University of Bari “Aldo Moro”, 70124 Bari, Italy; (A.D.G.); (R.P.)
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Gill PS, Clothier JL, Veerapandiyan A, Dweep H, Porter-Gill PA, Schaefer GB. Molecular Dysregulation in Autism Spectrum Disorder. J Pers Med 2021; 11:848. [PMID: 34575625 PMCID: PMC8466026 DOI: 10.3390/jpm11090848] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 12/14/2022] Open
Abstract
Autism Spectrum Disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders with a strong heritable genetic component. At present, ASD is diagnosed solely by behavioral criteria. Advances in genomic analysis have contributed to numerous candidate genes for the risk of ASD, where rare mutations and s common variants contribute to its susceptibility. Moreover, studies show rare de novo variants, copy number variation and single nucleotide polymorphisms (SNPs) also impact neurodevelopment signaling. Exploration of rare and common variants involved in common dysregulated pathways can provide new diagnostic and therapeutic strategies for ASD. Contributions of current innovative molecular strategies to understand etiology of ASD will be explored which are focused on whole exome sequencing (WES), whole genome sequencing (WGS), microRNA, long non-coding RNAs and CRISPR/Cas9 models. Some promising areas of pharmacogenomic and endophenotype directed therapies as novel personalized treatment and prevention will be discussed.
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Affiliation(s)
- Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Arkansas Children’s Research Institute, 13 Children’s Way, Little Rock, AR 72202, USA;
| | - Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Aravindhan Veerapandiyan
- Pediatric Neurology, Arkansas Children’s Hospital, 1 Children’s Way, Little Rock, AR 72202, USA;
| | - Harsh Dweep
- The Wistar Institute, 3601 Spruce St., Philadelphia, PA 19104, USA;
| | | | - G. Bradley Schaefer
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA
- Arkansas Children’s Hospital NW, Springdale, AR 72762, USA
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Choi L, An JY. Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies. Neurosci Biobehav Rev 2021; 128:244-257. [PMID: 34166716 DOI: 10.1016/j.neubiorev.2021.06.028] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 06/17/2021] [Accepted: 06/17/2021] [Indexed: 12/20/2022]
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a strong genetic component. Recently developed genomic technologies, including microarray and next-generation sequencing (NGS), have enabled researchers to genetic analyses aimed at identifying genetic variations associated with ASD and to elucidate the genetic architecture of the disorder. Large-scale microarray, exome sequencing analyses, and robust statistical methods have resulted in successful gene discovery and identification of high-confidence ASD genes from among de novo and inherited variants. Efforts have been made to understand the genetic architecture of ASD using whole-genome sequencing and genome-wide association studies aimed at identifying noncoding mutations and common variants associated with ASD. In addition, the development of systems biology approaches has resulted in the integration of genetic findings with functional genomic datasets, thereby providing a unique insight into the functional convergence of ASD risk genes and their neurobiology. In this review, we summarize the latest findings of ASD genetic studies involving large cohorts and discuss their implications in ASD neurobiology and in clinical practice.
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Affiliation(s)
- Leejee Choi
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul, 02841, Republic of Korea; Department of Integrated Biomedical and Life Science, Korea University, Seoul, 02841, Republic of Korea; Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, 02841, Republic of Korea; BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, 02841, Republic of Korea.
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Targeted sequencing and integrative analysis to prioritize candidate genes in neurodevelopmental disorders. Mol Neurobiol 2021; 58:3863-3873. [PMID: 33860439 PMCID: PMC8280036 DOI: 10.1007/s12035-021-02377-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/29/2021] [Indexed: 11/09/2022]
Abstract
Neurodevelopmental disorders (NDDs) are a group of diseases characterized by high heterogeneity and frequently co-occurring symptoms. The mutational spectrum in patients with NDDs is largely incomplete. Here, we sequenced 547 genes from 1102 patients with NDDs and validated 1271 potential functional variants, including 108 de novo variants (DNVs) in 78 autosomal genes and seven inherited hemizygous variants in six X chromosomal genes. Notably, 36 of these 78 genes are the first to be reported in Chinese patients with NDDs. By integrating our genetic data with public data, we prioritized 212 NDD candidate genes with FDR < 0.1, including 17 novel genes. The novel candidate genes interacted or were co-expressed with known candidate genes, forming a functional network involved in known pathways. We highlighted MSL2, which carried two de novo protein-truncating variants (p.L192Vfs*3 and p.S486Ifs*11) and was frequently connected with known candidate genes. This study provides the mutational spectrum of NDDs in China and prioritizes 212 NDD candidate genes for further functional validation and genetic counseling.
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Wang T, Zhang Y, Liu L, Wang Y, Chen H, Fan T, Li J, Xia K, Sun Z. Targeted sequencing and integrative analysis of 3,195 Chinese patients with neurodevelopmental disorders prioritized 26 novel candidate genes. J Genet Genomics 2021; 48:312-323. [PMID: 33994118 DOI: 10.1016/j.jgg.2021.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/05/2021] [Accepted: 03/07/2021] [Indexed: 02/06/2023]
Abstract
Neurodevelopmental disorders (NDDs) are a set of complex disorders characterized by diverse and co-occurring clinical symptoms. The genetic contribution in patients with NDDs remains largely unknown. Here, we sequence 519 NDD-related genes in 3,195 Chinese probands with neurodevelopmental phenotypes and identify 2,522 putative functional mutations consisting of 137 de novo mutations (DNMs) in 86 genes and 2,385 rare inherited mutations (RIMs) with 22 X-linked hemizygotes in 13 genes, 2 homozygous mutations in 2 genes and 23 compound heterozygous mutations in 10 genes. Furthermore, the DNMs of 16,807 probands with NDDs are retrieved from public datasets and combine in an integrated analysis with the mutation data of our Chinese NDD probands by taking 3,582 in-house controls of Chinese origin as background. We prioritize 26 novel candidate genes. Notably, six of these genes - ITSN1, UBR3, CADM1, RYR3, FLNA, and PLXNA3 - preferably contribute to autism spectrum disorders (ASDs), as demonstrated by high co-expression and/or interaction with ASD genes confirmed via rescue experiments in a mouse model. Importantly, these genes are differentially expressed in the ASD cortex in a significant manner and involved in ASD-associated networks. Together, our study expands the genetic spectrum of Chinese NDDs, further facilitating both basic and translational research.
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Affiliation(s)
- Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; DIAGenes Precision Medicine, Beijing 102600, China
| | - Yi Zhang
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China
| | - Liqui Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Huiqian Chen
- Shanghai Adeptus Biotechnology, Shanghai 200126, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410083, China; Department of Neurology, Xiangya Hospital, Central South University, Changsha Hunan, 410083, China.
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410083, China; CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China; School of Basic Medical Science, Central South University, Changsha, Hunan, 410083, China.
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
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Agarwala S, Veerappa AM, Ramachandra NB. Identification of primary copy number variations reveal enrichment of Calcium, and MAPK pathways sensitizing secondary sites for autism. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00091-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Autism is a neurodevelopmental condition with genetic heterogeneity. It is characterized by difficulties in reciprocal social interactions with strong repetitive behaviors and stereotyped interests. Copy number variations (CNVs) are genomic structural variations altering the genomic structure either by duplication or deletion. De novo or inherited CNVs are found in 5–10% of autistic subjects with a size range of few kilobases to several megabases. CNVs predispose humans to various diseases by altering gene regulation, generation of chimeric genes, and disruption of the coding region or through position effect. Although, CNVs are not the initiating event in pathogenesis; additional preceding mutations might be essential for disease manifestation. The present study is aimed to identify the primary CNVs responsible for autism susceptibility in healthy cohorts to sensitize secondary-hits. In the current investigation, primary-hit autism gene CNVs are characterized in 1715 healthy cohorts of varying ethnicities across 12 populations using Affymetrix high-resolution array study. Thirty-eight individuals from twelve families residing in Karnataka, India, with the age group of 13–73 years are included for the comparative CNV analysis. The findings are validated against global 179 autism whole-exome sequence datasets derived from Simons Simplex Collection. These datasets are deposited at the Simons Foundation Autism Research Initiative (SFARI) database.
Results
The study revealed that 34.8% of the subjects carried 2% primary-hit CNV burden with 73 singleton-autism genes in different clusters. Of these, three conserved CNV breakpoints were identified with ARHGAP11B, DUSP22, and CHRNA7 as the target genes across 12 populations. Enrichment analysis of the population-specific autism genes revealed two signaling pathways—calcium and mitogen-activated protein kinases (MAPK) in the CNV identified regions. These impaired pathways affected the downstream cascades of neuronal function and physiology, leading to autism behavior. The pathway analysis of enriched genes unravelled complex protein interaction networks, which sensitized secondary sites for autism. Further, the identification of miRNA targets associated with autism gene CNVs added severity to the condition.
Conclusion
These findings contribute to an atlas of primary-hit genes to detect autism susceptibility in healthy cohorts, indicating their impact on secondary sites for manifestation.
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Garcia-Forn M, Boitnott A, Akpinar Z, De Rubeis S. Linking Autism Risk Genes to Disruption of Cortical Development. Cells 2020; 9:cells9112500. [PMID: 33218123 PMCID: PMC7698947 DOI: 10.3390/cells9112500] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is a prevalent neurodevelopmental disorder characterized by impairments in social communication and social interaction, and the presence of repetitive behaviors and/or restricted interests. In the past few years, large-scale whole-exome sequencing and genome-wide association studies have made enormous progress in our understanding of the genetic risk architecture of ASD. While showing a complex and heterogeneous landscape, these studies have led to the identification of genetic loci associated with ASD risk. The intersection of genetic and transcriptomic analyses have also begun to shed light on functional convergences between risk genes, with the mid-fetal development of the cerebral cortex emerging as a critical nexus for ASD. In this review, we provide a concise summary of the latest genetic discoveries on ASD. We then discuss the studies in postmortem tissues, stem cell models, and rodent models that implicate recently identified ASD risk genes in cortical development.
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Affiliation(s)
- Marta Garcia-Forn
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- 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
| | - Andrea Boitnott
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- 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
| | - Zeynep Akpinar
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- 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 Psychology, College of Arts and Sciences, New York University, New York, NY 10003, USA
| | - Silvia De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; (M.G.-F.); (A.B.); (Z.A.)
- 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
- Correspondence: ; Tel.: +1-212-241-0179
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Xu YC, Guo YL. Less Is More, Natural Loss-of-Function Mutation Is a Strategy for Adaptation. PLANT COMMUNICATIONS 2020; 1:100103. [PMID: 33367264 PMCID: PMC7743898 DOI: 10.1016/j.xplc.2020.100103] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/08/2020] [Accepted: 08/12/2020] [Indexed: 05/12/2023]
Abstract
Gene gain and loss are crucial factors that shape the evolutionary success of diverse organisms. In the past two decades, more attention has been paid to the significance of gene gain through gene duplication or de novo genes. However, gene loss through natural loss-of-function (LoF) mutations, which is prevalent in the genomes of diverse organisms, has been largely ignored. With the development of sequencing techniques, many genomes have been sequenced across diverse species and can be used to study the evolutionary patterns of gene loss. In this review, we summarize recent advances in research on various aspects of LoF mutations, including their identification, evolutionary dynamics in natural populations, and functional effects. In particular, we discuss how LoF mutations can provide insights into the minimum gene set (or the essential gene set) of an organism. Furthermore, we emphasize their potential impact on adaptation. At the genome level, although most LoF mutations are neutral or deleterious, at least some of them are under positive selection and may contribute to biodiversity and adaptation. Overall, we highlight the importance of natural LoF mutations as a robust framework for understanding biological questions in general.
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Affiliation(s)
- Yong-Chao Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Long Guo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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39
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Breuss MW, Mamerto A, Renner T, Waters ER. The Evolution of the Mammalian ABCA6-like Genes: Analysis of Phylogenetic, Expression, and Population Genetic Data Reveals Complex Evolutionary Histories. Genome Biol Evol 2020; 12:2093-2106. [PMID: 32877505 PMCID: PMC7674697 DOI: 10.1093/gbe/evaa179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/21/2020] [Indexed: 01/25/2023] Open
Abstract
ABC membrane transporters are a large and complex superfamily of ATP-binding cassette transporters that are present in all domains of life. Both their essential function and complexity are reflected by their retention across large expanses of organismal diversity and by the extensive expansion of individual members and subfamilies during evolutionary history. This expansion has resulted in the diverse ABCA transporter family that has in turn evolved into multiple subfamilies. Here, we focus on the ABCA6-like subfamily of ABCA transporters with the goal of understanding their evolutionary history including potential functional changes in, or loss of, individual members. Our analysis finds that ABCA6-like genes, consisting of ABCA6, 8, 9, and 10, are absent from representatives of both monotremes and marsupials and thus the duplications that generated these families most likely occurred at the base of the Eutherian or placental mammals. We have found evidence of both positive and relaxed selection among the ABCA6-like genes, suggesting dynamic changes in function and the potential of gene redundancy. Analysis of the ABCA10 genes further suggests that this gene has undergone relaxed selection only within the human lineage. These findings are complemented by human population data, where we observe an excess of deactivating homozygous mutations. We describe the complex evolutionary history of this ABCA transporter subfamily and demonstrate through the combination of evolutionary and population genetic analysis that ABCA10 is undergoing pseudogenization within humans.
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Affiliation(s)
- Martin W Breuss
- Department of Neurosciences, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, California
| | - Allen Mamerto
- Department of Biology and Program in Biological and Medical Informatics, San Diego State University
| | - Tanya Renner
- Department of Entomology, The Pennsylvania State University, University Park
| | - Elizabeth R Waters
- Department of Biology and Program in Biological and Medical Informatics, San Diego State University
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40
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Wang L, Zhang Y, Li K, Wang Z, Wang X, Li B, Zhao G, Fang Z, Ling Z, Luo T, Xia L, Li Y, Guo H, Hu Z, Li J, Sun Z, Xia K. Functional relationships between recessive inherited genes and genes with de novo variants in autism spectrum disorder. Mol Autism 2020; 11:75. [PMID: 33023636 PMCID: PMC7541261 DOI: 10.1186/s13229-020-00382-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 09/22/2020] [Indexed: 12/19/2022] Open
Abstract
Background Both de novo variants and recessive inherited variants were associated with autism spectrum disorder (ASD). This study aimed to use exome data to prioritize recessive inherited genes (RIGs) with biallelically inherited variants in autosomes or X-linked inherited variants in males and investigate the functional relationships between RIGs and genes with de novo variants (DNGs).
Methods We used a bioinformatics pipeline to analyze whole-exome sequencing data from 1799 ASD quads (containing one proband, one unaffected sibling, and their parents) from the Simons Simplex Collection and prioritize candidate RIGs with rare biallelically inherited variants in autosomes or X-linked inherited variants in males. The relationships between RIGs and DNGs were characterized based on different genetic perspectives, including genetic variants, functional networks, and brain expression patterns. Results Among the biallelically or hemizygous constrained genes that were expressed in the brain, ASD probands carried significantly more biallelically inherited protein-truncating variants (PTVs) in autosomes (p = 0.038) and X-linked inherited PTVs in males (p = 0.026) than those in unaffected siblings. We prioritized eight autosomal, and 13 X-linked candidate RIGs, including 11 genes already associated with neurodevelopmental disorders. In total, we detected biallelically inherited variants or X-linked inherited variants of these 21 candidate RIGs in 26 (1.4%) of 1799 probands. We then integrated previously reported known or candidate genes in ASD, ultimately obtaining 70 RIGs and 87 DNGs for analysis. We found that RIGs were less likely to carry multiple recessive inherited variants than DNGs were to carry multiple de novo variants. Additionally, RIGs and DNGs were significantly co-expressed and interacted with each other, forming a network enriched in known functional ASD clusters, although RIGs were less likely to be enriched in these functional clusters compared with DNGs. Furthermore, although RIGs and DNGs presented comparable expression patterns in the human brain, RIGs were less likely to be associated with prenatal brain regions, the middle cortical layers, and excitatory neurons than DNGs. Limitations The RIGs analyzed in this study require functional validation, and the results should be replicated in more patients with ASD. Conclusions ASD RIGs were functionally associated with DNGs; however, they exhibited higher heterogeneity than DNGs.
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Affiliation(s)
- Lin Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Reproductive Medicine Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi Zhang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Kuokuo Li
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Zheng Wang
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xiaomeng Wang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guihu Zhao
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhenghuan Fang
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengbao Ling
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Luo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yanping Li
- Reproductive Medicine Center, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hui Guo
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Jinchen Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, China. .,Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, China.
| | - Kun Xia
- Center for Medical Genetics and Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China. .,CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai, China. .,School of Basic Medical Science, Central South University, Changsha, Hunan, China.
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41
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Schmitz-Abe K, Sanchez-Schmitz G, Doan RN, Hill RS, Chahrour MH, Mehta BK, Servattalab S, Ataman B, Lam ATN, Morrow EM, Greenberg ME, Yu TW, Walsh CA, Markianos K. Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder. Sci Rep 2020; 10:14045. [PMID: 32820185 PMCID: PMC7441318 DOI: 10.1038/s41598-020-70656-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
More than 98% of the human genome is made up of non-coding DNA, but techniques to ascertain its contribution to human disease have lagged far behind our understanding of protein coding variations. Autism spectrum disorder (ASD) has been mostly associated with coding variations via de novo single nucleotide variants (SNVs), recessive/homozygous SNVs, or de novo copy number variants (CNVs); however, most ASD cases continue to lack a genetic diagnosis. We analyzed 187 consanguineous ASD families for biallelic CNVs. Recessive deletions were significantly enriched in affected individuals relative to their unaffected siblings (17% versus 4%, p < 0.001). Only a small subset of biallelic deletions were predicted to result in coding exon disruption. In contrast, biallelic deletions in individuals with ASD were enriched for overlap with regulatory regions, with 23/28 CNVs disrupting histone peaks in ENCODE (p < 0.009). Overlap with regulatory regions was further demonstrated by comparisons to the 127-epigenome dataset released by the Roadmap Epigenomics project, with enrichment for enhancers found in primary brain tissue and neuronal progenitor cells. Our results suggest a novel noncoding mechanism of ASD, describe a powerful method to identify important noncoding regions in the human genome, and emphasize the potential significance of gene activation and regulation in cognitive and social function.
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Affiliation(s)
- Klaus Schmitz-Abe
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Divisions of Newborn Medicine and Manton Center for Orphan Disease Research, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA
| | - Guzman Sanchez-Schmitz
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Infectious Diseases, Department of Pediatrics and Precision Vaccines Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria H Chahrour
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bhaven K Mehta
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Servattalab
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bulent Ataman
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anh-Thu N Lam
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry and Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02912, USA
| | | | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Kyriacos Markianos
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Center for Data and Computational Sciences, Cooperative Studies Program, VA Boston Healthcare system, Boston, MA, 02130, USA.
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42
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Harms FL, Parthasarathy P, Zorndt D, Alawi M, Fuchs S, Halliday BJ, McKeown C, Sampaio H, Radhakrishnan N, Radhakrishnan SK, Gorce M, Navet B, Ziegler A, Sachdev R, Robertson SP, Nampoothiri S, Kutsche K. Biallelic loss-of-function variants in TBC1D2B cause a neurodevelopmental disorder with seizures and gingival overgrowth. Hum Mutat 2020; 41:1645-1661. [PMID: 32623794 DOI: 10.1002/humu.24071] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 06/08/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
The family of Tre2-Bub2-Cdc16 (TBC)-domain containing GTPase activating proteins (RABGAPs) is not only known as key regulatorof RAB GTPase activity but also has GAP-independent functions. Rab GTPases are implicated in membrane trafficking pathways, such as vesicular trafficking. We report biallelic loss-of-function variants in TBC1D2B, encoding a member of the TBC/RABGAP family with yet unknown function, as the underlying cause of cognitive impairment, seizures, and/or gingival overgrowth in three individuals from unrelated families. TBC1D2B messenger RNA amount was drastically reduced, and the protein was absent in fibroblasts of two patients. In immunofluorescence analysis, ectopically expressed TBC1D2B colocalized with vesicles positive for RAB5, a small GTPase orchestrating early endocytic vesicle trafficking. In two independent TBC1D2B CRISPR/Cas9 knockout HeLa cell lines that serve as cellular model of TBC1D2B deficiency, epidermal growth factor internalization was significantly reduced compared with the parental HeLa cell line suggesting a role of TBC1D2B in early endocytosis. Serum deprivation of TBC1D2B-deficient HeLa cell lines caused a decrease in cell viability and an increase in apoptosis. Our data reveal that loss of TBC1D2B causes a neurodevelopmental disorder with gingival overgrowth, possibly by deficits in vesicle trafficking and/or cell survival.
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Affiliation(s)
- Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Padmini Parthasarathy
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Dennis Zorndt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sigrid Fuchs
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Benjamin J Halliday
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Colina McKeown
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Hugo Sampaio
- Department of Women and Children's Health, University of New South Wales, Randwick Campus, Randwick, NSW, Australia.,Sydney Children's Hospital, Randwick, NSW, Australia
| | - Natasha Radhakrishnan
- Department of Ophthalmology, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Suresh K Radhakrishnan
- Department of Neurology, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Magali Gorce
- Department of Metabolic Disease, Children University Hospital, Toulouse, France
| | - Benjamin Navet
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France.,MitoLab, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers, France
| | - Alban Ziegler
- Department of Biochemistry and Genetics, University Hospital of Angers, Angers, France.,MitoLab, Institut MitoVasc, UMR CNRS6015, INSERM U1083, Angers, France
| | - Rani Sachdev
- Centre for Clinical Genetics, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Stephen P Robertson
- Department of Women's and Children's Health, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences and Research Centre, Cochin, Kerala, India
| | - Kerstin Kutsche
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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43
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Lin BD, Colas F, Nijman IJ, Medic J, Brands W, Parr JR, van Eijk KR, Klauck SM, Chiocchetti AG, Freitag CM, Maestrini E, Bacchelli E, Coon H, Vicente A, Oliveira G, Pagnamenta AT, Gallagher L, Ennis S, Anney R, Bourgeron T, Luykx JJ, Vorstman J. The role of rare compound heterozygous events in autism spectrum disorder. Transl Psychiatry 2020; 10:204. [PMID: 32572023 PMCID: PMC7308334 DOI: 10.1038/s41398-020-00866-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 05/05/2020] [Accepted: 05/15/2020] [Indexed: 11/30/2022] Open
Abstract
The identification of genetic variants underlying autism spectrum disorders (ASDs) may contribute to a better understanding of their underlying biology. To examine the possible role of a specific type of compound heterozygosity in ASD, namely, the occurrence of a deletion together with a functional nucleotide variant on the remaining allele, we sequenced 550 genes in 149 individuals with ASD and their deletion-transmitting parents. This approach allowed us to identify additional sequence variants occurring in the remaining allele of the deletion. Our main goal was to compare the rate of sequence variants in remaining alleles of deleted regions between probands and the deletion-transmitting parents. We also examined the predicted functional effect of the identified variants using Combined Annotation-Dependent Depletion (CADD) scores. The single nucleotide variant-deletion co-occurrence was observed in 13.4% of probands, compared with 8.1% of parents. The cumulative burden of sequence variants (n = 68) in pooled proband sequences was higher than the burden in pooled sequences from the deletion-transmitting parents (n = 41, X2 = 6.69, p = 0.0097). After filtering for those variants predicted to be most deleterious, we observed 21 of such variants in probands versus 8 in their deletion-transmitting parents (X2 = 5.82, p = 0.016). Finally, cumulative CADD scores conferred by these variants were significantly higher in probands than in deletion-transmitting parents (burden test, β = 0.13; p = 1.0 × 10-5). Our findings suggest that the compound heterozygosity described in the current study may be one of several mechanisms explaining variable penetrance of CNVs with known pathogenicity for ASD.
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Affiliation(s)
- Bochao Danae Lin
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Preventive Medicine, Institute of Biomedical Informatics, Bioinformatics Center, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Fabrice Colas
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Isaac J Nijman
- Department of Medical Informatics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jelena Medic
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - William Brands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jeremy R Parr
- Institute of Neuroscience, Newcastle University, Newcastle, UK
| | - Kristel R van Eijk
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Sabine M Klauck
- Division of Molecular Genome Analysis and Division of Cancer Genome Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas G Chiocchetti
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christine M Freitag
- Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, University Hospital Frankfurt, JW Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Elena Maestrini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Elena Bacchelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Hilary Coon
- Department of Psychiatry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Astrid Vicente
- Instituto Nacional de Saúde Doutor Ricardo Jorge, Avenida Padre Cruz, Lisboa, Portugal
| | | | - Alistair T Pagnamenta
- NIHR Oxford BRC, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Louise Gallagher
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity College Dublin, Trinity Centre for Health Sciences, Dublin, Ireland
| | - Sean Ennis
- Academic Centre on Rare Diseases, School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Richard Anney
- Medical Research Council Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Thomas Bourgeron
- Human Genetics and Cognitive Functions, Institut Pasteur, UMR3571 CNRS, Université de Paris, Paris, France
| | - Jurjen J Luykx
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
- GGNet Mental Health, Apeldoorn, The Netherlands
| | - Jacob Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
- Program in Genetics and Genome Biology, Research Institute, and Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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44
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Abstract
Recent advances in understanding the genetic architecture of autism spectrum disorder have allowed for unprecedented insight into its biological underpinnings. New studies have elucidated the contributions of a variety of forms of genetic variation to autism susceptibility. While the roles of de novo copy number variants and single-nucleotide variants-causing loss-of-function or missense changes-have been increasingly recognized and refined, mosaic single-nucleotide variants have been implicated more recently in some cases. Moreover, inherited variants (including common variants) and, more recently, rare recessive inherited variants have come into greater focus. Finally, noncoding variants-both inherited and de novo-have been implicated in the last few years. This work has revealed a convergence of diverse genetic drivers on common biological pathways and has highlighted the ongoing importance of increasing sample size and experimental innovation. Continuing to synthesize these genetic findings with functional and phenotypic evidence and translating these discoveries to clinical care remain considerable challenges for the field.
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Affiliation(s)
- Caroline M Dias
- Division of Developmental Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Christopher A Walsh
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts 02115, USA; .,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Department of Neurology, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts 02115, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
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45
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Lin JH, Masson E, Boulling A, Hayden M, Cooper DN, Férec C, Liao Z, Chen JM. 5' splice site GC>GT and GT>GC variants differ markedly in terms of their functionality and pathogenicity. Hum Mutat 2020; 41:1358-1364. [PMID: 32369867 DOI: 10.1002/humu.24029] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 03/27/2020] [Accepted: 04/19/2020] [Indexed: 12/11/2022]
Abstract
In the human genome, most 5' splice sites (~99%) employ the canonical GT dinucleotide whereas a small minority (~1%) use the noncanonical GC dinucleotide. The functionality and pathogenicity of 5' splice site GT>GC (+2T>C) variants have been extensively studied but we know very little about 5' splice site GC>GT (+2C>T) variants. Herein, we have addressed this deficiency by performing a meta-analysis of reported +2C>T "pathogenic" variants together with a functional analysis of engineered +2C>T substitutions using a cell culture-based full-length gene splicing assay. Our results establish proof of concept that +2C>T variants are qualitatively different from +2T>C variants in terms of their functionality and suggest that, in sharp contrast to +2T>C variants, most if not all +2C>T variants have no pathological relevance. Our findings have important implications for interpreting the clinical relevance of +2C>T variants and understanding the evolutionary switching between GT and GC 5' splice sites in mammalian genomes.
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Affiliation(s)
- Jin-Huan Lin
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Emmanuelle Masson
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France
| | | | - Matthew Hayden
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Claude Férec
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France.,CHRU Brest, Service de Génétique Médicale et de Biologie de la Reproduction, Brest, France
| | - Zhuan Liao
- Department of Gastroenterology, Changhai Hospital, Second Military Medical University, Shanghai, China.,Shanghai Institute of Pancreatic Diseases, Shanghai, China
| | - Jian-Min Chen
- EFS, Univ Brest, INSERM, UMR 1078, GGB, Brest, France
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46
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Li M, Shen L, Chen L, Huai C, Huang H, Wu X, Yang C, Ma J, Zhou W, Du H, Fan L, He L, Wan C, Qin S. Novel genetic susceptibility loci identified by family based whole exome sequencing in Han Chinese schizophrenia patients. Transl Psychiatry 2020; 10:5. [PMID: 32066673 PMCID: PMC7026419 DOI: 10.1038/s41398-020-0708-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 12/07/2019] [Accepted: 12/19/2019] [Indexed: 12/14/2022] Open
Abstract
Schizophrenia (SCZ) is a highly heritable psychiatric disorder that affects approximately 1% of population around the world. However, early relevant studies did not reach clear conclusions of the genetic mechanisms of SCZ, suggesting that additional susceptibility loci that exert significant influence on SCZ are yet to be revealed. So, in order to identify novel susceptibility genes that account for the genetic risk of SCZ, we performed a systematic family-based study using whole exome sequencing (WES) in 65 Han Chinese families. The analysis of 51 SCZ trios with both unaffected parents identified 22 exonic and 1 splice-site de novo mutations (DNMs) on a total of 23 genes, and showed that 12 genes carried rare protein-altering compound heterozygous mutations in more than one trio. In addition, we identified 26 exonic or splice-site single nucleotide polymorphisms (SNPs) on 18 genes with nominal significance (P < 5 × 10-4) using a transmission disequilibrium test (TDT) in all the families. Moreover, TDT result confirmed a SCZ susceptibility locus on 3p21.1, encompassing the multigenetic region NEK4-ITIH1-ITIH3-ITIH4. Through several different strategies to predict the potential pathogenic genes in silico, we revealed 4 previous discovered susceptibility genes (TSNARE1, PBRM1, STAB1 and OLIG2) and 4 novel susceptibility loci (PSEN1, TLR5, MGAT5B and SSPO) in Han Chinese SCZ patients. In summary, we identified a list of putative candidate genes for SCZ using a family-based WES approach, thus improving our understanding of the pathology of SCZ and providing critical clues to future functional validation.
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Affiliation(s)
- Mo Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Lu Shen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Luan Chen
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Cong Huai
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Hailiang Huang
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Xi Wu
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Chao Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jingsong Ma
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Wei Zhou
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Huihui Du
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Lingzi Fan
- Psychiatric Hospital of Zhumadian City, Henan, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
- The Third Affiliated Hospital, Guangzhou Medical University, Guangdong, China.
| | - Chunling Wan
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China.
- Collaborative Innovation Center, Jining Medical University, Shandong, China.
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47
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Zhang Y, Li N, Li C, Zhang Z, Teng H, Wang Y, Zhao T, Shi L, Zhang K, Xia K, Li J, Sun Z. Genetic evidence of gender difference in autism spectrum disorder supports the female-protective effect. Transl Psychiatry 2020; 10:4. [PMID: 32066658 PMCID: PMC7026157 DOI: 10.1038/s41398-020-0699-8] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 12/07/2019] [Accepted: 12/30/2019] [Indexed: 12/27/2022] Open
Abstract
Autism spectrum disorder (ASD) is a complex neurodevelopmental disorder with a male-to-female prevalence of 4:1. However, the genetic mechanisms underlying this gender difference remain unclear. Mutation burden analysis, a TADA model, and co-expression and functional network analyses were performed on de novo mutations (DNMs) and corresponding candidate genes. We found that the prevalence of putative functional DNMs (loss-of-function and predicted deleterious missense mutations) in females was significantly higher than that in males, suggesting that a higher genetic load was required in females to reach the threshold for a diagnosis. We then prioritized 174 candidate genes, including 60 shared genes, 91 male-specific genes, and 23 female-specific genes. All of the three subclasses of candidate genes were significantly more frequently co-expressed in female brains than male brains, suggesting that compensation effects of the deficiency of ASD candidate genes may be more likely in females. Nevertheless, the three subclasses of candidate genes were co-expressed with each other, suggesting a convergent functional network of male and female-specific genes. Our analysis of different aspects of genetic components provides suggestive evidence supporting the female-protective effect in ASD. Moreover, further study is needed to integrate neuronal and hormonal data to elucidate the underlying gender difference in ASD.
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Affiliation(s)
- Yi Zhang
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China ,grid.216417.70000 0001 0379 7164National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan 410008 China
| | - Na Li
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China
| | - Chao Li
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China
| | - Ze Zhang
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China
| | - Huajing Teng
- grid.9227.e0000000119573309Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, 100101 China
| | - Yan Wang
- grid.9227.e0000000119573309Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, 100101 China
| | - Tingting Zhao
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China
| | - Leisheng Shi
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China ,grid.9227.e0000000119573309Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Kun Zhang
- grid.268099.c0000 0001 0348 3990Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025 China
| | - Kun Xia
- grid.216417.70000 0001 0379 7164Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410008 China
| | - Jinchen Li
- National Clinical Research Centre for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China. .,Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410008, China.
| | - Zhongsheng Sun
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325025, China. .,Beijing Institutes of Life Science, Chinese Academy of Science, Beijing, 100101, China.
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48
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Watson AES, Goodkey K, Footz T, Voronova A. Regulation of CNS precursor function by neuronal chemokines. Neurosci Lett 2020; 715:134533. [DOI: 10.1016/j.neulet.2019.134533] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 02/07/2023]
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49
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Vorstman JAS, Olde Loohuis LM, Kahn RS, Ophoff RA. Double hits in schizophrenia. Hum Mol Genet 2019; 27:2755-2761. [PMID: 29767709 DOI: 10.1093/hmg/ddy175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 11/14/2022] Open
Abstract
The co-occurrence of a copy number variant (CNV) and a functional variant on the other allele may be a relevant genetic mechanism in schizophrenia. We hypothesized that the cumulative burden of such double hits-in particular those composed of a deletion and a coding single-nucleotide variation (SNV)-is increased in patients with schizophrenia. We combined CNV data with coding variants data in 795 patients with schizophrenia and 474 controls. To limit false CNV-detection, only CNVs called by two algorithms were included. CNV-affected genes were subsequently examined for coding SNVs, which we termed "CNV-SNVs." Correcting for total queried sequence, we assessed the CNV-SNV-burden and the combined predicted deleterious effect. We estimated P-values by permutation of the phenotype. We detected 105 CNV-SNVs; 67 in duplicated and 38 in deleted genic sequence. Although the difference in CNV-SNVs rates was not significant, the combined deleteriousness inferred by CNV-SNVs in deleted sequence was almost 4-fold higher in cases compared with controls (nominal P = 0.009). This effect may be driven by a higher number of CNV-SNVs and/or by a higher degree of predicted deleteriousness of CNV-SNVs. No such effect was observed for duplications. We provide early evidence that deletions co-occurring with a functional variant may be relevant, albeit of modest impact, for the genetic etiology of schizophrenia. Large-scale consortium studies are required to validate our findings. Sequence-based analyses would provide the best resolution for detection of CNVs as well as coding variants genome-wide.
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Affiliation(s)
- Jacob A S Vorstman
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Psychiatry, The Hospital for Sick Children and University of Toronto, Toronto, ON, Canada.,Program in Genetics and Genome Biology, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Loes M Olde Loohuis
- Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | | | - René S Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Psychiatry, Icahn School of Medicine, Mount Sinai, New York, NY, USA
| | - Roel A Ophoff
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, The Netherlands.,Center for Neurobehavioral Genetics, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
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50
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Pirooznia M, Niranjan T, Chen YC, Tunc I, Goes FS, Avramopoulos D, Potash JB, Huganir RL, Zandi PP, Wang T. Affected Sib-Pair Analyses Identify Signaling Networks Associated With Social Behavioral Deficits in Autism. Front Genet 2019; 10:1186. [PMID: 31827489 PMCID: PMC6892440 DOI: 10.3389/fgene.2019.01186] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/25/2019] [Indexed: 11/29/2022] Open
Abstract
Autism spectrum disorders (ASDs) are characterized by deficits in three core behavioral domains: reciprocal social interactions, communication, and restricted interests and/or repetitive behaviors. Several hundreds of risk genes for autism have been identified, however, it remains a challenge to associate these genes with specific core behavioral deficits. In multiplex autism families, affected sibs often show significant differences in severity of individual core phenotypes. We hypothesize that a higher mutation burden contributes to a larger difference in the severity of specific core phenotypes between affected sibs. We tested this hypothesis on social behavioral deficits in autism. We sequenced synaptome genes (n = 1,886) in affected male sib-pairs (n = 274) in families from the Autism Genetics Research Exchange (AGRE) and identified rare (MAF ≤ 1%) and predicted functional variants. We selected affected sib-pairs with a large (≥10; n = 92 pairs) or a small (≤4; n = 108 pairs) difference in total cumulative Autism Diagnostic Interview-Revised (ADI-R) social scores (SOCT_CS). We compared burdens of unshared variants present only in sibs with severe social deficits and found a higher burden in SOCT_CS≥10 compared to SOCT_CS ≤ 4 (SOCT_CS≥10: 705.1 ± 16.2; SOCT_CS ≤ 4, 668.3 ± 9.0; p = 0.025). Unshared SOCT_CS≥10 genes only in sibs with severe social deficits are significantly enriched in the SFARI gene set. Network analyses of these genes using InWeb_IM, molecular signatures database (MSigDB), and GeNetMeta identified enrichment for phosphoinositide 3-kinase (PI3K)-AKT-mammalian target of rapamycin (mTOR) (Enrichment Score [eScore] p value = 3.36E−07; n = 8 genes) and Nerve growth factor (NGF) (eScore p value = 8.94E−07; n = 9 genes) networks. These studies support a key role for these signaling networks in social behavioral deficits and present a novel approach to associate risk genes and signaling networks with core behavioral domains in autism.
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Affiliation(s)
- Mehdi Pirooznia
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States.,Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Tejasvi Niranjan
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yun-Ching Chen
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Ilker Tunc
- Bioinformatics and Computational Biology Core Facility, National Heart Lung and Blood Institute, NIH, Bethesda, MD, United States
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Dimitrios Avramopoulos
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - James B Potash
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Richard L Huganir
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Peter P Zandi
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Department of Mental Health and Epidemiology, Johns Hopkins University School of Public Health, Baltimore, MD, United States
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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