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Olfson E, Farhat LC, Liu W, Vitulano LA, Zai G, Lima MO, Parent J, Polanczyk GV, Cappi C, Kennedy JL, Fernandez TV. Rare de novo damaging DNA variants are enriched in attention-deficit/hyperactivity disorder and implicate risk genes. Nat Commun 2024; 15:5870. [PMID: 38997333 DOI: 10.1038/s41467-024-50247-7] [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: 08/18/2023] [Accepted: 06/29/2024] [Indexed: 07/14/2024] Open
Abstract
Research demonstrates the important role of genetic factors in attention-deficit/hyperactivity disorder (ADHD). DNA sequencing of families provides a powerful approach for identifying de novo (spontaneous) variants, leading to the discovery of hundreds of clinically informative risk genes for other childhood neurodevelopmental disorders. This approach has yet to be extensively leveraged in ADHD. We conduct whole-exome DNA sequencing in 152 families, comprising a child with ADHD and both biological parents, and demonstrate a significant enrichment of rare and ultra-rare de novo gene-damaging mutations in ADHD cases compared to unaffected controls. Combining these results with a large independent case-control DNA sequencing cohort (3206 ADHD cases and 5002 controls), we identify lysine demethylase 5B (KDM5B) as a high-confidence risk gene for ADHD and estimate that 1057 genes contribute to ADHD risk. Using our list of genes harboring ultra-rare de novo damaging variants, we show that these genes overlap with previously reported risk genes for other neuropsychiatric conditions and are enriched in several canonical biological pathways, suggesting early neurodevelopmental underpinnings of ADHD. This work provides insight into the biology of ADHD and demonstrates the discovery potential of DNA sequencing in larger parent-child trio cohorts.
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Affiliation(s)
- Emily Olfson
- Child Study Center, Yale University, New Haven, CT, USA.
- Wu Tsai Institute, Yale University, New Haven, CT, USA.
| | - Luis C Farhat
- Child Study Center, Yale University, New Haven, CT, USA
- Division of Child & Adolescent Psychiatry, Department of Psychiatry, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Wenzhong Liu
- Child Study Center, Yale University, New Haven, CT, USA
| | | | - Gwyneth Zai
- Tanenbaum Centre, Molecular Brain Sciences Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Monicke O Lima
- Division of Child & Adolescent Psychiatry, Department of Psychiatry, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Justin Parent
- University of Rhode Island, Kingston, RI, USA
- Bradley/Hasbro Children's Research Center, E.P. Bradley Hospital, Providence, RI, USA
- Alpert Medical School of Brown University, Providence, RI, USA
| | - Guilherme V Polanczyk
- Division of Child & Adolescent Psychiatry, Department of Psychiatry, Faculdade de Medicina FMUSP, Universidade de São Paulo, São Paulo, Brazil
| | - Carolina Cappi
- Department of Psychiatry at Icahn School of Medicine at Mount Sinai Hospital, New York, NY, USA
| | - James L Kennedy
- Tanenbaum Centre, Molecular Brain Sciences Department, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
- Institute of Medical Science and Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Thomas V Fernandez
- Child Study Center, Yale University, New Haven, CT, USA.
- Department of Psychiatry, Yale University, New Haven, CT, USA.
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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2024; 85:444-453. [PMID: 37940764 DOI: 10.1007/s12020-023-03581-7] [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: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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He MF, Liu LH, Luo S, Wang J, Guo JJ, Wang PY, Zhai QX, He SL, Zou DF, Liu XR, Li BM, Ma HY, Qiao JD, Zhou P, He N, Yi YH, Liao WP. ZFHX3 variants cause childhood partial epilepsy and infantile spasms with favourable outcomes. J Med Genet 2024; 61:652-660. [PMID: 38508705 PMCID: PMC11228202 DOI: 10.1136/jmg-2023-109725] [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: 11/01/2023] [Accepted: 02/18/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND The ZFHX3 gene plays vital roles in embryonic development, cell proliferation, neuronal differentiation and neuronal death. This study aims to explore the relationship between ZFHX3 variants and epilepsy. METHODS Whole-exome sequencing was performed in a cohort of 378 patients with partial (focal) epilepsy. A Drosophila Zfh2 knockdown model was used to validate the association between ZFHX3 and epilepsy. RESULTS Compound heterozygous ZFHX3 variants were identified in eight unrelated cases. The burden of ZFHX3 variants was significantly higher in the case cohort, shown by multiple/specific statistical analyses. In Zfh2 knockdown flies, the incidence and duration of seizure-like behaviour were significantly greater than those in the controls. The Zfh2 knockdown flies exhibited more firing in excitatory neurons. All patients presented partial seizures. The five patients with variants in the C-terminus/N-terminus presented mild partial epilepsy. The other three patients included one who experienced frequent non-convulsive status epilepticus and two who had early spasms. These three patients had also neurodevelopmental abnormalities and were diagnosed as developmental epileptic encephalopathy (DEE), but achieved seizure-free after antiepileptic-drug treatment without adrenocorticotropic-hormone/steroids. The analyses of temporal expression (genetic dependent stages) indicated that ZFHX3 orthologous were highly expressed in the embryonic stage and decreased dramatically after birth. CONCLUSION ZFHX3 is a novel causative gene of childhood partial epilepsy and DEE. The patients of infantile spasms achieved seizure-free after treatment without adrenocorticotropic-hormone/steroids implies a significance of genetic diagnosis in precise treatment. The genetic dependent stage provided an insight into the underlying mechanism of the evolutional course of illness.
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Affiliation(s)
- Ming-Feng He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Li-Hong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
- Department of Neurology, Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou 510630, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Juan Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Jia-Jun Guo
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Peng-Yu Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Qiong-Xiang Zhai
- Department of Pediatrics, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510120, China
| | - Su-Li He
- Department of Pediatrics, Shantou Chaonan Minsheng Hospital, Shantou 515000, China
| | - Dong-Fang Zou
- Epilepsy Center and Department of Neurology, Shenzhen Children's Hospital, Shenzhen 518029, China
| | - Xiao-Rong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Bing-Mei Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Hai-Yan Ma
- Department of Functional Neurosurgery, Affiliated Nanjing Brain Hospital of Nanjing Medical University, Nanjing 210029, China
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Peng Zhou
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Yong-Hong Yi
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou 510260, China
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4
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Ebstein F, Latypova X, Hung KYS, Prado MA, Lee BH, Möller S, Zieba BA, Florenceau L, Vignard V, Poirier L, Moroni I, Dubucs C, Chassaing N, Horvath J, Prokisch H, Küry S, Bézieau S, Paulo JA, Finley D, Krüger E, Ghezzi D, Isidor B. Biallelic USP14 variants cause a syndromic neurodevelopmental disorder. Genet Med 2024; 26:101120. [PMID: 38469793 PMCID: PMC11241549 DOI: 10.1016/j.gim.2024.101120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 03/13/2024] Open
Abstract
PURPOSE Imbalances in protein homeostasis affect human brain development, with the ubiquitin-proteasome system (UPS) and autophagy playing crucial roles in neurodevelopmental disorders (NDD). This study explores the impact of biallelic USP14 variants on neurodevelopment, focusing on its role as a key hub connecting UPS and autophagy. METHODS Here, we identified biallelic USP14 variants in 4 individuals from 3 unrelated families: 1 fetus, a newborn with a syndromic NDD and 2 siblings affected by a progressive neurological disease. Specifically, the 2 siblings from the latter family carried 2 compound heterozygous variants c.8T>C p.(Leu3Pro) and c.988C>T p.(Arg330∗), whereas the fetus had a homozygous frameshift c.899_902del p.(Lys300Serfs∗24) variant, and the newborn patient harbored a homozygous frameshift c.233_236del p.(Leu78Glnfs∗11) variant. Functional studies were conducted using sodium dodecyl-sulfate polyacrylamide gel electrophoresis, western blotting, and mass spectrometry analyses in both patient-derived and CRISPR-Cas9-generated cells. RESULTS Our investigations indicated that the USP14 variants correlated with reduced N-terminal methionine excision, along with profound alterations in proteasome, autophagy, and mitophagy activities. CONCLUSION Biallelic USP14 variants in NDD patients perturbed protein degradation pathways, potentially contributing to disorder etiology. Altered UPS, autophagy, and mitophagy activities underscore the intricate interplay, elucidating their significance in maintaining proper protein homeostasis during brain development.
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Affiliation(s)
- Frédéric Ebstein
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
| | - Xenia Latypova
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | | | - Miguel A. Prado
- Dept of Cell Biology, Harvard Medical School, Boston, MA, US
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Byung-Hoon Lee
- Dept of Cell Biology, Harvard Medical School, Boston, MA, US
- Dept of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, 42988, Korea
| | - Sophie Möller
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Barbara A. Zieba
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Laëtitia Florenceau
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
| | - Virginie Vignard
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Léa Poirier
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
| | - Isabella Moroni
- Department of Pediatric Neurosciences, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Charlotte Dubucs
- Département anatomie et cytologie pathologiques, CHU Toulouse, Toulouse, France
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Nicolas Chassaing
- Service de Génétique Médicale, Hôpital Purpan, CHU Toulouse, Toulouse, France
| | - Judit Horvath
- Institute for Human Genetics, University Hospital Muenster, Muenster, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Institute of Neurogenomics, Helmholtz Zentrum München, 85764 Munich, Germany
| | - Sébastien Küry
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Stéphane Bézieau
- Present address: Nantes Université, CNRS, INSERM, L’Institut du Thorax, 44000 Nantes, France
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
| | - Joao A. Paulo
- Dept of Cell Biology, Harvard Medical School, Boston, MA, US
| | - Daniel Finley
- Dept of Cell Biology, Harvard Medical School, Boston, MA, US
| | - Elke Krüger
- University Medicine Greifswald, Institute of Medical Biochemistry and Molecular Biology, Greifswald, Germany
| | - Daniele Ghezzi
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- Department of Pathophysiology and Transplantation, University of Milan, Milan, Italy
| | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 9 quai Moncousu, 44093 Nantes Cedex 1, France
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Pérez-Sisqués L, Bhatt SU, Matuleviciute R, Gileadi TE, Kramar E, Graham A, Garcia FG, Keiser A, Matheos DP, Cain JA, Pittman AM, Andreae LC, Fernandes C, Wood MA, Giese KP, Basson MA. The Intellectual Disability Risk Gene Kdm5b Regulates Long-Term Memory Consolidation in the Hippocampus. J Neurosci 2024; 44:e1544232024. [PMID: 38575342 PMCID: PMC11079963 DOI: 10.1523/jneurosci.1544-23.2024] [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: 02/18/2024] [Revised: 03/21/2024] [Accepted: 03/30/2024] [Indexed: 04/06/2024] Open
Abstract
The histone lysine demethylase KDM5B is implicated in recessive intellectual disability disorders, and heterozygous, protein-truncating variants in KDM5B are associated with reduced cognitive function in the population. The KDM5 family of lysine demethylases has developmental and homeostatic functions in the brain, some of which appear to be independent of lysine demethylase activity. To determine the functions of KDM5B in hippocampus-dependent learning and memory, we first studied male and female mice homozygous for a Kdm5b Δ ARID allele that lacks demethylase activity. Kdm5b Δ ARID/ Δ ARID mice exhibited hyperactivity and long-term memory deficits in hippocampus-dependent learning tasks. The expression of immediate early, activity-dependent genes was downregulated in these mice and hyperactivated upon a learning stimulus compared with wild-type (WT) mice. A number of other learning-associated genes were also significantly dysregulated in the Kdm5b Δ ARID/ Δ ARID hippocampus. Next, we knocked down Kdm5b specifically in the adult, WT mouse hippocampus with shRNA. Kdm5b knockdown resulted in spontaneous seizures, hyperactivity, and hippocampus-dependent long-term memory and long-term potentiation deficits. These findings identify KDM5B as a critical regulator of gene expression and synaptic plasticity in the adult hippocampus and suggest that at least some of the cognitive phenotypes associated with KDM5B gene variants are caused by direct effects on memory consolidation mechanisms.
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Affiliation(s)
- Leticia Pérez-Sisqués
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Shail U Bhatt
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Rugile Matuleviciute
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Talia E Gileadi
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Eniko Kramar
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Andrew Graham
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Franklin G Garcia
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Ashley Keiser
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - Dina P Matheos
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - James A Cain
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
| | - Alan M Pittman
- St. George's University of London, London SW17 0RE, United Kingdom
| | - Laura C Andreae
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
| | - Cathy Fernandes
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Social, Genetic & Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE5 8AB, United Kingdom
| | - Marcelo A Wood
- Department of Neurobiology and Behavior, School of Biological Sciences, University of California Irvine, Irvine, California, California 92697
| | - K Peter Giese
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London SE5 9RT, United Kingdom
| | - M Albert Basson
- Centre for Craniofacial and Regenerative Biology, Guy's Hospital, King's College London, London SE1 9RT, United Kingdom
- MRC Centre for Neurodevelopmental Disorders, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London SE1 1UL, United Kingdom
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Hatherly Laboratories, Exeter EX4 4PS, United Kingdom
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6
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Wigdor EM, Samocha KE, Eberhardt RY, Chundru VK, Firth HV, Wright CF, Hurles ME, Martin HC. Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders. Sci Rep 2024; 14:8708. [PMID: 38622173 PMCID: PMC11018828 DOI: 10.1038/s41598-024-58894-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Recent work has revealed an important role for rare, incompletely penetrant inherited coding variants in neurodevelopmental disorders (NDDs). Additionally, we have previously shown that common variants contribute to risk for rare NDDs. Here, we investigate whether common variants exert their effects by modifying gene expression, using multi-cis-expression quantitative trait loci (cis-eQTL) prediction models. We first performed a transcriptome-wide association study for NDDs using 6987 probands from the Deciphering Developmental Disorders (DDD) study and 9720 controls, and found one gene, RAB2A, that passed multiple testing correction (p = 6.7 × 10-7). We then investigated whether cis-eQTLs modify the penetrance of putatively damaging, rare coding variants inherited by NDD probands from their unaffected parents in a set of 1700 trios. We found no evidence that unaffected parents transmitting putatively damaging coding variants had higher genetically-predicted expression of the variant-harboring gene than their child. In probands carrying putatively damaging variants in constrained genes, the genetically-predicted expression of these genes in blood was lower than in controls (p = 2.7 × 10-3). However, results for proband-control comparisons were inconsistent across different sets of genes, variant filters and tissues. We find limited evidence that common cis-eQTLs modify penetrance of rare coding variants in a large cohort of NDD probands.
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Affiliation(s)
- Emilie M Wigdor
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Kaitlin E Samocha
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, USA
| | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - V Kartik Chundru
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Helen V Firth
- Department of Medical Genetics, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon and Exeter Hospital, Exeter, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Hilary C Martin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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7
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La Rocca LA, Frank J, Bentzen HB, Pantel JT, Gerischer K, Bovier A, Krawitz PM. Understanding recessive disease risk in multi-ethnic populations with different degrees of consanguinity. Am J Med Genet A 2024; 194:e63452. [PMID: 37921563 DOI: 10.1002/ajmg.a.63452] [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: 09/30/2023] [Accepted: 10/10/2023] [Indexed: 11/04/2023]
Abstract
Population medical genetics aims at translating clinically relevant findings from recent studies of large cohorts into healthcare for individuals. Genetic counseling concerning reproductive risks and options is still mainly based on family history, and consanguinity is viewed to increase the risk for recessive diseases regardless of the demographics. However, in an increasingly multi-ethnic society with diverse approaches to partner selection, healthcare professionals should also sharpen their intuition for the influence of different mating schemes in non-equilibrium dynamics. We, therefore, revisited the so-called out-of-Africa model and studied in forward simulations with discrete and not overlapping generations the effect of inbreeding on the average number of recessive lethals in the genome. We were able to reproduce in both frameworks the drop in the incidence of recessive disorders, which is a transient phenomenon during and after the growth phase of a population, and therefore showed their equivalence. With the simulation frameworks, we also provide the means to study and visualize the effect of different kin sizes and mating schemes on these parameters for educational purposes.
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Affiliation(s)
- Luis A La Rocca
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
| | - Julia Frank
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Heidi Beate Bentzen
- Centre for Medical Ethics, Faculty of Medicine, Univeristy of Oslo, Oslo, Norway
| | - Jean Tori Pantel
- Department of Digitalization and General Practice, University Hospital RWTH Aachen, Aachen, Germany
| | - Konrad Gerischer
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Anton Bovier
- Institute for Genomic Statistics and Bioinformatics, University of Bonn, Bonn, Germany
| | - Peter M Krawitz
- Institute for Applied Mathematics, University of Bonn, Bonn, Germany
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8
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Nadimpalli Kobren S, Moldovan MA, Reimers R, Traviglia D, Li X, Barnum D, Veit A, Willett J, Berselli M, Ronchetti W, Sherwood R, Krier J, Kohane IS, Sunyaev SR. Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.13.580158. [PMID: 38405764 PMCID: PMC10888768 DOI: 10.1101/2024.02.13.580158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform "N-of-1" analyses on individual patients. The increasing sizes of ultra-rare, "N-of-1" disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development.1,2 The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale N-of-1 analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We apply existing and introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We make our gene-level findings and variant-level information across the cohort available in a public-facing browser (https://dbmi-bgm.github.io/udn-browser/). These results show that N-of-1 efforts should be supplemented by a joint genomic analysis across cohorts.
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Affiliation(s)
| | | | | | - Daniel Traviglia
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Xinyun Li
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT
| | | | - Alexander Veit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Julian Willett
- Department of Neurology, Massachusetts General Hospital, Boston, MA
| | - Michele Berselli
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - William Ronchetti
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Richard Sherwood
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Joel Krier
- Department of Genetics, Atrius Health, Boston, MA
| | - Isaac S. Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | | | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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9
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Mušálková D, Přistoupilová A, Jedličková I, Hartmannová H, Trešlová H, Nosková L, Hodaňová K, Bittmanová P, Stránecký V, Jiřička V, Langmajerová M, Woodbury‐Smith M, Zarrei M, Trost B, Scherer SW, Bleyer AJ, Vevera J, Kmoch S. Increased burden of rare protein-truncating variants in constrained, brain-specific and synaptic genes in extremely impulsively violent males with antisocial personality disorder. GENES, BRAIN, AND BEHAVIOR 2024; 23:e12882. [PMID: 38359179 PMCID: PMC10869132 DOI: 10.1111/gbb.12882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 12/11/2023] [Accepted: 01/03/2024] [Indexed: 02/17/2024]
Abstract
The genetic correlates of extreme impulsive violence are poorly understood, and there have been few studies that have characterized a large group of affected individuals both clinically and genetically. We performed whole exome sequencing (WES) in 290 males with the life-course-persistent, extremely impulsively violent form of antisocial personality disorder (APD) and analyzed the spectrum of rare protein-truncating variants (rPTVs). Comparisons were made with 314 male controls and publicly available genotype data. Functional annotation tools were used for biological interpretation. Participants were significantly more likely to harbor rPTVs in genes that are intolerant to loss-of-function variants (odds ratio [OR] 2.06; p < 0.001), specifically expressed in brain (OR 2.80; p = 0.036) and enriched for those involved in neurotransmitter transport and synaptic processes. In 60 individuals (20%), we identified rPTVs that we classified as clinically relevant based on their clinical associations, biological function and gene expression patterns. Of these, 37 individuals harbored rPTVs in 23 genes that are associated with a monogenic neurological disorder, and 23 individuals harbored rPTVs in 20 genes reportedly intolerant to loss-of-function variants. The analysis presents evidence in support of a model where presence of either one or several private, functionally relevant mutations contribute significantly to individual risk of life-course-persistent APD and reveals multiple individuals who could be affected by clinically unrecognized neuropsychiatric Mendelian disease. Thus, Mendelian diseases and increased rPTV burden may represent important factors for the development of extremely impulsive violent life-course-persistent forms of APD irrespective of their clinical presentation.
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Affiliation(s)
- Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Petra Bittmanová
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
| | - Václav Jiřička
- Department of PsychologyPrison Service of the Czech RepublicPragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Michaela Langmajerová
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
| | - Marc Woodbury‐Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Faculty of Medical Sciences, Biosciences InstituteNewcastle UniversityNewcastle upon TyneUK
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Brett Trost
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick ChildrenTorontoOntarioCanada
- Department of Molecular Genetics and McLaughlin CentreUniversity of TorontoTorontoOntarioCanada
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Section on Nephrology, Wake Forest School of MedicineWinston‐SalemNorth CarolinaUSA
| | - Jan Vevera
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
- Department of PsychiatryUniversity Hospital PilsenPilsenCzech Republic
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Inherited Metabolic Disorders, First Faculty of MedicineCharles University in Prague and General University Hospital in PraguePragueCzech Republic
- Department of Psychiatry, Faculty of Medicine in PilsenCharles UniversityPilsenCzech Republic
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10
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Sun J, Noss S, Banerjee D, Das M, Girirajan S. Strategies for dissecting the complexity of neurodevelopmental disorders. Trends Genet 2024; 40:187-202. [PMID: 37949722 PMCID: PMC10872993 DOI: 10.1016/j.tig.2023.10.009] [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: 05/27/2023] [Revised: 09/20/2023] [Accepted: 10/16/2023] [Indexed: 11/12/2023]
Abstract
Neurodevelopmental disorders (NDDs) are associated with a wide range of clinical features, affecting multiple pathways involved in brain development and function. Recent advances in high-throughput sequencing have unveiled numerous genetic variants associated with NDDs, which further contribute to disease complexity and make it challenging to infer disease causation and underlying mechanisms. Herein, we review current strategies for dissecting the complexity of NDDs using model organisms, induced pluripotent stem cells, single-cell sequencing technologies, and massively parallel reporter assays. We further highlight single-cell CRISPR-based screening techniques that allow genomic investigation of cellular transcriptomes with high efficiency, accuracy, and throughput. Overall, we provide an integrated review of experimental approaches that can be applicable for investigating a broad range of complex disorders.
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Affiliation(s)
- Jiawan Sun
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Serena Noss
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Deepro Banerjee
- Bioinformatics and Genomics Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Maitreya Das
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA
| | - Santhosh Girirajan
- Molecular, Cellular, and Integrative Biosciences Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA; Bioinformatics and Genomics Graduate Program, The Huck Institutes of Life Sciences, University Park, PA 16802, USA; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA.
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11
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Young AS, Martin HC. Discovering genes that affect cognitive ability. Trends Genet 2023; 39:810-812. [PMID: 37596117 DOI: 10.1016/j.tig.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/20/2023]
Abstract
Twin and genomic studies indicate that genes play an important role in the development of cognitive ability. However, data limitations have made it difficult to pinpoint specific genes with a large impact. By examining the full gene sequences of >300 000 individuals, Chen et al. find eight such genes.
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Affiliation(s)
- Alexander Strudwick Young
- University of California Los Angeles (UCLA) Anderson School of Management, Los Angeles, CA, USA; Human Genetics Department, UCLA David Geffen School of Medicine, Los Angeles, CA, USA.
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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12
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Malawsky DS, van Walree E, Jacobs BM, Heng TH, Huang QQ, Sabir AH, Rahman S, Sharif SM, Khan A, Mirkov MU, Kuwahara H, Gao X, Alkuraya FS, Posthuma D, Newman WG, Griffiths CJ, Mathur R, van Heel DA, Finer S, O'Connell J, Martin HC. Influence of autozygosity on common disease risk across the phenotypic spectrum. Cell 2023; 186:4514-4527.e14. [PMID: 37757828 PMCID: PMC10580289 DOI: 10.1016/j.cell.2023.08.028] [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: 02/02/2023] [Revised: 07/11/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023]
Abstract
Autozygosity is associated with rare Mendelian disorders and clinically relevant quantitative traits. We investigated associations between the fraction of the genome in runs of homozygosity (FROH) and common diseases in Genes & Health (n = 23,978 British South Asians), UK Biobank (n = 397,184), and 23andMe. We show that restricting analysis to offspring of first cousins is an effective way of reducing confounding due to social/environmental correlates of FROH. Within this group in G&H+UK Biobank, we found experiment-wide significant associations between FROH and twelve common diseases. We replicated associations with type 2 diabetes (T2D) and post-traumatic stress disorder via within-sibling analysis in 23andMe (median n = 480,282). We estimated that autozygosity due to consanguinity accounts for 5%-18% of T2D cases among British Pakistanis. Our work highlights the possibility of widespread non-additive genetic effects on common diseases and has important implications for global populations with high rates of consanguinity.
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Affiliation(s)
| | - Eva van Walree
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, the Netherlands; Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands
| | - Benjamin M Jacobs
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Teng Hiang Heng
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Qin Qin Huang
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ataf H Sabir
- West Midlands Regional Clinical Genetics Unit, Birmingham Women's and Children's NHS FT, Birmingham, UK; Institute of Cancer and Genomics, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Saadia Rahman
- Queen Square Institute of Neurology, University College London, London, UK
| | - Saghira Malik Sharif
- Yorkshire Regional Genetics Service, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Ahsan Khan
- Waltham Forest Council, Waltham Forest Town Hall, Forest Road, Walthamstow E17 4JF, UK
| | - Maša Umićević Mirkov
- Congenica Limited, BioData Innovation Centre, Wellcome Genome Campus, Hinxton, UK
| | - Hiroyuki Kuwahara
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955, Saudi Arabia
| | - Fowzan S Alkuraya
- Department of Translational Genomics, Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Danielle Posthuma
- Department of Complex Trait Genetics Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, VU Amsterdam, Amsterdam, the Netherlands
| | - William G Newman
- Division of Evolution, Infection and Genomics, Faculty of Biology, Medicine and Human Sciences, University of Manchester, Manchester M13 9PL, UK; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester M13 9WL, UK
| | - Christopher J Griffiths
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK; MRC and Asthma UK Centre in Allergic Mechanisms of Asthma, King's College London, London, UK
| | - Rohini Mathur
- Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - David A van Heel
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Sarah Finer
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK; Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | | | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
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13
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Fernandez TV, Williams ZP, Kline T, Rajendran S, Augustine F, Wright N, Sullivan CAW, Olfson E, Abdallah SB, Liu W, Hoffman EJ, Gupta AR, Singer HS. Primary complex motor stereotypies are associated with de novo damaging DNA coding mutations that identify KDM5B as a risk gene. PLoS One 2023; 18:e0291978. [PMID: 37788244 PMCID: PMC10547198 DOI: 10.1371/journal.pone.0291978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/10/2023] [Indexed: 10/05/2023] Open
Abstract
Motor stereotypies are common in children with autism spectrum disorder (ASD), intellectual disability, or sensory deprivation, as well as in typically developing children ("primary" stereotypies, pCMS). The precise pathophysiological mechanism for motor stereotypies is unknown, although genetic etiologies have been suggested. In this study, we perform whole-exome DNA sequencing in 129 parent-child trios with pCMS and 853 control trios (118 cases and 750 controls after quality control). We report an increased rate of de novo predicted-damaging DNA coding variants in pCMS versus controls, identifying KDM5B as a high-confidence risk gene and estimating 184 genes conferring risk. Genes harboring de novo damaging variants in pCMS probands show significant overlap with those in Tourette syndrome, ASD, and those in ASD probands with high versus low stereotypy scores. An exploratory analysis of these pCMS gene expression patterns finds clustering within the cortex and striatum during early mid-fetal development. Exploratory gene ontology and network analyses highlight functional convergence in calcium ion transport, demethylation, cell signaling, cell cycle and development. Continued sequencing of pCMS trios will identify additional risk genes and provide greater insights into biological mechanisms of stereotypies across diagnostic boundaries.
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Affiliation(s)
- Thomas V. Fernandez
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
- Department of Psychiatry, Yale University School of Medicine, New Haven, CT, United States America
| | - Zsanett P. Williams
- Department of Psychiatry, Vanderbilt University School of Nursing, Nashville, TN, United States America
| | - Tina Kline
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Shreenath Rajendran
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Farhan Augustine
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
| | - Nicole Wright
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Catherine A. W. Sullivan
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States America
| | - Emily Olfson
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Sarah B. Abdallah
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Wenzhong Liu
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Ellen J. Hoffman
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
| | - Abha R. Gupta
- Yale Child Study Center, Yale University School of Medicine, New Haven, CT, United States America
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, United States America
| | - Harvey S. Singer
- Departments of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States America
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14
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Guo R, Rippert A, Cook EB, Alves CAP, Bird LM, Izumi K. Expansion of clinical and variant spectrum of EEF2-related neurodevelopmental disorder: Report of two additional cases. Am J Med Genet A 2023; 191:2602-2609. [PMID: 37159414 PMCID: PMC10527330 DOI: 10.1002/ajmg.a.63230] [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: 01/31/2023] [Revised: 04/14/2023] [Accepted: 04/24/2023] [Indexed: 05/11/2023]
Abstract
Eukaryotic translation elongation factor 2 (eEF2), encoded by the gene EEF2, is an essential factor involved in the elongation phase of protein translation. A specific heterozygous missense variant (p.P596H) in EEF2 was originally identified in association with autosomal dominant adult-onset spinocerebellar ataxia-26 (SCA26). More recently, additional heterozygous missense variants in this gene have been described to cause a novel, childhood-onset neurodevelopmental disorder with benign external hydrocephalus. Herein, we report two unrelated individuals with a similar gene-disease correlation to support this latter observation. Patient 1 is a 7-year-old male with a previously reported, de novo missense variant (p.V28M) who has motor and speech delay, autism spectrum disorder, failure to thrive with relative macrocephaly, unilateral microphthalmia with coloboma and eczema. Patient 2 is a 4-year-old female with a novel de novo nonsense variant (p.Q145X) with motor and speech delay, hypotonia, macrocephaly with benign ventricular enlargement, and keratosis pilaris. These additional cases help to further expand the genotypic and phenotypic spectrum of this newly described EEF2-related neurodevelopmental syndrome.
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Affiliation(s)
- Rose Guo
- Division of Human Genetics, Children’s Hospital of Philadelphia, Pennsylvania, Pennsylvania, USA
| | - Alyssa Rippert
- Division of Human Genetics, Children’s Hospital of Philadelphia, Pennsylvania, Pennsylvania, USA
| | - Edward B Cook
- Division of Human Genetics, Children’s Hospital of Philadelphia, Pennsylvania, Pennsylvania, USA
| | - Cesar Augusto P Alves
- Department of Radiology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Lynne M Bird
- Department of Pediatrics, University of California San Diego; Division of Dysmorphology/Genetics, Rady Children’s Hospital San Diego, San Diego, California, USA
| | - Kosuke Izumi
- Division of Human Genetics, Children’s Hospital of Philadelphia, Pennsylvania, Pennsylvania, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Current affiliation: Division of Genetics and Metabolism, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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15
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Ye T, Zhang J, Wang J, Lan S, Zeng T, Wang H, He X, Li BM, Deng W, Liao WP, Liu XR. Variants in BSN gene associated with epilepsy with favourable outcome. J Med Genet 2023; 60:776-783. [PMID: 36600631 PMCID: PMC10439262 DOI: 10.1136/jmg-2022-108865] [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: 08/11/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
BACKGROUND BSN gene encodes Bassoon, an essential protein to assemble the cytomatrix at the active zone of neurotransmitter release. This study aims to explore the relationship between BSN variants and epilepsy. METHODS Whole-exome sequencing was performed in a cohort of 313 cases (trios) with epilepsies of unknown causes. Additional cases with BSN variants were collected from China Epilepsy Gene V.1.0 Matching Platform. The Clinical Validity Framework of ClinGen was used to evaluate the relationship between BSN variants and epilepsy. RESULTS Four pairs of compound heterozygous variants and one cosegregating heterozygous missense variant in BSN were identified in five unrelated families. These variants presented statistically higher frequency in the case cohort than in controls. Additional two de novo heterozygous nonsense variants and one cosegregating heterozygous missense variant were identified in three unrelated cases from the gene matching platform, which were not present in the Genome Aggregation Database. The missense variants tended to be located in C-terminus, including the two monoallelic missense variants. Protein modelling showed that at least one missense variant in each pair of compound heterozygous variants had hydrogen bond alterations. Clinically, two cases were diagnosed as idiopathic generalised epilepsy, two as focal epilepsy and the remaining four as epilepsy with febrile seizures plus. Seven out of eight probands showed infancy or childhood-onset epilepsy. Eight out of 10 affected individuals had a history of febrile convulsions. All the cases were seizure-free. The cases with monoallelic variants achieved seizure-free without treatment or under monotherapy, while cases with biallelic missense variants mostly required combined therapy. The evidence from ClinGen Framework suggested an association between BSN variants and epilepsy. CONCLUSION The BSN gene was potentially a novel candidate gene for epilepsy. The phenotypical severity was associated with the genotypes and the molecular subregional effects of the variants.
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Affiliation(s)
- Tingting Ye
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Jiwei Zhang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Song Lan
- Department of Neurology, Maoming People's Hospital, Maoming, Guangdong, China
| | - Tao Zeng
- Department of Neurology, Guangzhou First People's Hospital, Guangzhou, China
| | - Huaili Wang
- Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xuelian He
- Precision Medical Center, Wuhan Childrens Hospital, Wuhan, China
| | - Bing-Mei Li
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Weiwen Deng
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiao-Rong Liu
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
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16
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Huang Y, Bodnar D, Chen CY, Sanchez-Andrade G, Sanderson M, Shi J, Meilleur KG, Hurles ME, Gerety SS, Tsai EA, Runz H. Rare genetic variants impact muscle strength. Nat Commun 2023; 14:3449. [PMID: 37301943 PMCID: PMC10257725 DOI: 10.1038/s41467-023-39247-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/05/2023] [Indexed: 06/12/2023] Open
Abstract
Muscle strength is highly heritable and predictive for multiple adverse health outcomes including mortality. Here, we present a rare protein-coding variant association study in 340,319 individuals for hand grip strength, a proxy measure of muscle strength. We show that the exome-wide burden of rare protein-truncating and damaging missense variants is associated with a reduction in hand grip strength. We identify six significant hand grip strength genes, KDM5B, OBSCN, GIGYF1, TTN, RB1CC1, and EIF3J. In the example of the titin (TTN) locus we demonstrate a convergence of rare with common variant association signals and uncover genetic relationships between reduced hand grip strength and disease. Finally, we identify shared mechanisms between brain and muscle function and uncover additive effects between rare and common genetic variation on muscle strength.
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Affiliation(s)
- Yunfeng Huang
- Research and Development, Biogen Inc., Cambridge, MA, USA.
| | - Dora Bodnar
- Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Chia-Yen Chen
- Research and Development, Biogen Inc., Cambridge, MA, USA
| | | | - Mark Sanderson
- Wellcome Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Jun Shi
- Research and Development, Biogen Inc., Cambridge, MA, USA
| | | | | | | | - Ellen A Tsai
- Research and Development, Biogen Inc., Cambridge, MA, USA
| | - Heiko Runz
- Research and Development, Biogen Inc., Cambridge, MA, USA.
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17
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Chen CY, Tian R, Ge T, Lam M, Sanchez-Andrade G, Singh T, Urpa L, Liu JZ, Sanderson M, Rowley C, Ironfield H, Fang T, Daly M, Palotie A, Tsai EA, Huang H, Hurles ME, Gerety SS, Lencz T, Runz H. The impact of rare protein coding genetic variation on adult cognitive function. Nat Genet 2023:10.1038/s41588-023-01398-8. [PMID: 37231097 DOI: 10.1038/s41588-023-01398-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 04/13/2023] [Indexed: 05/27/2023]
Abstract
Compelling evidence suggests that human cognitive function is strongly influenced by genetics. Here, we conduct a large-scale exome study to examine whether rare protein-coding variants impact cognitive function in the adult population (n = 485,930). We identify eight genes (ADGRB2, KDM5B, GIGYF1, ANKRD12, SLC8A1, RC3H2, CACNA1A and BCAS3) that are associated with adult cognitive function through rare coding variants with large effects. Rare genetic architecture for cognitive function partially overlaps with that of neurodevelopmental disorders. In the case of KDM5B we show how the genetic dosage of one of these genes may determine the variability of cognitive, behavioral and molecular traits in mice and humans. We further provide evidence that rare and common variants overlap in association signals and contribute additively to cognitive function. Our study introduces the relevance of rare coding variants for cognitive function and unveils high-impact monogenic contributions to how cognitive function is distributed in the normal adult population.
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Affiliation(s)
- Chia-Yen Chen
- Research and Development, Biogen Inc, Cambridge, MA, USA.
| | - Ruoyu Tian
- Research and Development, Biogen Inc, Cambridge, MA, USA
- Dewpoint Therapeutics, Boston, MA, USA
| | - Tian Ge
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Max Lam
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | | | - Tarjinder Singh
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Lea Urpa
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Jimmy Z Liu
- Research and Development, Biogen Inc, Cambridge, MA, USA
- GlaxoSmithKline, Philadelphia, PA, USA
| | | | | | | | - Terry Fang
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Mark Daly
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Aarno Palotie
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ellen A Tsai
- Research and Development, Biogen Inc, Cambridge, MA, USA
| | - Hailiang Huang
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | | | | | - Todd Lencz
- Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health, Glen Oaks, NY, USA
- Institute of Behavioral Science, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Department of Psychiatry, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
- Department of Molecular Medicine, Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Heiko Runz
- Research and Development, Biogen Inc, Cambridge, MA, USA.
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18
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Wright CF, Campbell P, Eberhardt RY, Aitken S, Perrett D, Brent S, Danecek P, Gardner EJ, Chundru VK, Lindsay SJ, Andrews K, Hampstead J, Kaplanis J, Samocha KE, Middleton A, Foreman J, Hobson RJ, Parker MJ, Martin HC, FitzPatrick DR, Hurles ME, Firth HV. Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland. N Engl J Med 2023; 388:1559-1571. [PMID: 37043637 PMCID: PMC7614484 DOI: 10.1056/nejmoa2209046] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
BACKGROUND Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits. METHODS We conducted a large-scale sequencing study involving more than 13,500 families with probands with severe, probably monogenic, difficult-to-diagnose developmental disorders from 24 regional genetics services in the United Kingdom and Ireland. Standardized phenotypic data were collected, and exome sequencing and microarray analyses were performed to investigate novel genetic causes. We developed an iterative variant analysis pipeline and reported candidate variants to clinical teams for validation and diagnostic interpretation to inform communication with families. Multiple regression analyses were performed to evaluate factors affecting the probability of diagnosis. RESULTS A total of 13,449 probands were included in the analyses. On average, we reported 1.0 candidate variant per parent-offspring trio and 2.5 variants per singleton proband. Using clinical and computational approaches to variant classification, we made a diagnosis in approximately 41% of probands (5502 of 13,449). Of 3599 probands in trios who received a diagnosis by clinical assertion, approximately 76% had a pathogenic de novo variant. Another 22% of probands (2997 of 13,449) had variants of uncertain significance in genes that were strongly linked to monogenic developmental disorders. Recruitment in a parent-offspring trio had the largest effect on the probability of diagnosis (odds ratio, 4.70; 95% confidence interval [CI], 4.16 to 5.31). Probands were less likely to receive a diagnosis if they were born extremely prematurely (i.e., 22 to 27 weeks' gestation; odds ratio, 0.39; 95% CI, 0.22 to 0.68), had in utero exposure to antiepileptic medications (odds ratio, 0.44; 95% CI, 0.29 to 0.67), had mothers with diabetes (odds ratio, 0.52; 95% CI, 0.41 to 0.67), or were of African ancestry (odds ratio, 0.51; 95% CI, 0.31 to 0.78). CONCLUSIONS Among probands with severe, probably monogenic, difficult-to-diagnose developmental disorders, multimodal analysis of genomewide data had good diagnostic power, even after previous attempts at diagnosis. (Funded by the Health Innovation Challenge Fund and Wellcome Sanger Institute.).
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Affiliation(s)
- Caroline F. Wright
- Department of Clinical and Biomedical Sciences, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter UK, EX2 5DW
| | - Patrick Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
| | - Ruth Y. Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Stuart Aitken
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Daniel Perrett
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Simon Brent
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Eugene J. Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - V. Kartik Chundru
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Sarah J. Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Katrina Andrews
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Juliet Hampstead
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Joanna Kaplanis
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Kaitlin E. Samocha
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Anna Middleton
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, Cambridge, UK, CB10 1SA
| | - Julia Foreman
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SD
| | - Rachel J. Hobson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Michael J. Parker
- Wellcome Centre for Ethics and Humanities/Ethox Centre, Oxford Population Health, University of Oxford, Big Data Institute, Old Road Campus, Oxford, UK, OX3 7LF
| | - Hilary C. Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - David R. FitzPatrick
- MRC Human Genetics Unit, Institute of Genetic and Cancer, University of Edinburgh, Edinburgh UK, EH4 2XU
| | - Matthew E. Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
| | - Helen V. Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge UK, CB10 1SA
- Cambridge University Hospitals Foundation Trust, Addenbrooke’s Hospital, Cambridge UK, CB2 0QQ
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19
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Kildal ESM, Quintana DS, Szabo A, Tronstad C, Andreassen O, Nærland T, Hassel B. Heart rate monitoring to detect acute pain in non-verbal patients: a study protocol for a randomized controlled clinical trial. BMC Psychiatry 2023; 23:252. [PMID: 37060049 PMCID: PMC10103503 DOI: 10.1186/s12888-023-04757-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 04/06/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Autism entails reduced communicative abilities. Approximately 30% of individuals with autism have intellectual disability (ID). Some people with autism and ID are virtually non-communicative and unable to notify their caregivers when they are in pain. In a pilot study, we showed that heart rate (HR) monitoring may identify painful situations in this patient group, as HR increases in acutely painful situations. OBJECTIVES This study aims to generate knowledge to reduce the number of painful episodes in non-communicative patients' everyday lives. We will 1) assess the effectiveness of HR as a tool for identifying potentially painful care procedures, 2) test the effect of HR-informed changes in potentially painful care procedures on biomarkers of pain, and 3) assess how six weeks of communication through HR affects the quality of communication between patient and caregiver. METHODS We will recruit 38 non-communicative patients with autism and ID residing in care homes. ASSESSMENTS HR is measured continuously to identify acutely painful situations. HR variability and pain-related cytokines (MCP-1, IL-1RA, IL-8, TGFβ1, and IL-17) are collected as measures of long-term pain. Caregivers will be asked to what degree they observe pain in their patients and how well they believe they understand their patient's expressions of emotion and pain. Pre-intervention: HR is measured 8 h/day over 2 weeks to identify potentially painful situations across four settings: physiotherapy, cast use, lifting, and personal hygiene. INTERVENTION Changes in procedures for identified painful situations are in the form of changes in 1) physiotherapy techniques, 2) preparations for putting on casts, 3) lifting techniques or 4) personal hygiene procedures. DESIGN Nineteen patients will start intervention in week 3 while 19 patients will continue data collection for another 2 weeks before procedure changes are introduced. This is done to distinguish between specific effects of changes in procedures and non-specific effects, such as caregivers increased attention. DISCUSSION This study will advance the field of wearable physiological sensor use in patient care. TRIAL REGISTRATION Registered prospectively at ClinicalTrials.gov (NCT05738278).
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Affiliation(s)
- Emilie S M Kildal
- K.G. Jebsen, Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway.
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Department of Psychiatry, Lovisenberg Diakonale Sykehus, Oslo, Norway.
| | - Daniel S Quintana
- K.G. Jebsen, Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- Department of Psychology, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, University of Oslo, Oslo, Norway
- NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway
| | - Attila Szabo
- K.G. Jebsen, Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, University of Oslo, Oslo, Norway
| | - Christian Tronstad
- Department of Clinical and Biomedical Engineering, Oslo University Hospital, Oslo, Norway
| | - Ole Andreassen
- K.G. Jebsen, Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway
- NORMENT, Division of Mental Health and Addiction, University of Oslo, Oslo, Norway
| | - Terje Nærland
- K.G. Jebsen, Centre for Neurodevelopmental Disorders, University of Oslo, Oslo, Norway.
- NevSom, Department of Rare Disorders, Oslo University Hospital, Oslo, Norway.
| | - Bjørnar Hassel
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Neurohabilitation, Oslo University Hospital, Oslo, Norway
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20
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Valkovskaya M, Hassan A, Zartaloudi E, Hussain F, Umar M, Khizar B, Khattak I, Gill SA, Khan SUDA, Dogar IA, Mustafa AB, Ansari MA, Qalb I Hyder S, Ali M, Ilyas N, Channar P, Mughal N, Channa S, Mufti K, Mufti AA, Hussain MI, Shafiq S, Tariq M, Khan MK, Chaudhry ST, Choudhary AR, Ali MN, Ali G, Hussain A, Rehman M, Ahmad N, Farooq S, Naeem F, Nasr T, Lewis G, Knowles JA, Ayub M, Kuchenbaecker K. Study protocol of DIVERGE, the first genetic epidemiological study of major depressive disorder in Pakistan. Psychiatr Genet 2023; 33:69-78. [PMID: 36538573 PMCID: PMC9997631 DOI: 10.1097/ypg.0000000000000333] [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: 08/31/2022] [Accepted: 11/22/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Globally, 80% of the burdenof major depressive disorder (MDD) pertains to low- and middle-income countries. Research into genetic and environmental risk factors has the potential to uncover disease mechanisms that may contribute to better diagnosis and treatment of mental illness, yet has so far been largely limited to participants with European ancestry from high-income countries. The DIVERGE study was established to help overcome this gap and investigate genetic and environmental risk factors for MDD in Pakistan. METHODS DIVERGE aims to enrol 9000 cases and 4000 controls in hospitals across the country. Here, we provide the rationale for DIVERGE, describe the study protocol and characterise the sample using data from the first 500 cases. Exploratory data analysis is performed to describe demographics, socioeconomic status, environmental risk factors, family history of mental illness and psychopathology. RESULTS AND DISCUSSION Many participants had severe depression with 74% of patients who experienced multiple depressive episodes. It was a common practice to seek help for mental health struggles from faith healers and religious leaders. Socioeconomic variables reflected the local context with a large proportion of women not having access to any education and the majority of participants reporting no savings. CONCLUSION DIVERGE is a carefully designed case-control study of MDD in Pakistan that captures diverse risk factors. As the largest genetic study in Pakistan, DIVERGE helps address the severe underrepresentation of people from South Asian countries in genetic as well as psychiatric research.
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Affiliation(s)
| | - Arsalan Hassan
- Department of Pharmacy, University of Peshawar, Peshawar, Pakistan
| | - Eirini Zartaloudi
- Institute of Clinical Trials and Methodology, University College London, London, UK
| | - Fahad Hussain
- Lahore Institute of Research and Development, Lahore
| | - Muhammad Umar
- Lahore Institute of Research and Development, Lahore
| | - Bakht Khizar
- Lahore Institute of Research and Development, Lahore
| | | | | | | | | | - Ali Burhan Mustafa
- Department of Psychiatry and Behavioural Sciences, Sheikh Zayed Medical College/Hospital, Rahim Yar Khan
| | - Moin Ahmed Ansari
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Syed Qalb I Hyder
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Muhammad Ali
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Nilofar Ilyas
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Parveen Channar
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Nazish Mughal
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | - Sumera Channa
- Sir Cowasjee Jehangir Institute of Psychiatric and Behavioral Sciences, Hyderabad
| | | | | | | | | | | | | | | | | | | | - Gohar Ali
- Department of Psychiatry, Saidu Teaching Hospital
| | | | | | - Noman Ahmad
- Punjab Institute of Mental Health (PIMH), Lahore, Pakistan
| | - Saeed Farooq
- School of Medicine, Keele University, Keele
- Innovation Department, Midlands Partnership NHS Foundation Trust, Staffotdshire, UK
| | - Farooq Naeem
- Department of Psychiatry, University of Toronto
- Center for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Tanveer Nasr
- Lahore Institute of Research and Development, Lahore
| | - Glyn Lewis
- Division of Psychiatry, University College London, London, UK
| | - James A. Knowles
- Human Genetics Institute of New Jersey (HGINJ), Rutgers University, New Brunswick, New Jersey, USA
| | - Muhammad Ayub
- Division of Psychiatry, University College London, London, UK
| | - Karoline Kuchenbaecker
- Division of Psychiatry, University College London, London, UK
- UCL Genetics Institute, University College London, London, UK
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21
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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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22
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Gupta N. Deciphering Intellectual Disability. Indian J Pediatr 2023; 90:160-167. [PMID: 36441387 DOI: 10.1007/s12098-022-04345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) is a common cause of referral to the pediatricians, geneticists, and pediatric neurologists. A thorough clinical evaluation and a stepwise investigative approach using a combination of traditional genetic techniques and appropriate latest genomic technologies can help in arriving at a diagnosis. In the current "omics" era, adopting a multiomics approach would further assist in solving the undiagnosed cases with intellectual disability.
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Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, Ansari Nagar, Old OT Block, New Delhi, 110029, India.
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23
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Wiel L, Hampstead JE, Venselaar H, Vissers LE, Brunner HG, Pfundt R, Vriend G, Veltman JA, Gilissen C. De novo mutation hotspots in homologous protein domains identify function-altering mutations in neurodevelopmental disorders. Am J Hum Genet 2023; 110:92-104. [PMID: 36563679 PMCID: PMC9892778 DOI: 10.1016/j.ajhg.2022.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
Variant interpretation remains a major challenge in medical genetics. We developed Meta-Domain HotSpot (MDHS) to identify mutational hotspots across homologous protein domains. We applied MDHS to a dataset of 45,221 de novo mutations (DNMs) from 31,058 individuals with neurodevelopmental disorders (NDDs) and identified three significantly enriched missense DNM hotspots in the ion transport protein domain family (PF00520). The 37 unique missense DNMs that drive enrichment affect 25 genes, 19 of which were previously associated with NDDs. 3D protein structure modeling supports the hypothesis of function-altering effects of these mutations. Hotspot genes have a unique expression pattern in tissue, and we used this pattern alongside in silico predictors and population constraint information to identify candidate NDD-associated genes. We also propose a lenient version of our method, which identifies 32 hotspot positions across 16 different protein domains. These positions are enriched for likely pathogenic variation in clinical databases and DNMs in other genetic disorders.
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Affiliation(s)
- Laurens Wiel
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Department of Medicine, Division of Cardiovascular Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Juliet E. Hampstead
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Hanka Venselaar
- Centre for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Lisenka E.L.M. Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Han G. Brunner
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands
| | - Gerrit Vriend
- Baco Institute of Protein Science, Baco, 5201 Mindoro, Philippines
| | - Joris A. Veltman
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
| | - Christian Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen 6525 GA, the Netherlands,Corresponding author
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24
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Proteomic Analysis of Murine Bone Marrow Very Small Embryonic-like Stem Cells at Steady-State Conditions and after In Vivo Stimulation by Nicotinamide and Follicle-Stimulating Factor Reflects their Germ-Lineage Origin and Multi Germ Layer Differentiation Potential. Stem Cell Rev Rep 2023; 19:120-132. [PMID: 35986128 PMCID: PMC9823037 DOI: 10.1007/s12015-022-10445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2022] [Indexed: 01/29/2023]
Abstract
Very small embryonic-like stem cells (VSELs) are a dormant population of development early stem cells deposited in adult tissues that as demonstrated contribute to tissue/organ repair and regeneration. We postulated developmental relationship of these cells to migrating primordial germ cells (PGCs) and explained the quiescent state of these cells by the erasure of differently methylated regions (DMRs) at some of the paternally imprinted genes involved in embryogenesis. Recently, we reported that VSELs began to proliferate and expand in vivo in murine bone marrow (BM) after exposure to nicotinamide (NAM) and selected pituitary and gonadal sex hormones. In the current report, we performed proteomic analysis of VSELs purified from murine bone marrow (BM) after repeated injections of NAM + Follicle-Stimulating Hormone (FSH) that in our previous studies turned out to be an effective combination to expand these cells. By employing the Gene Ontology (GO) resources, we have performed a combination of standard GO annotations (GO-CAM) to produce a network between BM steady-state conditions VSELs (SSC-VSELS) and FSH + NAM expanded VSELs (FSH + NAM VSELs). We have identified several GO biological processes regulating development, organogenesis, gene expression, signal transduction, Wnt signaling, insulin signaling, cytoskeleton organization, cell adhesion, inhibiting apoptosis, responses to extra- and intracellular stimuli, protein transport and stabilization, protein phosphorylation and ubiquitination, DNA repair, immune response, and regulation of circadian rhythm. We report that VSELs express a unique panel of proteins that only partially overlapped with the proteome of BM - derived hematopoietic stem cells (HSCs) and hematopoietic mononuclear cells (MNCs) and respond to FSH + NAM stimulation by expressing proteins involved in the development of all three germ layers. Thus, our current data supports further germ-lineage origin and multi germ layer differentiation potential of these cells.
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25
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Regulation, functions and transmission of bivalent chromatin during mammalian development. Nat Rev Mol Cell Biol 2023; 24:6-26. [PMID: 36028557 DOI: 10.1038/s41580-022-00518-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2022] [Indexed: 12/25/2022]
Abstract
Cells differentiate and progress through development guided by a dynamic chromatin landscape that mediates gene expression programmes. During development, mammalian cells display a paradoxical chromatin state: histone modifications associated with gene activation (trimethylated histone H3 Lys4 (H3K4me3)) and with gene repression (trimethylated H3 Lys27 (H3K27me3)) co-occur at promoters of developmental genes. This bivalent chromatin modification state is thought to poise important regulatory genes for expression or repression during cell-lineage specification. In this Review, we discuss recent work that has expanded our understanding of the molecular basis of bivalent chromatin and its contributions to mammalian development. We describe the factors that establish bivalency, especially histone-lysine N-methyltransferase 2B (KMT2B) and Polycomb repressive complex 2 (PRC2), and consider evidence indicating that PRC1 shapes bivalency and may contribute to its transmission between generations. We posit that bivalency is a key feature of germline and embryonic stem cells, as well as other types of stem and progenitor cells. Finally, we discuss the relevance of bivalent chromtin to human development and cancer, and outline avenues of future research.
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26
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Bilches Medinas D, Malik S, Yıldız‐Bölükbaşı E, Borgonovo J, Saaranen MJ, Urra H, Pulgar E, Afzal M, Contreras D, Wright MT, Bodaleo F, Quiroz G, Rozas P, Mumtaz S, Díaz R, Rozas C, Cabral‐Miranda F, Piña R, Valenzuela V, Uyan O, Reardon C, Woehlbier U, Brown RH, Sena‐Esteves M, Gonzalez‐Billault C, Morales B, Plate L, Ruddock LW, Concha ML, Hetz C, Tolun A. Mutation in protein disulfide isomerase A3 causes neurodevelopmental defects by disturbing endoplasmic reticulum proteostasis. EMBO J 2022; 41:e105531. [PMID: 34904718 PMCID: PMC8762563 DOI: 10.15252/embj.2020105531] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 09/23/2021] [Accepted: 10/14/2021] [Indexed: 01/19/2023] Open
Abstract
Recessive gene mutations underlie many developmental disorders and often lead to disabling neurological problems. Here, we report identification of a homozygous c.170G>A (p.Cys57Tyr or C57Y) mutation in the gene coding for protein disulfide isomerase A3 (PDIA3, also known as ERp57), an enzyme that catalyzes formation of disulfide bonds in the endoplasmic reticulum, to be associated with syndromic intellectual disability. Experiments in zebrafish embryos show that PDIA3C57Y expression is pathogenic and causes developmental defects such as axonal disorganization as well as skeletal abnormalities. Expression of PDIA3C57Y in the mouse hippocampus results in impaired synaptic plasticity and memory consolidation. Proteomic and functional analyses reveal that PDIA3C57Y expression leads to dysregulation of cell adhesion and actin cytoskeleton dynamics, associated with altered integrin biogenesis and reduced neuritogenesis. Biochemical studies show that PDIA3C57Y has decreased catalytic activity and forms disulfide-crosslinked aggregates that abnormally interact with chaperones in the endoplasmic reticulum. Thus, rare disease gene variant can provide insight into how perturbations of neuronal proteostasis can affect the function of the nervous system.
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27
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Tian M, Liu X, Lin S, Wang J, Luo S, Gao L, Chen X, Liang X, Liu Z, He N, Yi Y, Liao W. Variants in BRWD3 associated with X-linked partial epilepsy without intellectual disability. CNS Neurosci Ther 2022; 29:727-735. [PMID: 36514184 PMCID: PMC9873514 DOI: 10.1111/cns.14057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 11/23/2022] [Accepted: 11/27/2022] [Indexed: 12/15/2022] Open
Abstract
AIMS Etiology of the majority patients with idiopathic partial epilepsy (IPE) remains elusive. We thus screened the potential disease-associated variants in the patients with IPE. METHODS Trios-based whole exome sequencing was performed in a cohort of 320 patients with IPE. Frequency and molecular effects of variants were predicted. RESULTS Three novel BRWD3 variants were identified in five unrelated cases with IPE, which were four male cases and one female case. The variants included two recurrent missense variants (c.836C>T/p.Thr279Ile and c.4234A>C/p.Ile1412Leu) and one intronic variant close to splice site (c.2475 + 6A>G). The two missense variants were located in WD40 repeat domain and bromodomain, respectively. They were predicted to be damaging by silico tools and change hydrogen bonds with surrounding amino acids. The frequency of mutant alleles in this cohort was significantly higher than that in the controls of East Asian and all population of gnomAD. All these variants were inherited from the asymptomatic mothers. Four male cases presented frequent seizures at onset, while the female case only had two fever-triggered seizures. They showed good responses to valproate and lamotrigine, then finally became seizure free. All the cases had no intellectual disability. Further analysis demonstrated that all previously reported destructive variants of BRWD3 caused intellectual disability, while missense variants located in WD40 repeat domains and bromodomains of BRWD3 were associated with epilepsy. CONCLUSION BRWD3 gene is potentially associated with X-linked partial epilepsy without intellectual disability. The genotypes and locations of BRWD3 variants may explain for their phenotypic variation.
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Affiliation(s)
- Mao‐Qiang Tian
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina,Department of PediatricsAffiliated Hospital of Zunyi Medical UniversityZunyiChina
| | - Xiao‐Rong Liu
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Si‐Mei Lin
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Jie Wang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Sheng Luo
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Liang‐Di Gao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Xiao‐Bin Chen
- Department of PediatricsThe 900th Hospital of Joint Logistic Support ForceFuzhouChina
| | - Xiao‐Yu Liang
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Zhi‐Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare HospitalSouthern Medical UniversityFoshanChina
| | - Na He
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Yong‐Hong Yi
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
| | - Wei‐Ping Liao
- Institute of Neuroscience and Department of Neurology of the Second Affiliated Hospital of Guangzhou Medical UniversityKey Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of ChinaGuangzhouChina
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28
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Yoo J, Kim GW, Jeon YH, Kim JY, Lee SW, Kwon SH. Drawing a line between histone demethylase KDM5A and KDM5B: their roles in development and tumorigenesis. Exp Mol Med 2022; 54:2107-2117. [PMID: 36509829 PMCID: PMC9794821 DOI: 10.1038/s12276-022-00902-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 12/14/2022] Open
Abstract
Distinct epigenetic modifiers ensure coordinated control over genes that govern a myriad of cellular processes. Growing evidence shows that dynamic regulation of histone methylation is critical for almost all stages of development. Notably, the KDM5 subfamily of histone lysine-specific demethylases plays essential roles in the proper development and differentiation of tissues, and aberrant regulation of KDM5 proteins during development can lead to chronic developmental defects and even cancer. In this review, we adopt a unique perspective regarding the context-dependent roles of KDM5A and KDM5B in development and tumorigenesis. It is well known that these two proteins show a high degree of sequence homology, with overlapping functions. However, we provide deeper insights into their substrate specificity and distinctive function in gene regulation that at times divert from each other. We also highlight both the possibility of targeting KDM5A and KDM5B to improve cancer treatment and the limitations that must be overcome to increase the efficacy of current drugs.
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Affiliation(s)
- Jung Yoo
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Go Woon Kim
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Yu Hyun Jeon
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Ji Yoon Kim
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - Sang Wu Lee
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
| | - So Hee Kwon
- grid.15444.300000 0004 0470 5454College of Pharmacy, Yonsei Institute of Pharmaceutical Sciences, Yonsei University, Incheon, 21983 Republic of Korea
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29
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Abstract
Age is the key risk factor for diseases and disabilities of the elderly. Efforts to tackle age-related diseases and increase healthspan have suggested targeting the ageing process itself to 'rejuvenate' physiological functioning. However, achieving this aim requires measures of biological age and rates of ageing at the molecular level. Spurred by recent advances in high-throughput omics technologies, a new generation of tools to measure biological ageing now enables the quantitative characterization of ageing at molecular resolution. Epigenomic, transcriptomic, proteomic and metabolomic data can be harnessed with machine learning to build 'ageing clocks' with demonstrated capacity to identify new biomarkers of biological ageing.
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Affiliation(s)
- Jarod Rutledge
- Department of Genetics, Stanford University, Stanford, CA, USA
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
| | - Hamilton Oh
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA
- Graduate Program in Stem Cell and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Ageing, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA.
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30
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Hatch HAM, Secombe J. Molecular and cellular events linking variants in the histone demethylase KDM5C to the intellectual disability disorder Claes-Jensen syndrome. FEBS J 2022; 289:7776-7787. [PMID: 34536985 PMCID: PMC8930784 DOI: 10.1111/febs.16204] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 01/14/2023]
Abstract
The widespread availability of genetic testing for those with neurodevelopmental disorders has highlighted the importance of many genes necessary for the proper development and function of the nervous system. One gene found to be genetically altered in the X-linked intellectual disability disorder Claes-Jensen syndrome is KDM5C, which encodes a histone demethylase that regulates transcription by altering chromatin. While the genetic link between KDM5C and cognitive (dys)function is clear, how KDM5C functions to control transcriptional programs within neurons to impact their growth and activity remains the subject of ongoing research. Here, we review our current knowledge of Claes-Jensen syndrome and discuss important new data using model organisms that have revealed the importance of KDM5C in regulating aspects of neuronal development and function. Continued research into the molecular and cellular activities regulated by KDM5C is expected to provide critical etiological insights into Claes-Jensen syndrome and highlight potential targets for developing therapies to improve the quality of life of those affected.
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Affiliation(s)
- Hayden A M Hatch
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Secombe
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
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31
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Sun H, Wu M, Wang M, Zhang X, Zhu J. The regulatory role of endoplasmic reticulum chaperone proteins in neurodevelopment. Front Neurosci 2022; 16:1032607. [DOI: 10.3389/fnins.2022.1032607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/25/2022] [Indexed: 11/16/2022] Open
Abstract
The endoplasmic reticulum (ER) is the largest tubular reticular organelle spanning the cell. As the main site of protein synthesis, Ca2+ homeostasis maintenance and lipid metabolism, the ER plays a variety of essential roles in eukaryotic cells, with ER molecular chaperones participate in all these processes. In recent years, it has been reported that the abnormal expression of ER chaperones often leads to a variety of neurodevelopmental disorders (NDDs), including abnormal neuronal migration, neuronal morphogenesis, and synaptic function. Neuronal development is a complex and precisely regulated process. Currently, the mechanism by which neural development is regulated at the ER level remains under investigation. Therefore, in this work, we reviewed the recent advances in the roles of ER chaperones in neural development and developmental disorders caused by the deficiency of these molecular chaperones.
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32
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Gunne E, Lambert DM, Ward AJ, Murphy DN, Treacy EP, Lynch SA. An estimate of the cumulative paediatric prevalence of rare diseases in Ireland and comment on the literature. Eur J Hum Genet 2022; 30:1211-1215. [PMID: 35853949 PMCID: PMC9626478 DOI: 10.1038/s41431-022-01144-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/22/2022] [Accepted: 06/27/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Emer Gunne
- Children's University Hospital, Temple Street, Dublin, Republic of Ireland.
| | - Deborah M Lambert
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Republic of Ireland
| | - Alana J Ward
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Republic of Ireland
| | - Daniel N Murphy
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Republic of Ireland
| | - Eileen P Treacy
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Republic of Ireland
| | - Sally Ann Lynch
- Children's University Hospital, Temple Street, Dublin, Republic of Ireland
- National Rare Disease Office, Mater Misericordiae University Hospital, Dublin, Republic of Ireland
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33
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Jolly LA, Kumar R, Penzes P, Piper M, Gecz J. The DUB Club: Deubiquitinating Enzymes and Neurodevelopmental Disorders. Biol Psychiatry 2022; 92:614-625. [PMID: 35662507 PMCID: PMC10084722 DOI: 10.1016/j.biopsych.2022.03.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/28/2022] [Accepted: 03/28/2022] [Indexed: 02/08/2023]
Abstract
Protein ubiquitination is a widespread, multifunctional, posttranslational protein modification, best known for its ability to direct protein degradation via the ubiquitin proteasome system (UPS). Ubiquitination is also reversible, and the human genome encodes over 90 deubiquitinating enzymes (DUBs), many of which appear to target specific subsets of ubiquitinated proteins. This review focuses on the roles of DUBs in neurodevelopmental disorders (NDDs). We present the current genetic evidence connecting 12 DUBs to a range of NDDs and the functional studies implicating at least 19 additional DUBs as candidate NDD genes. We highlight how the study of DUBs in NDDs offers critical insights into the role of protein degradation during brain development. Because one of the major known functions of a DUB is to antagonize the UPS, loss of function of DUB genes has been shown to culminate in loss of abundance of its protein substrates. The identification and study of NDD DUB substrates in the developing brain is revealing that they regulate networks of proteins that themselves are encoded by NDD genes. We describe the new technologies that are enabling the full resolution of DUB protein networks in the developing brain, with the view that this knowledge can direct the development of new therapeutic paradigms. The fact that the abundance of many NDD proteins is regulated by the UPS presents an exciting opportunity to combat NDDs caused by haploinsufficiency, because the loss of abundance of NDD proteins can be potentially rectified by antagonizing their UPS-based degradation.
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Affiliation(s)
- Lachlan A Jolly
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia.
| | - Raman Kumar
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia
| | - Peter Penzes
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Michael Piper
- School of Biomedical Sciences and Queensland Brain Institute, University of Queensland, Brisbane, Queensland, Australia
| | - Jozef Gecz
- University of Adelaide and Robinson Research Institute, Adelaide, South Australia, Australia; South Australian Health and Medical Research Institute, Adelaide, South Australia, Australia
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34
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Chen Z, Luo S, Liu ZG, Deng YC, He SL, Liu XR, Yi YH, Wang J, Gao LD, Li BM, Wu ZJ, Ye ZL, Liang DH, Bian WJ, Liao WP. CELSR1 variants are associated with partial epilepsy of childhood. Am J Med Genet B Neuropsychiatr Genet 2022; 189:247-256. [PMID: 36453712 DOI: 10.1002/ajmg.b.32916] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 01/25/2022] [Accepted: 07/26/2022] [Indexed: 02/01/2023]
Abstract
CELSR1 gene, encoding cadherin EGF LAG seven-pass G-type receptor 1, is mainly expressed in neural stem cells during the embryonic period. It plays an important role in neurodevelopment. However, the relationship between CELSR1 and disease of the central nervous system has not been defined. In this study, we performed trios-based whole-exome sequencing in a cohort of 356 unrelated cases with partial epilepsy without acquired causes and identified CELSR1 variants in six unrelated cases. The variants included one de novo heterozygous nonsense variant, one de novo heterozygous missense variant, and four compound heterozygous missense variants that had one variant was located in the extracellular region and the other in the cytoplasm. The patients with biallelic variants presented severe epileptic phenotypes, whereas those with heterozygous variants were associated with a mild epileptic phenotype of benign epilepsy with centrotemporal spikes (BECTS). These variants had no or low allele frequency in the gnomAD database. The frequencies of the CELSR1 variants in this cohort were significantly higher than those in the control populations. The evidence from ClinGen Clinical-Validity Framework suggested a strong association between CELSR1 variants and epilepsy. These findings provide evidence that CELSR1 is potentially a candidate pathogenic gene of partial epilepsy of childhood.
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Affiliation(s)
- Zheng Chen
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China.,Department of Pediatrics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Sheng Luo
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Zhi-Gang Liu
- Department of Pediatrics, Affiliated Foshan Maternity and Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Yan-Chun Deng
- Department of Neurology, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
| | - Su-Li He
- Department of Pediatrics, Shantou Chaonan Minsheng Hospital, Shantou, China
| | - Xiao-Rong Liu
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Yong-Hong Yi
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Liang-Di Gao
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Bing-Mei Li
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Zhi-Jun Wu
- Department of Neurology, Second Hospital of Lanzhou University, Lanzhou University, Lanzhou, China
| | - Zi-Long Ye
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - De-Hai Liang
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Wen-Jun Bian
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
| | - Wei-Ping Liao
- Institute of Neuroscience, Department of Neurology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.,Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province, The Ministry of Education of China, Guangzhou, China
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35
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Beaumont RN, Wright CF. Estimating diagnostic noise in panel-based genomic analysis. Genet Med 2022; 24:2042-2050. [PMID: 35920826 DOI: 10.1016/j.gim.2022.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
PURPOSE Gene panels with a series of strict variant filtering rules are often used for clinical analysis of exomes and genomes. Panel sizes vary, affecting the test's sensitivity and specificity. We investigated the background rate of candidate variants in a population setting using gene panels developed to diagnose a range of heterogeneous monogenic diseases. METHODS We used the Gene2Phenotype database with the Variant Effect Predictor plugin to identify rare nonsynonymous variants in exome sequence data from 200,643 individuals in UK Biobank. We evaluated 5 clinically curated gene panels of varying sizes (50-1700 genes). RESULTS Bigger gene panels resulted in more prioritized variants, varying from an average of approximately 0.3 to 3.5 variants per person. The number of individuals with prioritized variants varied linearly with coding sequence length for monoallelic genes (∼300 individuals per 1000 base pairs) and quadratically for biallelic genes, with notable outliers. CONCLUSION Although large gene panels may be the best strategy to maximize diagnostic yield in genetically heterogeneous diseases, they frequently prioritize likely benign variants requiring follow up. Most individuals have ≥1 rare nonsynonymous variant in panels containing >500 disease genes. Extreme caution should be applied when interpreting candidate variants, particularly in the absence of relevant phenotypes.
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Affiliation(s)
- Robin N Beaumont
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, College of Medicine and Health, University of Exeter Medical School, University of Exeter, Exeter, United Kingdom.
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36
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Yuan B, Schulze KV, Assia Batzir N, Sinson J, Dai H, Zhu W, Bocanegra F, Fong CT, Holder J, Nguyen J, Schaaf CP, Yang Y, Bi W, Eng C, Shaw C, Lupski JR, Liu P. Sequencing individual genomes with recurrent genomic disorder deletions: an approach to characterize genes for autosomal recessive rare disease traits. Genome Med 2022; 14:113. [PMID: 36180924 PMCID: PMC9526336 DOI: 10.1186/s13073-022-01113-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 09/02/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND In medical genetics, discovery and characterization of disease trait contributory genes and alleles depends on genetic reasoning, study design, and patient ascertainment; we suggest a segmental haploid genetics approach to enhance gene discovery and molecular diagnostics. METHODS We constructed a genome-wide map for nonallelic homologous recombination (NAHR)-mediated recurrent genomic deletions and used this map to estimate population frequencies of NAHR deletions based on large-scale population cohorts and region-specific studies. We calculated recessive disease carrier burden using high-quality pathogenic or likely pathogenic variants from ClinVar and gnomAD. We developed a NIRD (NAHR deletion Impact to Recessive Disease) score for recessive disorders by quantifying the contribution of NAHR deletion to the overall allele load that enumerated all pairwise combinations of disease-causing alleles; we used a Punnett square approach based on an assumption of random mating. Literature mining was conducted to identify all reported patients with defects in a gene with a high NIRD score; meta-analysis was performed on these patients to estimate the representation of NAHR deletions in recessive traits from contemporary human genomics studies. Retrospective analyses of extant clinical exome sequencing (cES) were performed for novel rare recessive disease trait gene and allele discovery from individuals with NAHR deletions. RESULTS We present novel genomic insights regarding the genome-wide impact of NAHR recurrent segmental variants on recessive disease burden; we demonstrate the utility of NAHR recurrent deletions to enhance discovery in the challenging context of autosomal recessive (AR) traits and biallelic variation. Computational results demonstrate new mutations mediated by NAHR, involving recurrent deletions at 30 genomic regions, likely drive recessive disease burden for over 74% of loci within these segmental deletions or at least 2% of loci genome-wide. Meta-analyses on 170 literature-reported patients implicate that NAHR deletions are depleted from the ascertained pool of AR trait alleles. Exome reanalysis of personal genomes from subjects harboring recurrent deletions uncovered new disease-contributing variants in genes including COX10, ERCC6, PRRT2, and OTUD7A. CONCLUSIONS Our results demonstrate that genomic sequencing of personal genomes with NAHR deletions could dramatically improve allele and gene discovery and enhance clinical molecular diagnosis. Moreover, results suggest NAHR events could potentially enable human haploid genetic screens as an approach to experimental inquiry into disease biology.
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Affiliation(s)
- Bo Yuan
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA
| | - Katharina V. Schulze
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Nurit Assia Batzir
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Jefferson Sinson
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Hongzheng Dai
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Wenmiao Zhu
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | | | - Chin-To Fong
- grid.412750.50000 0004 1936 9166Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Jimmy Holder
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA
| | - Joanne Nguyen
- grid.267308.80000 0000 9206 2401Department of Pediatrics, University of Texas Health Science Center, Houston, TX USA
| | - Christian P. Schaaf
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.7700.00000 0001 2190 4373Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - Yaping Yang
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA
| | - Weimin Bi
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Christine Eng
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.510928.7Baylor Genetics, Houston, TX USA
| | - Chad Shaw
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.21940.3e0000 0004 1936 8278Department of Statistics, Rice University, Houston, TX USA
| | - James R. Lupski
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX USA ,grid.39382.330000 0001 2160 926XDepartment of Pediatrics, Baylor College of Medicine, Houston, TX USA ,grid.416975.80000 0001 2200 2638Texas Children’s Hospital, Houston, TX USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX, 77030, USA. .,Baylor Genetics, Houston, TX, USA.
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Lee T, Lee H, Kim S, Park KJ, An JY, Kim HW. Brief Report: Risk Variants Could Inform Early Neurodevelopmental Outcome in Children with Developmental Disabilities. J Autism Dev Disord 2022:10.1007/s10803-022-05735-4. [PMID: 36071318 DOI: 10.1007/s10803-022-05735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/28/2022] [Indexed: 11/30/2022]
Abstract
The aim of this study was to examine genetic variations underlying the early neurodevelopmental outcome of developmental disabilities (DDs). The study cohort consisted of 191 children with DDs. Diagnosis was assessed at baseline and at the index age (72-84 months). Exome sequencing was conducted and putative risk variants were identified. According to the diagnostic improvement, children were categorized into the improvement group (n = 19) and the non-improvement group (n = 172). Compared to the non-improvement group, the improvement group had lower number of risk variants in known DD genes and haploinsufficient genes, and lower number of overall putative risk variants. Our results may serve as a preliminary basis for developing a model that informs clinical outcome by sequencing analysis.
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Affiliation(s)
- Taeyeop Lee
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Hyeji Lee
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
| | - Soowhee Kim
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea
- Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, Republic of Korea
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, Republic of Korea
| | - Kee Jeong Park
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Joon-Yong An
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, Republic of Korea.
- Department of Integrated Biomedical and Life Science, Korea University, Seoul, Republic of Korea.
- Transdisciplinary Major in Learning Health Systems, Department of Healthcare Sciences, Graduate School, Korea University, Seoul, Republic of Korea.
- BK21FOUR R&E Center for Learning Health Systems, Korea University, Seoul, Republic of Korea.
| | - Hyo-Won Kim
- Department of Psychiatry, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea.
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38
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Zhou X, Feliciano P, Shu C, Wang T, Astrovskaya I, Hall JB, Obiajulu JU, Wright JR, Murali SC, Xu SX, Brueggeman L, Thomas TR, Marchenko O, Fleisch C, Barns SD, Snyder LG, Han B, Chang TS, Turner TN, Harvey WT, Nishida A, O'Roak BJ, Geschwind DH, Michaelson JJ, Volfovsky N, Eichler EE, Shen Y, Chung WK. Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nat Genet 2022; 54:1305-1319. [PMID: 35982159 PMCID: PMC9470534 DOI: 10.1038/s41588-022-01148-2] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 06/28/2022] [Indexed: 12/16/2022]
Abstract
To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P < 2.5 × 10-6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes (NAV3, ITSN1, SCAF1 and HNRNPUL2; n = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes (CHD8, SCN2A, ADNP, FOXP1 and SHANK3) (59% vs 88%, P = 1.9 × 10-6). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.
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Affiliation(s)
- Xueya Zhou
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Chang Shu
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | - Tianyun Wang
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Department of Medical Genetics, Center for Medical Genetics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China.,Neuroscience Research Institute, Department of Neurobiology, School of Basic Medical Sciences, Peking University Health Science Center; Key Laboratory for Neuroscience, Ministry of Education of China & National Health Commission of China, Beijing, China
| | | | | | - Joseph U Obiajulu
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA.,Department of Systems Biology, Columbia University Medical Center, New York, NY, USA
| | | | - Shwetha C Murali
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Leo Brueggeman
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | - Taylor R Thomas
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | | | | | | | - Bing Han
- Simons Foundation, New York, NY, USA
| | - Timothy S Chang
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Tychele N Turner
- Department of Genetics, Washington University, St. Louis, MO, USA
| | - William T Harvey
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Andrew Nishida
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Brian J O'Roak
- Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | | | - Jacob J Michaelson
- Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA
| | | | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University Medical Center, New York, NY, USA.,Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA. .,Simons Foundation, New York, NY, USA. .,Department of Medicine, Columbia University Medical Center, New York, NY, USA.
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39
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Boonsawat P, Horn AHC, Steindl K, Baumer A, Joset P, Kraemer D, Bahr A, Ivanovski I, Cabello EM, Papik M, Zweier M, Oneda B, Sirleto P, Burkhardt T, Sticht H, Rauch A. Assessing clinical utility of preconception expanded carrier screening regarding residual risk for neurodevelopmental disorders. NPJ Genom Med 2022; 7:45. [PMID: 35906228 PMCID: PMC9338263 DOI: 10.1038/s41525-022-00316-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/15/2022] [Indexed: 11/10/2022] Open
Abstract
The magnitude of clinical utility of preconception expanded carrier screening (ECS) concerning its potential to reduce the risk of affected offspring is unknown. Since neurodevelopmental disorders (NDDs) in their offspring is a major concern of parents-to-be, we addressed the question of residual risk by assessing the risk-reduction potential for NDDs in a retrospective study investigating ECS with different criteria for gene selection and definition of pathogenicity. We used exome sequencing data from 700 parents of children with NDDs and blindly screened for carrier-alleles in up to 3046 recessive/X-linked genes. Depending on variant pathogenicity thresholds and gene content, NDD-risk-reduction potential was up to 43.5% in consanguineous, and 5.1% in nonconsanguineous couples. The risk-reduction-potential was compromised by underestimation of pathogenicity of missense variants (false-negative-rate 4.6%), inherited copy-number variants and compound heterozygosity of one inherited and one de novo variant (0.9% each). Adherence to the ACMG recommendations of restricting ECS to high-frequency genes in nonconsanguineous couples would more than halve the detectable inherited NDD-risk. Thus, for optimized clinical utility of ECS, screening in recessive/X-linked genes regardless of their frequency (ACMG Tier-4) and sensible pathogenicity thresholds should be considered for all couples seeking ECS.
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Affiliation(s)
| | - Anselm H C Horn
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland.,Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Alessandra Baumer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pascal Joset
- Medical Genetics, University Hospital Basel, Basel, Switzerland
| | - Dennis Kraemer
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Ivan Ivanovski
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Elena M Cabello
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Michael Papik
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Markus Zweier
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Beatrice Oneda
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Pietro Sirleto
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland
| | - Tilo Burkhardt
- University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Heinrich Sticht
- Institute of Biochemistry, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Zurich, Switzerland. .,University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Harrington J, Wheway G, Willaime-Morawek S, Gibson J, Walters ZS. Pathogenic KDM5B variants in the context of developmental disorders. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194848. [PMID: 35905858 DOI: 10.1016/j.bbagrm.2022.194848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/30/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
Histone modifying enzymes are involved in the posttranslational modification of histones and the epigenetic control of gene expression. They play a critical role in normal development, and there is increasing evidence of their role in developmental disorders (DDs). DDs are a group of chronic, severe conditions that impact the physical, intellectual, language and/or behavioral development of an individual. There are very few treatment options available for DDs such that these are conditions with significant unmet clinical need. Recessive variants in the gene encoding histone modifying enzyme KDM5B are associated with a DD characterized by developmental delay, facial dysmorphism and camptodactyly. KDM5B is responsible for the demethylation of lysine 4 on the amino tail of histone 3 and plays a vital role in normal development and regulating cell differentiation. This review explores the literature on KDM5B and what is currently known about its roles in development and developmental disorders.
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Affiliation(s)
- Jack Harrington
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Gabrielle Wheway
- School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | | | - Jane Gibson
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - Zoë S Walters
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK.
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Two Genetic Mechanisms in Two Siblings with Intellectual Disability, Autism Spectrum Disorder, and Psychosis. J Pers Med 2022; 12:jpm12061013. [PMID: 35743796 PMCID: PMC9224546 DOI: 10.3390/jpm12061013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/17/2022] [Indexed: 12/04/2022] Open
Abstract
Intellectual disability (ID) and autism spectrum disorder (ASD) are complex neurodevelopmental disorders with high heritability. To search for the genetic deficits in two siblings affected with ID and ASD in a family, we first performed a genome-wide copy number variation (CNV) analysis using chromosomal microarray analysis (CMA). We found a 3.7 Mb microdeletion at 22q13.3 in the younger sister. This de novo microdeletion resulted in the haploinsufficiency of SHANK3 and several nearby genes involved in neurodevelopment disorders. Hence, she was diagnosed with Phelan–McDermid syndrome (PMS, OMIM#606232). We further performed whole-genome sequencing (WGS) analysis in this family. We did not detect pathogenic mutations with significant impacts on the phenotypes of the elder brother. Instead, we identified several rare, likely pathogenic variants in seven genes implicated in neurodevelopmental disorders: KLHL17, TDO2, TRRAP, EIF3F, ATP10A, DICER1, and CDH15. These variants were transmitted from his unaffected parents, indicating these variants have only moderate clinical effects. We propose that these variants worked together and led to the clinical phenotypes in the elder brother. We also suggest that the combination of multiple genes with moderate effects is part of the genetic mechanism of neurodevelopmental disorders.
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42
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Ojaimi MA, Banimortada BJ, Othman A, Riedhammer KM, Almannai M, El-Hattab AW. Disorders of histone methylation: molecular basis and clinical syndromes. Clin Genet 2022; 102:169-181. [PMID: 35713103 DOI: 10.1111/cge.14181] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/12/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
Epigenetic modifications of DNA and histone tails are essential for gene expression regulation. They play an essential role in neurodevelopment as nervous system development is a complex process requiring a dynamic pattern of gene expression. Histone methylation is one of the vital epigenetic regulators and mostly occurs on lysine residues of histones H3 and H4. Histone methylation is catalyzed by two sets of enzymes: histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). KMT2 enzymes form a distinct multi-subunit complex known as COMPASS to enhance their catalytic activity and diversify their biologic functions. Several neurodevelopmental syndromes result from defects of histone methylation which can be caused by deficiencies in histone methyltransferases and demethylases, loss of the histone methyltransferase activator TASP1, or derangements in COMPASS formation. In this review article, the molecular mechanism of histone methylation is discussed followed by summarizing clinical syndromes caused by monogenic defects in histone methylation.
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Affiliation(s)
- Mode Al Ojaimi
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Amna Othman
- Genetics and Genomic Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Mohammed Almannai
- Genetics and Precision Medicine Department, King Abdullah Specialized Children's Hospital, Riyadh, Saudi Arabia
| | - Ayman W El-Hattab
- College of Medicine, University of Sharjah, Sharjah, United Arab Emirates.,Pediatrics Department, University Hospital Sharjah, Sharjah, United Arab Emirates.,Genetics and Metabolic Department, KidsHeart Medical Center, Abu Dhabi, United Arab Emirates
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43
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Inherited variants in CHD3 show variable expressivity in Snijders Blok-Campeau syndrome. Genet Med 2022; 24:1283-1296. [PMID: 35346573 DOI: 10.1016/j.gim.2022.02.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
PURPOSE Common diagnostic next-generation sequencing strategies are not optimized to identify inherited variants in genes associated with dominant neurodevelopmental disorders as causal when the transmitting parent is clinically unaffected, leaving a significant number of cases with neurodevelopmental disorders undiagnosed. METHODS We characterized 21 families with inherited heterozygous missense or protein-truncating variants in CHD3, a gene in which de novo variants cause Snijders Blok-Campeau syndrome. RESULTS Computational facial and Human Phenotype Ontology-based comparisons showed that the phenotype of probands with inherited CHD3 variants overlaps with the phenotype previously associated with de novo CHD3 variants, whereas heterozygote parents are mildly or not affected, suggesting variable expressivity. In addition, similarly reduced expression levels of CHD3 protein in cells of an affected proband and of healthy family members with a CHD3 protein-truncating variant suggested that compensation of expression from the wild-type allele is unlikely to be an underlying mechanism. Notably, most inherited CHD3 variants were maternally transmitted. CONCLUSION Our results point to a significant role of inherited variation in Snijders Blok-Campeau syndrome, a finding that is critical for correct variant interpretation and genetic counseling and warrants further investigation toward understanding the broader contributions of such variation to the landscape of human disease.
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44
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Chung WK, Berg JS, Botkin JR, Brenner SE, Brosco JP, Brothers KB, Currier RJ, Gaviglio A, Kowtoniuk WE, Olson C, Lloyd-Puryear M, Saarinen A, Sahin M, Shen Y, Sherr EH, Watson MS, Hu Z. Newborn screening for neurodevelopmental diseases: Are we there yet? AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2022; 190:222-230. [PMID: 35838066 PMCID: PMC9796120 DOI: 10.1002/ajmg.c.31988] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 01/01/2023]
Abstract
In the US, newborn screening (NBS) is a unique health program that supports health equity and screens virtually every baby after birth, and has brought timely treatments to babies since the 1960's. With the decreasing cost of sequencing and the improving methods to interpret genetic data, there is an opportunity to add DNA sequencing as a screening method to facilitate the identification of babies with treatable conditions that cannot be identified in any other scalable way, including highly penetrant genetic neurodevelopmental disorders (NDD). However, the lack of effective dietary or drug-based treatments has made it nearly impossible to consider NDDs in the current NBS framework, yet it is anticipated that any treatment will be maximally effective if started early. Hence there is a critical need for large scale pilot studies to assess if and how NDDs can be effectively screened at birth, if parents desire that information, and what impact early diagnosis may have. Here we attempt to provide an overview of the recent advances in NDD treatments, explore the possible framework of setting up a pilot study to genetically screen for NDDs, highlight key technical, practical, and ethical considerations and challenges, and examine the policy and health system implications.
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Affiliation(s)
- Wendy K Chung
- Department of Pediatrics and Medicine, Columbia University, New York, New York, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jeffrey R Botkin
- Department of Pediatrics, University of Utah, Salt Lake City, Utah, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Jeffrey P Brosco
- Institute for Bioethics and Health Policy, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, Kentucky, USA
| | - Robert J Currier
- School of Medicine, University of California, San Francisco, California, USA
| | - Amy Gaviglio
- Connetics Consulting, Minneapolis, Minnesota, USA
| | | | - Colleen Olson
- Steinhardt Graduate School of Education, New York University, New York, New York, USA
| | | | | | - Mustafa Sahin
- Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yufeng Shen
- Department of Systems Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
| | - Elliott H Sherr
- Department of Neurology, Weill Institute of Neurosciences, University of California, San Francisco, California, USA
| | - Michael S Watson
- Department of Pediatrics, School of Medicine, Washington University (Adjunct), St. Louis, Missouri, USA
| | - Zhanzhi Hu
- Department of Systems Biology, Columbia University, New York, New York, USA.,Department of Biomedical Informatics, Columbia University, New York, New York, USA
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Luo S, Liu ZG, Wang J, Luo JX, Ye XG, Li X, Zhai QX, Liu XR, Wang J, Gao LD, Liu FL, Ye ZL, Li H, Gao ZF, Guo QH, Li BM, Yi YH, Liao WP. Recessive LAMA5 Variants Associated With Partial Epilepsy and Spasms in Infancy. Front Mol Neurosci 2022; 15:825390. [PMID: 35663266 PMCID: PMC9162154 DOI: 10.3389/fnmol.2022.825390] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 04/19/2022] [Indexed: 12/23/2022] Open
Abstract
Objective The LAMA5 gene encodes the laminin subunit α5, the most abundant laminin α subunit in the human brain. It forms heterotrimers with the subunit β1/β2 and γ1/γ3 and regulates neurodevelopmental processes. Genes encoding subunits of the laminin heterotrimers containing subunit α5 have been reported to be associated with human diseases. Among LAMAs encoding the laminin α subunit, LAMA1-4 have also been reported to be associated with human disease. In this study, we investigated the association between LAMA5 and epilepsy. Methods Trios-based whole-exome sequencing was performed in a cohort of 118 infants suffering from focal seizures with or without spasms. Protein modeling was used to assess the damaging effects of variations. The LAMAs expression was analyzed with data from the GTEX and VarCards databases. Results Six pairs of compound heterozygous missense variants in LAMA5 were identified in six unrelated patients. All affected individuals suffered from focal seizures with mild developmental delay, and three patients presented also spasms. These variants had no or low allele frequencies in controls and presented statistically higher frequency in the case cohort than in controls. The recessive burden analysis showed that recessive LAMA5 variants identified in this cohort were significantly more than the expected number in the East Asian population. Protein modeling showed that at least one variant in each pair of biallelic variants affected hydrogen bonds with surrounding amino acids. Among the biallelic variants in cases with only focal seizures, two variants of each pair were located in different structural domains or domains/links, whereas in the cases with spasms, the biallelic variants were constituted by two variants in the identical functional domains or both with hydrogen bond changes. Conclusion Recessive LAMA5 variants were potentially associated with infant epilepsy. The establishment of the association between LAMA5 and epilepsy will facilitate the genetic diagnosis and management in patients with infant epilepsy.
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Affiliation(s)
- Sheng Luo
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zhi-Gang Liu
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Juan Wang
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jun-Xia Luo
- Epilepsy Center, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Xing-Guang Ye
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Pediatrics, Affiliated Foshan Maternity & Child Healthcare Hospital, Southern Medical University, Foshan, China
| | - Xin Li
- Department of Pediatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Qiong-Xiang Zhai
- Department of Neurology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xiao-Rong Liu
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jie Wang
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Liang-Di Gao
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Fu-Li Liu
- Department of Neurology, The First People’s Hospital of Foshan, Foshan, China
| | - Zi-Long Ye
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Huan Li
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Zai-Fen Gao
- Epilepsy Center, Qilu Children’s Hospital of Shandong University, Jinan, China
| | - Qing-Hui Guo
- Department of Pediatrics, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Bing-Mei Li
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Yong-Hong Yi
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wei-Ping Liao
- Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, Department of Neurology, Institute of Neuroscience, Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- *Correspondence: Wei-Ping Liao,
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Wang JY, Wang J, Lu XG, Song W, Luo S, Zou DF, Hua LD, Peng Q, Tian Y, Gao LD, Liao WP, He N. Recessive PKD1 Mutations Are Associated With Febrile Seizures and Epilepsy With Antecedent Febrile Seizures and the Genotype-Phenotype Correlation. Front Mol Neurosci 2022; 15:861159. [PMID: 35620448 PMCID: PMC9128595 DOI: 10.3389/fnmol.2022.861159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/05/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveThe PKD1 encodes polycystin-1, a large transmembrane protein that plays important roles in cell proliferation, apoptosis, and cation transport. Previous studies have identified PKD1 mutations in autosomal dominant polycystic kidney disease (ADPKD). However, the expression of PKD1 in the brain is much higher than that in the kidney. This study aimed to explore the association between PKD1 and epilepsy.MethodsTrios-based whole-exome sequencing was performed in a cohort of 314 patients with febrile seizures or epilepsy with antecedent febrile seizures. The damaging effects of variants was predicted by protein modeling and multiple in silico tools. The genotype-phenotype association of PKD1 mutations was systematically reviewed and analyzed.ResultsEight pairs of compound heterozygous missense variants in PKD1 were identified in eight unrelated patients. All patients suffered from febrile seizures or epilepsy with antecedent febrile seizures with favorable prognosis. All of the 16 heterozygous variants presented no or low allele frequencies in the gnomAD database, and presented statistically higher frequency in the case-cohort than that in controls. These missense variants were predicted to be damaging and/or affect hydrogen bonding or free energy stability of amino acids. Five patients showed generalized tonic-clonic seizures (GTCS), who all had one of the paired missense mutations located in the PKD repeat domain, suggesting that mutations in the PKD domains were possibly associated with GTCS. Further analysis demonstrated that monoallelic mutations with haploinsufficiency of PKD1 potentially caused kidney disease, compound heterozygotes with superimposed effects of two missense mutations were associated with epilepsy, whereas the homozygotes with complete loss of PKD1 would be embryonically lethal.ConclusionPKD1 gene was potentially a novel causative gene of epilepsy. The genotype-phenotype relationship of PKD1 mutations suggested a quantitative correlation between genetic impairment and phenotypic variation, which will facilitate the genetic diagnosis and management in patients with PKD1 mutations.
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Affiliation(s)
- Jing-Yang Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Jie Wang
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Xin-Guo Lu
- Epilepsy Center, Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Wang Song
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Sheng Luo
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Dong-Fang Zou
- Epilepsy Center, Department of Neurology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Li-Dong Hua
- Translational Medicine Center, Guangdong Women and Children Hospital, Guangzhou, China
| | - Qian Peng
- Department of Pediatrics, Dongguan City Maternal and Child Health Hospital, Southern Medical University, Dongguan, China
| | - Yang Tian
- Department of Neurology, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Liang-Di Gao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Wei-Ping Liao
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
| | - Na He
- Department of Neurology, Institute of Neuroscience, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory of Neurogenetics and Channelopathies of the Ministry of Education of China, Guangzhou, China
- *Correspondence: Na He,
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47
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Lynch MT, Maloney KA, Pollin TI, Streeten EA, Puffenberger EG, Strauss KA, Shuldiner AR, Mitchell BD. Impact of parental relatedness on reproductive outcomes among the Old Order Amish of Lancaster County. Am J Med Genet A 2022; 188:2119-2128. [PMID: 35442562 DOI: 10.1002/ajmg.a.62757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/01/2022] [Accepted: 03/18/2022] [Indexed: 11/06/2022]
Abstract
Genetically isolated populations that arise due to recent bottleneck events have reduced genetic variation reflecting the common set of founders. Increased genetic relatedness among members of isolated populations puts them at increased risk for some recessive disorders that are rare in outbred populations. To assess the burden on reproductive health, we compared frequencies of adverse reproductive outcomes between Amish couples who were both heterozygous carriers of a highly penetrant pathogenic or likely pathogenic variant and noncarrier couples from the same Amish community. In addition, we evaluated whether overall genetic relatedness of parents was associated with reproductive outcomes. Of the 1824 couples included in our study, 11.1% were at risk of producing a child with an autosomal recessive disorder. Carrier couples reported a lower number of miscarriages compared to noncarrier couples (p = 0.02), although the number of stillbirths (p = 0.3), live births (p = 0.9), and number of pregnancies (p = 0.9) did not differ significantly between groups. In contrast, higher overall relatedness between spouses was positively correlated with number of live births (p < 0.0001), pregnancies (p < 0.0001), and stillbirths (p = 0.03), although not with the number of miscarriages (p = 0.4). These results highlight a complex association between relatedness of parents and reproductive health outcomes in this community.
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Affiliation(s)
- Megan T Lynch
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Kristin A Maloney
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Toni I Pollin
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Elizabeth A Streeten
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA
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- Regeneron Genetics Center LLC, Tarrytown, New York, USA
| | | | - Braxton D Mitchell
- Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Department of Medicine Baltimore, University of Maryland School of Medicine, Baltimore, Maryland, USA.,Geriatrics Research and Education Clinical Center, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
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48
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Perry LD, Hogg SL, Bowdin S, Ambegaonkar G, Parker AP. Fifteen-minute consultation: The efficient investigation of infantile and childhood epileptic encephalopathies in the era of modern genomics. Arch Dis Child Educ Pract Ed 2022; 107:80-87. [PMID: 33414255 DOI: 10.1136/archdischild-2020-320606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 11/05/2020] [Accepted: 12/09/2020] [Indexed: 11/03/2022]
Abstract
The investigation of children presenting with infantile and childhood epileptic encephalopathies (ICEE) is challenging due to diverse aetiologies, overlapping phenotypes and the relatively low diagnostic yield of MRI, electroencephalography (EEG) and biochemical investigations. Careful history and thorough examination remain essential as these may identify an acquired cause or indicate more targeted investigation for a genetic disorder. Whole exome sequencing (WES) with analysis of a panel of candidate epilepsy genes has increased the diagnostic yield. Whole genome sequencing (WGS), particularly as a trio with both parents' DNA, is likely to supersede WES. Modern genomic investigation impacts on the timing and necessity of other testing. We propose a structured approach for children presenting with ICEE where there is diagnostic uncertainty, emphasising the importance of WGS or, if unavailable, WES early in the investigative process. We note the importance of expert review of all investigations, including radiology, neurophysiology and biochemistry, to confirm the technique used was appropriate as well as the results. It is essential to counsel families on the risks associated with the procedures, the yield of the procedures, findings that are difficult to interpret and implication of 'negative' results. Where children remain without a diagnosis despite comprehensive investigation, we note the importance of ongoing multidisciplinary care.
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Affiliation(s)
- Luke Daniel Perry
- Developmental Neurosciences, University College London, Great Ormond Street Institute of Child Health, London, UK
| | - Sarah Louise Hogg
- Biochemical Genetics Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Sarah Bowdin
- Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Gautam Ambegaonkar
- Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Alasdair Pj Parker
- Paediatric Neurology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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49
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Davis KW, Bilancia CG, Martin M, Vanzo R, Rimmasch M, Hom Y, Uddin M, Serrano MA. NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system. Sci Rep 2022; 12:5427. [PMID: 35361823 PMCID: PMC8971396 DOI: 10.1038/s41598-022-08938-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 03/08/2022] [Indexed: 02/06/2023] Open
Abstract
To identify candidate disease genes of central nervous system (CNS) phenotypes, we created the Neurogenetic Systematic Correlation of Omics-Related Evidence (NeuroSCORE). We identified five genome-wide metrics highly associated with CNS phenotypes to score 19,601 protein-coding genes. Genes scored one point per metric (range: 0-5), identifying 8298 scored genes (scores ≥ 1) and 1601 "high scoring" genes (scores ≥ 3). Using logistic regression, we determined the odds ratio that genes with a NeuroSCORE from 1 to 5 would be associated with known CNS-related phenotypes compared to genes that scored zero. We tested NeuroSCORE using microarray copy number variants (CNVs) in case-control cohorts and aggregate mouse model data. High scoring genes are associated with CNS phenotypes (OR = 5.5, p < 2E-16), enriched in case CNVs, and mouse ortholog genes that cause behavioral and nervous system abnormalities. We identified 1058 high scoring genes with no disease association in OMIM. Transforming the logistic regression results indicates high scoring genes have an 84-92% chance of being associated with a CNS phenotype. Top scoring genes include GRIA1, MAP4K4, SF1, TNPO2, and ZSWIM8. Finally, we interrogated CNVs in the Clinical Genome Resource, finding the majority of clinically significant CNVs contain high scoring genes. These findings can direct future research and improve molecular diagnostics.
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Affiliation(s)
- Kyle W Davis
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Colleen G Bilancia
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Megan Martin
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Rena Vanzo
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Megan Rimmasch
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Yolanda Hom
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, UAE
- Cellular Intelligence (Ci) Lab, GenomeArc Inc., Toronto, ON, Canada
| | - Moises A Serrano
- Bionano Genomics, Lineagen Division, Inc., 9540 Towne Center, Dr. #100, San Diego, CA, 92121, USA.
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50
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Drosophila Model for Studying Gut Microbiota in Behaviors and Neurodegenerative Diseases. Biomedicines 2022; 10:biomedicines10030596. [PMID: 35327401 PMCID: PMC8945323 DOI: 10.3390/biomedicines10030596] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/01/2022] [Indexed: 01/14/2023] Open
Abstract
Mounting evidence indicates that the gut microbiota is linked to several physiological processes and disease development in mammals; however, the underlying mechanisms remained unexplored mostly due to the complexity of the mammalian gut microbiome. The fruit fly, Drosophila melanogaster, is a valuable animal model for studying host-gut microbiota interactions in translational aspects. The availability of powerful genetic tools and resources in Drosophila allowed the scientists to unravel the mechanisms by which the gut microbes affect fitness, health, and behavior of their hosts. Drosophila models have been extensively used not only to study animal behaviors (i.e., courtship, aggression, sleep, and learning & memory), but also some human related neurodegenerative diseases (i.e., Alzheimer’s disease and Parkinson’s disease) in the past. This review comprehensively summarizes the current understanding of the gut microbiota of Drosophila and its impact on fly behavior, physiology, and neurodegenerative diseases.
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