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Chen H, Wu Y, Zhu Y, Luo K, Zheng S, Tang H, Xuan R, Huang Y, Li J, Xiong R, Fang X, Wang L, Gong Y, Miao J, Zhou J, Tan H, Wang Y, Wu L, Ouyang J, Huang M, Yan X. Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose. Evol Appl 2024; 17:e13768. [PMID: 39175938 PMCID: PMC11340016 DOI: 10.1111/eva.13768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non-synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.
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Affiliation(s)
- Hao Chen
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yan Wu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yihao Zhu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Keyi Luo
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Sumei Zheng
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Hongbo Tang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Rui Xuan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yuxuan Huang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jiawei Li
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Rui Xiong
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Xinyan Fang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Lei Wang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yujie Gong
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Junjie Miao
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jing Zhou
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Hongli Tan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yanan Wang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Liping Wu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jing Ouyang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Min Huang
- College of Animal Sciences & TechnologyZhejiang A&F UniversityHangzhouChina
| | - Xueming Yan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
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Sorrentino U, Boesch S, Doummar D, Ravelli C, Serranova T, Indelicato E, Winkelmann J, Burglen L, Jech R, Zech M. CHD8-related disorders redefined: an expanding spectrum of dystonic phenotypes. J Neurol 2024; 271:2859-2865. [PMID: 38441608 PMCID: PMC11055771 DOI: 10.1007/s00415-024-12271-x] [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: 01/08/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 04/28/2024]
Abstract
BACKGROUND Heterozygous loss-of-function variants in CHD8 have been associated with a syndromic neurodevelopmental-disease spectrum, collectively referred to as CHD8-related neurodevelopmental disorders. Several different clinical manifestations, affecting neurodevelopmental and systemic domains, have been described, presenting with highly variable expressivity. Some expressions are well established and comprise autism spectrum disorders, psychomotor delay with cognitive impairment, postnatal overgrowth with macrocephaly, structural brain abnormalities, gastrointestinal disturbances, and behavioral and sleep-pattern problems. However, the complete phenotypic spectrum of CHD8-related disorders is still undefined. In 2021, our group described two singular female patients with CHD8-related neurodevelopmental disorder and striking dystonic manifestations, prompting the suggestion that dystonia should be considered a possible component of this condition. CASE SERIES PRESENTATION We describe three additional unrelated female individuals, each carrying a different CHD8 frameshift variant and whose clinical presentations were primarily characterized by young-onset dystonia. Their dystonic manifestations were remarkably heterogeneous and ranged from focal, exercise-dependent, apparently isolated forms to generalized permanent phenotypes accompanied by spasticity and tremor. Neurocognitive impairment and autistic behaviors, typical of CHD8-related disorders, were virtually absent or at the mild end of the spectrum. CONCLUSIONS This work validates our previous observation that dystonia is part of the phenotypic spectrum of CHD8-related neurodevelopmental disorders with potential female preponderance, raising new challenges and opportunities in the diagnosis and management of this condition. It also highlights the importance of in-depth neurologic phenotyping of patients carrying variants associated with neurodevelopmental disorders, as the connection between neurodevelopmental and movement disorders is proving closer than previously appreciated.
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Affiliation(s)
- Ugo Sorrentino
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany.
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany.
- Clinical Genetics Unit, Department of Women's and Children's Health, University of Padova, Padua, Italy.
| | - Sylvia Boesch
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Diane Doummar
- Sorbonne Université, Service de Neuropédiatrie-Pathologie du Développement, Centre de Référence Neurogénétique, Hôpital Trousseau AP-HP.SU, HU I2D2, Paris, France
| | - Claudia Ravelli
- Sorbonne Université, Service de Neuropédiatrie-Pathologie du Développement, Centre de Référence Neurogénétique, Hôpital Trousseau AP-HP.SU, HU I2D2, Paris, France
| | - Tereza Serranova
- Department of Neurology and Centre of Clinical Neuroscience, General University Hospital and First Faculty of Medicine, Charles University, Kateřinská 30, 12 800, Prague, Czech Republic
| | - Elisabetta Indelicato
- Center for Rare Movement Disorders Innsbruck, Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Juliane Winkelmann
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- DZPG, Deutsches Zentrum Für Psychische Gesundheit, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Lydie Burglen
- Cerebellar Malformations and Congenital Diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP. Sorbonne Université, Paris, France
- Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Robert Jech
- Department of Neurology and Centre of Clinical Neuroscience, General University Hospital and First Faculty of Medicine, Charles University, Kateřinská 30, 12 800, Prague, Czech Republic
| | - Michael Zech
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
- Institute of Neurogenomics, Helmholtz Munich, Neuherberg, Germany
- Institute for Advanced Study, Technical University of Munich, Garching, Germany
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3
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Lui JC, Baron J. Epigenetic Causes of Overgrowth Syndromes. J Clin Endocrinol Metab 2024; 109:312-320. [PMID: 37450557 PMCID: PMC11032252 DOI: 10.1210/clinem/dgad420] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 06/21/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Human overgrowth disorders are characterized by excessive prenatal and/or postnatal growth of various tissues. These disorders often present with tall stature, macrocephaly, and/or abdominal organomegaly and are sometimes associated with additional phenotypic abnormalities such as intellectual disability and increased cancer risk. As the genetic etiology of these disorders have been elucidated, a surprising pattern has emerged. Multiple monogenic overgrowth syndromes result from variants in epigenetic regulators: variants in histone methyltransferases NSD1 and EZH2 cause Sotos syndrome and Weaver syndrome, respectively, variants in DNA methyltransferase DNMT3A cause Tatton-Brown-Rahman syndrome, and variants in chromatin remodeler CHD8 cause an autism spectrum disorder with overgrowth. In addition, very recently, a variant in histone reader protein SPIN4 was identified in a new X-linked overgrowth disorder. In this review, we discuss the genetics of these overgrowth disorders and explore possible common underlying mechanisms by which epigenetic pathways regulate human body size.
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Affiliation(s)
- Julian C Lui
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jeffrey Baron
- Section on Growth and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
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4
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Kim C, Noh ES, Cho SY. A Korean boy with a CHD8 mutation who presented with overgrowth, intellectual disability, and autism. Ann Pediatr Endocrinol Metab 2023; 28:S12-S13. [PMID: 36731504 PMCID: PMC10783926 DOI: 10.6065/apem.2244130.065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/28/2022] [Accepted: 08/09/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Chiwoo Kim
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Eu-seon Noh
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Yoon Cho
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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5
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Davidson EA, Holingue C, Jimenez-Gomez A, Dallman JE, Moshiree B. Gastrointestinal Dysfunction in Genetically Defined Neurodevelopmental Disorders. Semin Neurol 2023; 43:645-660. [PMID: 37586397 PMCID: PMC10895389 DOI: 10.1055/s-0043-1771460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Gastrointestinal symptoms are common in most forms of neurodevelopment disorders (NDDs) such as in autism spectrum disorders (ASD). The current patient-reported outcome measures with validated questionnaires used in the general population of children without NDDS cannot be used in the autistic individuals. We explore here the multifactorial pathophysiology of ASD and the role of genetics and the environment in this disease spectrum and focus instead on possible diagnostics that could provide future objective insight into the connection of the gut-brain-microbiome in this disease entity. We provide our own data from both humans and a zebrafish model of ASD called Phelan-McDermid Syndrome. We hope that this review highlights the gaps in our current knowledge on many of these profound NDDs and that it provides a future framework upon which clinicians and researchers can build and network with other interested multidisciplinary specialties.
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Affiliation(s)
| | - Calliope Holingue
- Center for Autism and Related Disorders, Kennedy Krieger Institute, Baltimore, Maryland
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Andres Jimenez-Gomez
- Neuroscience Center, Joe DiMaggio Children’s Hospital, Hollywood, Florida
- Department of Child Neurology, Florida Atlantic University Stiles - Nicholson Brain Institute, Jupiter, Florida
| | - Julia E. Dallman
- Department of Biology, University of Miami, Coral Gables, Miami, Florida
| | - Baharak Moshiree
- Atrium Health, Wake Forest Medical University, Charlotte, North Carolina
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6
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Tabbaa M, Knoll A, Levitt P. Mouse population genetics phenocopies heterogeneity of human Chd8 haploinsufficiency. Neuron 2023; 111:539-556.e5. [PMID: 36738737 PMCID: PMC9960295 DOI: 10.1016/j.neuron.2023.01.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/13/2022] [Accepted: 01/11/2023] [Indexed: 02/05/2023]
Abstract
Preclinical models of neurodevelopmental disorders typically use single inbred mouse strains, which fail to capture the genetic diversity and symptom heterogeneity that is common clinically. We tested whether modeling genetic background diversity in mouse genetic reference panels would recapitulate population and individual differences in responses to a syndromic mutation in the high-confidence autism risk gene, CHD8. We measured clinically relevant phenotypes in >1,000 mice from 33 strains, including brain and body weights and cognition, activity, anxiety, and social behaviors, using 5 behavioral assays: cued fear conditioning, open field tests in dark and bright light, direct social interaction, and social dominance. Trait disruptions mimicked those seen clinically, with robust strain and sex differences. Some strains exhibited large effect-size trait disruptions, sometimes in opposite directions, and-remarkably-others expressed resilience. Therefore, systematically introducing genetic diversity into models of neurodevelopmental disorders provides a better framework for discovering individual differences in symptom etiologies.
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Affiliation(s)
- Manal Tabbaa
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Allison Knoll
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA
| | - Pat Levitt
- Children's Hospital Los Angeles, The Saban Research Institute, Los Angeles, CA 90027, USA; Keck School of Medicine of the University of Southern California, Los Angeles, CA 90033, USA.
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7
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Web-accessible application for identifying pathogenic transcripts with RNA-seq: Increased sensitivity in diagnosis of neurodevelopmental disorders. Am J Hum Genet 2023; 110:251-272. [PMID: 36669495 PMCID: PMC9943747 DOI: 10.1016/j.ajhg.2022.12.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
For neurodevelopmental disorders (NDDs), a molecular diagnosis is key for management, predicting outcome, and counseling. Often, routine DNA-based tests fail to establish a genetic diagnosis in NDDs. Transcriptome analysis (RNA sequencing [RNA-seq]) promises to improve the diagnostic yield but has not been applied to NDDs in routine diagnostics. Here, we explored the diagnostic potential of RNA-seq in 96 individuals including 67 undiagnosed subjects with NDDs. We performed RNA-seq on single individuals' cultured skin fibroblasts, with and without cycloheximide treatment, and used modified OUTRIDER Z scores to detect gene expression outliers and mis-splicing by exonic and intronic outliers. Analysis was performed by a user-friendly web application, and candidate pathogenic transcriptional events were confirmed by secondary assays. We identified intragenic deletions, monoallelic expression, and pseudoexonic insertions but also synonymous and non-synonymous variants with deleterious effects on transcription, increasing the diagnostic yield for NDDs by 13%. We found that cycloheximide treatment and exonic/intronic Z score analysis increased detection and resolution of aberrant splicing. Importantly, in one individual mis-splicing was found in a candidate gene nearly matching the individual's specific phenotype. However, pathogenic splicing occurred in another neuronal-expressed gene and provided a molecular diagnosis, stressing the need to customize RNA-seq. Lastly, our web browser application allowed custom analysis settings that facilitate diagnostic application and ranked pathogenic transcripts as top candidates. Our results demonstrate that RNA-seq is a complementary method in the genomic diagnosis of NDDs and, by providing accessible analysis with improved sensitivity, our transcriptome analysis approach facilitates wider implementation of RNA-seq in routine genome diagnostics.
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8
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Wang L, Wang B, Wu C, Wang J, Sun M. Autism Spectrum Disorder: Neurodevelopmental Risk Factors, Biological Mechanism, and Precision Therapy. Int J Mol Sci 2023; 24:ijms24031819. [PMID: 36768153 PMCID: PMC9915249 DOI: 10.3390/ijms24031819] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 01/19/2023] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous, behaviorally defined neurodevelopmental disorder. Over the past two decades, the prevalence of autism spectrum disorders has progressively increased, however, no clear diagnostic markers and specifically targeted medications for autism have emerged. As a result, neurobehavioral abnormalities, neurobiological alterations in ASD, and the development of novel ASD pharmacological therapy necessitate multidisciplinary collaboration. In this review, we discuss the development of multiple animal models of ASD to contribute to the disease mechanisms of ASD, as well as new studies from multiple disciplines to assess the behavioral pathology of ASD. In addition, we summarize and highlight the mechanistic advances regarding gene transcription, RNA and non-coding RNA translation, abnormal synaptic signaling pathways, epigenetic post-translational modifications, brain-gut axis, immune inflammation and neural loop abnormalities in autism to provide a theoretical basis for the next step of precision therapy. Furthermore, we review existing autism therapy tactics and limits and present challenges and opportunities for translating multidisciplinary knowledge of ASD into clinical practice.
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9
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Hayot G, Massonot M, Keime C, Faure E, Golzio C. Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balance. Life Sci Alliance 2023; 6:e202201456. [PMID: 36375841 PMCID: PMC9664244 DOI: 10.26508/lsa.202201456] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/19/2022] [Accepted: 10/21/2022] [Indexed: 11/16/2022] Open
Abstract
Individuals with mutations in CHD8 present with gastrointestinal complaints, yet the underlying mechanisms are understudied. Here, using a stable constitutive chd8 mutant zebrafish model, we found that the loss of chd8 leads to a reduced number of vagal neural crest cells (NCCs), enteric neural and glial progenitors, emigrating from the neural tube, and that their early migration capability was altered. At later stages, although the intestinal colonization by NCCs was complete, we found the decreased numbers of both serotonin-producing enterochromaffin cells and NCC-derived serotonergic neurons, suggesting an intestinal hyposerotonemia in the absence of chd8 Furthermore, transcriptomic analyses revealed an altered expression of key receptors and enzymes in serotonin and acetylcholine signaling pathways. The tissue examination of chd8 mutants revealed a thinner intestinal epithelium accompanied by an accumulation of neutrophils and the decreased numbers of goblet cells and eosinophils. Last, single-cell sequencing of whole intestines showed a global disruption of the immune balance with a perturbed expression of inflammatory interleukins and changes in immune cell clusters. Our findings propose a causal developmental link between chd8, NCC development, intestinal homeostasis, and autism-associated gastrointestinal complaints.
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Affiliation(s)
- Gaëlle Hayot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Mathieu Massonot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Céline Keime
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Elodie Faure
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
| | - Christelle Golzio
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France
- Centre National de la Recherche Scientifique, Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, Illkirch, France
- Université de Strasbourg, Strasbourg, France
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10
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The phenotypic spectrum and genotype-phenotype correlations in 106 patients with variants in major autism gene CHD8. Transl Psychiatry 2022; 12:421. [PMID: 36182950 PMCID: PMC9526704 DOI: 10.1038/s41398-022-02189-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 09/07/2022] [Accepted: 09/15/2022] [Indexed: 12/08/2022] Open
Abstract
CHD8, a major autism gene, functions in chromatin remodelling and has various roles involving several biological pathways. Therefore, unsurprisingly, previous studies have shown that intellectual developmental disorder with autism and macrocephaly (IDDAM), the syndrome caused by pathogenic variants in CHD8, consists of a broad range of phenotypic abnormalities. We collected and reviewed 106 individuals with IDDAM, including 36 individuals not previously published, thus enabling thorough genotype-phenotype analyses, involving the CHD8 mutation spectrum, characterization of the CHD8 DNA methylation episignature, and the systematic analysis of phenotypes collected in Human Phenotype Ontology (HPO). We identified 29 unique nonsense, 25 frameshift, 24 missense, and 12 splice site variants. Furthermore, two unique inframe deletions, one larger deletion (exons 26-28), and one translocation were observed. Methylation analysis was performed for 13 patients, 11 of which showed the previously established episignature for IDDAM (85%) associated with CHD8 haploinsufficiency, one analysis was inconclusive, and one showing a possible gain-of-function signature instead of the expected haploinsufficiency signature was observed. Consistent with previous studies, phenotypical abnormalities affected multiple organ systems. Many neurological abnormalities, like intellectual disability (68%) and hypotonia (29%) were observed, as well as a wide variety of behavioural abnormalities (88%). Most frequently observed behavioural problems included autism spectrum disorder (76%), short attention span (32%), abnormal social behaviour (31%), sleep disturbance (29%) and impaired social interactions (28%). Furthermore, abnormalities in the digestive (53%), musculoskeletal (79%) and genitourinary systems (18%) were noted. Although no significant difference in severity was observed between males and females, individuals with a missense variant were less severely affected. Our study provides an extensive review of all phenotypic abnormalities in patients with IDDAM and provides clinical recommendations, which will be of significant value to individuals with a pathogenic variant in CHD8, their families, and clinicians as it gives a more refined insight into the clinical and molecular spectrum of IDDAM, which is essential for accurate care and counselling.
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11
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Hardcastle A, Berry AM, Campbell IM, Zhao X, Liu P, Gerard AE, Rosenfeld JA, Sisoudiya SD, Hernandez-Garcia A, Loddo S, Di Tommaso S, Novelli A, Dentici ML, Capolino R, Digilio MC, Graziani L, Rustad CF, Neas K, Ferrero GB, Brusco A, Di Gregorio E, Wellesley D, Beneteau C, Joubert M, Van Den Bogaert K, Boogaerts A, McMullan DJ, Dean J, Giuffrida MG, Bernardini L, Varghese V, Shannon NL, Harrison RE, Lam WWK, McKee S, Turnpenny PD, Cole T, Morton J, Eason J, Jones MC, Hall R, Wright M, Horridge K, Shaw CA, Chung WK, Scott DA. Identifying phenotypic expansions for congenital diaphragmatic hernia plus (CDH+) using DECIPHER data. Am J Med Genet A 2022; 188:2958-2968. [PMID: 35904974 PMCID: PMC9474674 DOI: 10.1002/ajmg.a.62919] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/28/2022] [Accepted: 07/10/2022] [Indexed: 01/31/2023]
Abstract
Congenital diaphragmatic hernia (CDH) can occur in isolation or in conjunction with other birth defects (CDH+). A molecular etiology can only be identified in a subset of CDH cases. This is due, in part, to an incomplete understanding of the genes that contribute to diaphragm development. Here, we used clinical and molecular data from 36 individuals with CDH+ who are cataloged in the DECIPHER database to identify genes that may play a role in diaphragm development and to discover new phenotypic expansions. Among this group, we identified individuals who carried putatively deleterious sequence or copy number variants affecting CREBBP, SMARCA4, UBA2, and USP9X. The role of these genes in diaphragm development was supported by their expression in the developing mouse diaphragm, their similarity to known CDH genes using data from a previously published and validated machine learning algorithm, and/or the presence of CDH in other individuals with their associated genetic disorders. Our results demonstrate how data from DECIPHER, and other public databases, can be used to identify new phenotypic expansions and suggest that CREBBP, SMARCA4, UBA2, and USP9X play a role in diaphragm development.
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Affiliation(s)
- Amy Hardcastle
- Department of Microbiology and Molecular Biology, College of Life Sciences, Brigham Young University, Provo, UT, USA
| | - Aliska M. Berry
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Ian M. Campbell
- Division of Human Genetics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Xiaonan Zhao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Baylor Genetics, Houston, TX, USA
| | - Amanda E. Gerard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
| | - Jill A. Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Saumya D. Sisoudiya
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Sara Loddo
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Silvia Di Tommaso
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Translational Cytogenomics Research Unit, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
| | - Maria L. Dentici
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Maria C. Digilio
- Medical Genetics Unit, Academic Department of Pediatrics, Bambino Gesù Children’s Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Ludovico Graziani
- Genetics and Rare Disease Research Division, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
- Medical Genetics Unit, Tor Vergata Hospital, Rome, Italy
| | - Cecilie F. Rustad
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | | | - Giovanni B. Ferrero
- Department of Clinical and Biological Sciences, University of Torino, Orbassano, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Torino, Italy
- Città della Salute e della Scienza University Hospital, Torino, Italy
| | | | - Diana Wellesley
- Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, Hampshire, UK
- University Hospital Southampton, Southampton, Hampshire, UK
| | - Claire Beneteau
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Madeleine Joubert
- Nantes Université, CHU de Nantes, UF 9321 de Fœtopathologie et Génétique, Nantes, France
| | - Kris Van Den Bogaert
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Anneleen Boogaerts
- Center for Human Genetics, University Hospitals Leuven–KU Leuven, Leuven, Belgium
| | - Dominic J. McMullan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, UK
| | - John Dean
- Clinical Genetics Service, Ashgrove House, NHS Grampian, Aberdeen, UK
| | - Maria G. Giuffrida
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Laura Bernardini
- Medical Genetics Unit, Fondazione IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | | | - Nora L Shannon
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Rachel E. Harrison
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Wayne W. K. Lam
- South East of Scotland Clinical Genetics Service, Western General Hospital, Edinburgh, Scotland
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast, UK
| | - Peter D. Turnpenny
- Clinical Genetics Department, Royal Devon and Exeter Hospital, Exeter, UK
| | - Trevor Cole
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics Unit, Birmingham Women’s Hospital, Birmingham, UK
| | - Jacqueline Eason
- Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Marilyn C. Jones
- University of California, San Diego and Rady Children’s Hospital, San Diego, CA, USA
| | - Rebecca Hall
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Michael Wright
- The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Karen Horridge
- South Tyneside and Sunderland NHS Foundation Trust, Sunderland, UK
| | - Chad A. Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wendy K. Chung
- Department of Pediatrics, Columbia University, New York, NY, USA
- Department of Medicine, Columbia University, New York, NY, USA
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Texas Children’s Hospital, Houston, TX, USA
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX, USA
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12
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Velmans C, O'Donnell-Luria AH, Argilli E, Tran Mau-Them F, Vitobello A, Chan MC, Fung JLF, Rech M, Abicht A, Aubert Mucca M, Carmichael J, Chassaing N, Clark R, Coubes C, Denommé-Pichon AS, de Dios JK, England E, Funalot B, Gerard M, Joseph M, Kennedy C, Kumps C, Willems M, van de Laar IMBH, Aarts-Tesselaar C, van Slegtenhorst M, Lehalle D, Leppig K, Lessmeier L, Pais LS, Paterson H, Ramanathan S, Rodan LH, Superti-Furga A, Chung BHY, Sherr E, Netzer C, Schaaf CP, Erger F. O'Donnell-Luria-Rodan syndrome: description of a second multinational cohort and refinement of the phenotypic spectrum. J Med Genet 2022; 59:697-705. [PMID: 34321323 DOI: 10.1136/jmedgenet-2020-107470] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 07/02/2021] [Indexed: 12/29/2022]
Abstract
BACKGROUND O'Donnell-Luria-Rodan syndrome (ODLURO) is an autosomal-dominant neurodevelopmental disorder caused by pathogenic, mostly truncating variants in KMT2E. It was first described by O'Donnell-Luria et al in 2019 in a cohort of 38 patients. Clinical features encompass macrocephaly, mild intellectual disability (ID), autism spectrum disorder (ASD) susceptibility and seizure susceptibility. METHODS Affected individuals were ascertained at paediatric and genetic centres in various countries by diagnostic chromosome microarray or exome/genome sequencing. Patients were collected into a case cohort and were systematically phenotyped where possible. RESULTS We report 18 additional patients from 17 families with genetically confirmed ODLURO. We identified 15 different heterozygous likely pathogenic or pathogenic sequence variants (14 novel) and two partial microdeletions of KMT2E. We confirm and refine the phenotypic spectrum of the KMT2E-related neurodevelopmental disorder, especially concerning cognitive development, with rather mild ID and macrocephaly with subtle facial features in most patients. We observe a high prevalence of ASD in our cohort (41%), while seizures are present in only two patients. We extend the phenotypic spectrum by sleep disturbances. CONCLUSION Our study, bringing the total of known patients with ODLURO to more than 60 within 2 years of the first publication, suggests an unexpectedly high relative frequency of this syndrome worldwide. It seems likely that ODLURO, although just recently described, is among the more common single-gene aetiologies of neurodevelopmental delay and ASD. We present the second systematic case series of patients with ODLURO, further refining the mutational and phenotypic spectrum of this not-so-rare syndrome.
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Affiliation(s)
- Clara Velmans
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Anne H O'Donnell-Luria
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Emanuela Argilli
- Brain Development Research Program, Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Frederic Tran Mau-Them
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Antonio Vitobello
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Marcus Cy Chan
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Jasmine Lee-Fong Fung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Megan Rech
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Marion Aubert Mucca
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, Midi-Pyrénées, France
| | - Jason Carmichael
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Nicolas Chassaing
- Department of Medical Genetics, University Hospital Centre Toulouse, Toulouse, Midi-Pyrénées, France
| | - Robin Clark
- Pediatrics Specialty Clinics, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Christine Coubes
- Department of Medical Genetics, University Hospital Center Montpellier, Montpellier, Languedoc-Roussillon, France
| | - Anne-Sophie Denommé-Pichon
- UFR Des Sciences de Santé, INSERM UMR1231 GAD Génétique des Anomalies du Développement, FHU-TRANSLAD, Université de Bourgogne, Dijon, Bourgogne, France.,Unité Fonctionnelle d'Innovation diagnostique des maladies rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - John Karl de Dios
- Department of Medical Genetics, Dayton Children's Hospital, Dayton, Ohio, USA
| | - Eleina England
- Center for Mendelian Genomics and Medical and Population Genetics Program, Broad Institute, Cambridge, Massachusetts, USA
| | - Benoit Funalot
- Department of Clinical Genetics, Hopital Henri Mondor, Creteil, Île-de-France, France
| | - Marion Gerard
- Service de Génétique, Centre Hospitalier Universitaire de Caen, Caen, Basse-Normandie, France
| | - Maries Joseph
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Colleen Kennedy
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, California, USA
| | - Camille Kumps
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, VD, Switzerland
| | - Marjolaine Willems
- Medical Genetic Department for Rare Diseases and Personalized Medicine, Reference Center AD SOOR, AnDDI-RARE, Groupe DI, Inserm U1298, Montpellier University, Centre Hospitalier Universitaire de Montpellier, Montpellier, France
| | - Ingrid M B H van de Laar
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Marjon van Slegtenhorst
- Department of Clinical Genetics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Daphné Lehalle
- Department of Clinical Genetics, Hopital Henri Mondor, Creteil, Île-de-France, France
| | - Kathleen Leppig
- Genetic Services, Kaiser Permanente Washington, Seattle, Washington, USA
| | - Lennart Lessmeier
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Lynn S Pais
- Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts, USA
| | - Heather Paterson
- Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, Massachusetts, USA.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Subhadra Ramanathan
- Pediatrics Specialty Clinics, Loma Linda University Medical Center, Loma Linda, California, USA
| | - Lance H Rodan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Andrea Superti-Furga
- Division of Genetic Medicine, Lausanne University Hospital, Lausanne, VD, Switzerland
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, Hong Kong, Hong Kong
| | - Elliott Sherr
- Brain Development Research Program, Department of Neurology, University of California San Francisco Division of Hospital Medicine, San Francisco, California, USA
| | - Christian Netzer
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
| | - Christian P Schaaf
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.,Institute of Human Genetics, Heidelberg University, Heidelberg, Baden-Württemberg, Germany.,Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas, USA
| | - Florian Erger
- Institute of Human Genetics, University Hospital Cologne, Cologne, Nordrhein-Westfalen, Germany
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13
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Garavaglia B, Vallian S, Romito LM, Straccia G, Capecci M, Invernizzi F, Andrenelli E, Kazemi A, Boesch S, Kopajtich R, Olfati N, Shariati M, Shoeibi A, Sadr-Nabavi A, Prokisch H, Winkelmann J, Zech M. AOPEP variants as a novel cause of recessive dystonia: Generalized dystonia and dystonia-parkinsonism. Parkinsonism Relat Disord 2022; 97:52-56. [PMID: 35306330 DOI: 10.1016/j.parkreldis.2022.03.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/16/2022]
Abstract
INTRODUCTION The genetic basis of autosomal-recessive dystonia remains poorly understood. Our objective was to report identification of additional individuals with variants in AOPEP, a recently described gene for recessively inherited dystonic disorders (OMIM:619565). METHODS Ongoing analysis on a high-throughput genetic platform and international case-recruitment efforts were undertaken. RESULTS Novel biallelic, likely pathogenic loss-of-function alleles were identified in two pedigrees of different ethnic background. Two members of a consanguineous Iranian family shared a homozygous c.1917-1G>A essential splice-site variant and featured presentations of adolescence-onset generalized dystonia. An individual of Chinese descent, homozygous for the nonsense variant c.1909G>T (p.Glu637*), displayed childhood-onset generalized dystonia combined with later-manifesting parkinsonism. One additional Iranian patient with adolescence-onset generalized dystonia carried an ultrarare, likely protein-damaging homozygous missense variant (c.1201C>T [p.Arg401Trp]). CONCLUSIONS These findings support the implication of AOPEP in recessive forms of generalized dystonia and dystonia-parkinsonism. Biallelic AOPEP variants represent a worldwide cause of dystonic movement-disorder phenotypes and should be considered in dystonia molecular testing approaches.
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Affiliation(s)
- Barbara Garavaglia
- Department of Diagnostic and Technology, Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico "C.Besta", Milan, Italy
| | - Sadeq Vallian
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Islamic Republic of Iran
| | - Luigi M Romito
- Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico "C.Besta", Milan, Italy
| | - Giulia Straccia
- Department of Clinical Neurosciences, Parkinson and Movement Disorders Unit, Fondazione IRCCS Istituto Neurologico "C.Besta", Milan, Italy
| | - Marianna Capecci
- Department of Experimental and Clinical Medicine, Neurorehabilitation Clinic, University Hospital "Ospedali Riuniti di Ancona", "Politecnica delle Marche" University, Ancona, Italy
| | - Federica Invernizzi
- Department of Diagnostic and Technology, Medical Genetics and Neurogenetics Unit, Fondazione IRCCS Istituto Neurologico "C.Besta", Milan, Italy
| | - Elisa Andrenelli
- Department of Experimental and Clinical Medicine, Neurorehabilitation Clinic, University Hospital "Ospedali Riuniti di Ancona", "Politecnica delle Marche" University, Ancona, Italy
| | - Arezu Kazemi
- Department of Cell and Molecular Biology and Microbiology, Faculty of Science and Technology, University of Isfahan, Isfahan, Islamic Republic of Iran
| | - Sylvia Boesch
- Department of Neurology, Medical University of Innsbruck, Innsbruck, Austria
| | - Robert Kopajtich
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Technical University of Munich, School of Medicine, Institute of Human Genetics, Munich, Germany
| | - Nahid Olfati
- Department of Neurology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohammad Shariati
- Department of Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Qaem Medical Center, Mashhad, Iran; Academic Center for Education, Culture and Research (ACECR)-Khorasan Razavi, Mashhad, Iran
| | - Ali Shoeibi
- Department of Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Qaem Medical Center, Mashhad, Iran
| | - Ariane Sadr-Nabavi
- Department of Neurology, Faculty of Medicine, Mashhad University of Medical Sciences, Qaem Medical Center, Mashhad, Iran; Academic Center for Education, Culture and Research (ACECR)-Khorasan Razavi, Mashhad, Iran; Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Holger Prokisch
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Technical University of Munich, School of Medicine, Institute of Human Genetics, Munich, Germany
| | - Juliane Winkelmann
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Technical University of Munich, School of Medicine, Institute of Human Genetics, Munich, Germany; Lehrstuhl für Neurogenetik, Technische Universität München, Munich, Germany; Munich Cluster for Systems Neurology, SyNergy, Munich, Germany
| | - Michael Zech
- Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany; Technical University of Munich, School of Medicine, Institute of Human Genetics, Munich, Germany.
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14
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Zarantonello G, Arnoldi M, Filosi M, Tebaldi T, Spirito G, Barbieri A, Gustincich S, Sanges R, Domenici E, Di Leva F, Biagioli M. Natural SINEUP RNAs in Autism Spectrum Disorders: RAB11B-AS1 Dysregulation in a Neuronal CHD8 Suppression Model Leads to RAB11B Protein Increase. Front Genet 2021; 12:745229. [PMID: 34880900 PMCID: PMC8647803 DOI: 10.3389/fgene.2021.745229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 10/20/2021] [Indexed: 11/26/2022] Open
Abstract
CHD8 represents one of the highest confidence genetic risk factors implied in Autism Spectrum Disorders, with most mutations leading to CHD8 haploinsufficiency and the insurgence of specific phenotypes, such as macrocephaly, facial dysmorphisms, intellectual disability, and gastrointestinal complaints. While extensive studies have been conducted on the possible consequences of CHD8 suppression and protein coding RNAs dysregulation during neuronal development, the effects of transcriptional changes of long non-coding RNAs (lncRNAs) remain unclear. In this study, we focused on a peculiar class of natural antisense lncRNAs, SINEUPs, that enhance translation of a target mRNA through the activity of two RNA domains, an embedded transposable element sequence and an antisense region. By looking at dysregulated transcripts following CHD8 knock down (KD), we first identified RAB11B-AS1 as a potential SINEUP RNA for its domain configuration. Then we demonstrated that such lncRNA is able to increase endogenous RAB11B protein amounts without affecting its transcriptional levels. RAB11B has a pivotal role in vesicular trafficking, and mutations on this gene correlate with intellectual disability and microcephaly. Thus, our study discloses an additional layer of molecular regulation which is altered by CHD8 suppression. This represents the first experimental confirmation that naturally occurring SINEUP could be involved in ASD pathogenesis and underscores the importance of dysregulation of functional lncRNAs in neurodevelopment.
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Affiliation(s)
- Giulia Zarantonello
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michele Arnoldi
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Michele Filosi
- Laboratory of Neurogenomic Biomarkers, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Toma Tebaldi
- Section of Hematology, Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, United States.,Laboratory of RNA and Disease Data Science, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Giovanni Spirito
- Laboratory of Computational Genomics, Area of Neuroscience, International School of Advanced Studies (SISSA), Trieste, Italy.,Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Anna Barbieri
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Stefano Gustincich
- Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Remo Sanges
- Laboratory of Computational Genomics, Area of Neuroscience, International School of Advanced Studies (SISSA), Trieste, Italy.,Central RNA Laboratory, Italian Institute of Technology (IIT), Genova, Italy
| | - Enrico Domenici
- Laboratory of Neurogenomic Biomarkers, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy.,Fondazione The Microsoft Research - University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Francesca Di Leva
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Marta Biagioli
- Laboratory of Neuroepigenetics, Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
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15
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Rosenberg AGW, Pater MRA, Pellikaan K, Davidse K, Kattentidt-Mouravieva AA, Kersseboom R, Bos-Roubos AG, van Eeghen A, Veen JMC, van der Meulen JJ, van Aalst-van Wieringen N, Hoekstra FME, van der Lely AJ, de Graaff LCG. What Every Internist-Endocrinologist Should Know about Rare Genetic Syndromes in Order to Prevent Needless Diagnostics, Missed Diagnoses and Medical Complications: Five Years of 'Internal Medicine for Rare Genetic Syndromes'. J Clin Med 2021; 10:jcm10225457. [PMID: 34830739 PMCID: PMC8622899 DOI: 10.3390/jcm10225457] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 11/11/2021] [Accepted: 11/17/2021] [Indexed: 02/06/2023] Open
Abstract
Patients with complex rare genetic syndromes (CRGS) have combined medical problems affecting multiple organ systems. Pediatric multidisciplinary (MD) care has improved life expectancy, however, transfer to internal medicine is hindered by the lack of adequate MD care for adults. We have launched an MD outpatient clinic providing syndrome-specific care for adults with CRGS, which, to our knowledge, is the first one worldwide in the field of internal medicine. Between 2015 and 2020, we have treated 720 adults with over 60 syndromes. Eighty-nine percent of the syndromes were associated with endocrine problems. We describe case series of missed diagnoses and patients who had undergone extensive diagnostic testing for symptoms that could actually be explained by their syndrome. Based on our experiences and review of the literature, we provide an algorithm for the clinical approach of health problems in CRGS adults. We conclude that missed diagnoses and needless invasive tests seem common in CRGS adults. Due to the increased life expectancy, an increasing number of patients with CRGS will transfer to adult endocrinology. Internist-endocrinologists (in training) should be aware of their special needs and medical pitfalls of CRGS will help prevent the burden of unnecessary diagnostics and under- and overtreatment.
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Affiliation(s)
- Anna G. W. Rosenberg
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
- Dutch Center of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Minke R. A. Pater
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
| | - Karlijn Pellikaan
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
- Dutch Center of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | - Kirsten Davidse
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
- Dutch Center of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
| | | | - Rogier Kersseboom
- Stichting Zuidwester, 3241 LB Middelharnis, The Netherlands; (A.A.K.-M.); (R.K.)
| | - Anja G. Bos-Roubos
- Center of Excellence for Neuropsychiatry, Vincent van Gogh, 5803 DN Venray, The Netherlands;
| | - Agnies van Eeghen
- ‘s Heeren Loo, Care Group, 3818 LA Amersfoort, The Netherlands;
- Department of Pediatrics, Amsterdam University Medical Center, 1105 AZ Amsterdam, The Netherlands
- Academic Center for Growth Disorders, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - José M. C. Veen
- ‘s Heeren Loo, Care Providing Agency, 6733 SC Wekerom, The Netherlands; (J.M.C.V.); (J.J.v.d.M.)
| | - Jiske J. van der Meulen
- ‘s Heeren Loo, Care Providing Agency, 6733 SC Wekerom, The Netherlands; (J.M.C.V.); (J.J.v.d.M.)
| | - Nina van Aalst-van Wieringen
- Department of Physical Therapy, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands;
| | - Franciska M. E. Hoekstra
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
- Department of Internal Medicine, Reinier de Graaf Hospital, 2625 AD Delft, The Netherlands
| | - Aart J. van der Lely
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
| | - Laura C. G. de Graaff
- Department of Internal Medicine, Division of Endocrinology, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands; (A.G.W.R.); (M.R.A.P.); (K.P.); (K.D.); (F.M.E.H.); (A.J.v.d.L.)
- Dutch Center of Reference for Prader-Willi Syndrome, 3015 GD Rotterdam, The Netherlands
- Academic Center for Growth Disorders, Erasmus MC, University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
- ENCORE—Dutch Center of Reference for Neurodevelopmental Disorders, 3015 GD Rotterdam, The Netherlands
- Dutch Center of Reference for Turner Syndrome, 3015 GD Rotterdam, The Netherlands
- Dutch Center of Reference for Disorders of Sex Development, 3015 GD Rotterdam, The Netherlands
- Correspondence:
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16
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Wade AA, van den Ameele J, Cheetham SW, Yakob R, Brand AH, Nord AS. In vivo targeted DamID identifies CHD8 genomic targets in fetal mouse brain. iScience 2021; 24:103234. [PMID: 34746699 PMCID: PMC8551073 DOI: 10.1016/j.isci.2021.103234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/11/2021] [Accepted: 10/04/2021] [Indexed: 01/15/2023] Open
Abstract
Genetic studies of autism have revealed causal roles for chromatin remodeling gene mutations. Chromodomain helicase DNA binding protein 8 (CHD8) encodes a chromatin remodeler with significant de novo mutation rates in sporadic autism. However, relationships between CHD8 genomic function and autism-relevant biology remain poorly elucidated. Published studies utilizing ChIP-seq to map CHD8 protein-DNA interactions have high variability, consistent with technical challenges and limitations associated with this method. Thus, complementary approaches are needed to establish CHD8 genomic targets and regulatory functions in developing brain. We used in utero CHD8 Targeted DamID followed by sequencing (TaDa-seq) to characterize CHD8 binding in embryonic mouse cortex. CHD8 TaDa-seq reproduced interaction patterns observed from ChIP-seq and further highlighted CHD8 distal interactions associated with neuronal loci. This study establishes TaDa-seq as a useful alternative for mapping protein-DNA interactions in vivo and provides insights into the regulatory targets of CHD8 and autism-relevant pathophysiology associated with CHD8 mutations.
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Affiliation(s)
- A. Ayanna Wade
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
| | - Jelle van den Ameele
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Seth W. Cheetham
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Rebecca Yakob
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Andrea H. Brand
- The Gurdon Institute and Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, CB2 1TN, UK
| | - Alex S. Nord
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA 95616, USA
- Department of Neurobiology, Physiology and Behavior, University of California, Davis, Davis, CA 95616, USA
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17
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Ciptasari U, van Bokhoven H. The phenomenal epigenome in neurodevelopmental disorders. Hum Mol Genet 2021; 29:R42-R50. [PMID: 32766754 PMCID: PMC7530535 DOI: 10.1093/hmg/ddaa175] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 07/16/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Disruption of chromatin structure due to epimutations is a leading genetic etiology of neurodevelopmental disorders, collectively known as chromatinopathies. We show that there is an increasing level of convergence from the high diversity of genes that are affected by mutations to the molecular networks and pathways involving the respective proteins, the disrupted cellular and subcellular processes, and their consequence for higher order cellular network function. This convergence is ultimately reflected by specific phenotypic features shared across the various chromatinopathies. Based on these observations, we propose that the commonly disrupted molecular and cellular anomalies might provide a rational target for the development of symptomatic interventions for defined groups of genetically distinct neurodevelopmental disorders.
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Affiliation(s)
- Ummi Ciptasari
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands.,Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behavior, Radboud university medical center, 6500 HB Nijmegen, The Netherlands
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18
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Doummar D, Treven M, Qebibo L, Devos D, Ghoumid J, Ravelli C, Kranz G, Krenn M, Demailly D, Cif L, Davion JB, Zimprich F, Burglen L, Zech M. Childhood-onset progressive dystonia associated with pathogenic truncating variants in CHD8. Ann Clin Transl Neurol 2021; 8:1986-1990. [PMID: 34415117 PMCID: PMC8528468 DOI: 10.1002/acn3.51444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/06/2021] [Accepted: 08/06/2021] [Indexed: 12/28/2022] Open
Abstract
Originally described as a risk factor for autism, CHD8 loss‐of‐function variants have recently been associated with a wider spectrum of neurodevelopmental abnormalities. We further expand the CHD8‐related phenotype with the description of two unrelated patients who presented with childhood‐onset progressive dystonia. Whole‐exome sequencing conducted in two independent laboratories revealed a CHD8 nonsense variant in one patient and a frameshift variant in the second. The patients had strongly overlapping phenotypes characterized by generalized dystonia with mild‐to‐moderate neurodevelopmental comorbidity. Deep brain stimulation led to clinical improvement in both cases. We suggest that CHD8 should be added to the growing list of neurodevelopmental disorder‐associated genes whose mutations can also result in dystonia‐dominant phenotypes.
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Affiliation(s)
- Diane Doummar
- Pediatric Neurology Department, Movement Disorders Center, Armand Trousseau Hospital, AP-HP.Sorbonne Université, Paris, France
| | - Marco Treven
- Department of Neurology, Medical University of Vienna, Vienna, Austria.,Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, 3400, Austria
| | - Leila Qebibo
- Cerebellar Malformations and Congenital diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP.Sorbonne Université, Paris, France
| | - David Devos
- Université de Lille, INSERM, U1172, CHU-Lille, Lille, France.,Neuroscience Cognition Research Centre, Lille, France.,Neurology and Movement Disorders Department, CHU Lille, Licend, Lille, 59000, France
| | - Jamal Ghoumid
- CHU Lille, University of Lille, ULR7364 RADEME, Lille, France
| | - Claudia Ravelli
- Pediatric Neurology Department, Movement Disorders Center, Armand Trousseau Hospital, AP-HP.Sorbonne Université, Paris, France
| | | | - Martin Krenn
- Department of Neurology, Medical University of Vienna, Vienna, Austria.,School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany
| | - Diane Demailly
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | - Laura Cif
- Département de Neurochirurgie, Unité des Pathologies Cérébrales Résistantes, Unité de Recherche sur les Comportements et Mouvements Anormaux, Hôpital Gui de Chauliac, Centre Hospitalier Régional Montpellier, Montpellier, France.,Faculté de médecine, Université de Montpellier, France
| | | | - Fritz Zimprich
- Department of Neurology, Medical University of Vienna, Vienna, Austria
| | - Lydie Burglen
- Cerebellar Malformations and Congenital diseases Reference Center and Neurogenetics Lab, Department of Genetics, Armand Trousseau Hospital, AP-HP.Sorbonne Université, Paris, France.,Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, Paris, France
| | - Michael Zech
- School of Medicine, Institute of Human Genetics, Technical University of Munich, Munich, Germany.,Institute of Neurogenomics, Helmholtz Zentrum München, Munich, Germany
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19
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Weissberg O, Elliott E. The Mechanisms of CHD8 in Neurodevelopment and Autism Spectrum Disorders. Genes (Basel) 2021; 12:genes12081133. [PMID: 34440307 PMCID: PMC8393912 DOI: 10.3390/genes12081133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Chromodomain-helicase-DNA-binding protein 8 (CHD8) has been identified as one of the genes with the strongest association with autism. The CHD8 protein is a transcriptional regulator that is expressed in nearly all cell types and has been implicated in multiple cellular processes, including cell cycle, cell adhesion, neuronal development, myelination, and synaptogenesis. Considering the central role of CHD8 in the genetics of autism, a deeper understanding of the physiological functions of CHD8 is important to understand the development of the autism phenotype and potential therapeutic targets. Different CHD8 mutant mouse models were developed to determine autism-like phenotypes and to fully understand their mechanisms. Here, we review the current knowledge on CHD8, with an emphasis on mechanistic lessons gained from animal models that have been studied.
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20
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Moirangthem A, Mandal K, Saxena D, Srivastava P, Gambhir PS, Agrawal N, Shambhavi A, Nampoothiri S, Phadke SR. Genetic heterogeneity of disorders with overgrowth and intellectual disability: Experience from a center in North India. Am J Med Genet A 2021; 185:2345-2355. [PMID: 33942996 DOI: 10.1002/ajmg.a.62241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/25/2021] [Accepted: 04/10/2021] [Indexed: 12/24/2022]
Abstract
Overgrowth, defined as height and/or OFC ≥ +2SD, characterizes a subset of patients with syndromic intellectual disability (ID). Many of the disorders with overgrowth and ID (OGID) are rare and the full phenotypic and genotypic spectra have not been unraveled. This study was undertaken to characterize the phenotypic and genotypic profile of patients with OGID. Patients with OGID were ascertained from the cohort of patients who underwent cytogenetic microarray (CMA) and/or exome sequencing (ES) at our center over a period of 6 years. Thirty-one subjects (six females) formed the study group with ages between 3.5 months and 13 years. CMA identified pathogenic deletions in two patients. In another 11 patients, a disease causing variant was detected by ES. The spectrum of disorders encompassed aberrations in genes involved in the two main pathways associated with OGID. These were genes involved in epigenetic regulation like NSD1, NFIX, FOXP1, and those in the PI3K-AKT pathway like PTEN, AKT3, TSC2, PPP2R5D. Five novel pathogenic variants were added by this study. NSD1-related Sotos syndrome was the most common disorder, seen in five patients. A causative variant was identified in 61.5% of patients who underwent only ES compared to the low yield of 11.1% in the CMA group. The molecular etiology could be confirmed in 13 subjects with OGID giving a diagnostic yield of 42%. The major burden was formed by autosomal dominant monogenic disorders. Hence, ES maybe a better first-tier genomic test rather than CMA in OGID.
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Affiliation(s)
- Amita Moirangthem
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Kausik Mandal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Deepti Saxena
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Priyanka Srivastava
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Poonam Singh Gambhir
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Neha Agrawal
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Arya Shambhavi
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
| | - Sheela Nampoothiri
- Department of Pediatric Genetics, Amrita Institute of Medical Sciences & Research Centre, AIMS, Cochin, Kerala, India
| | - Shubha R Phadke
- Department of Medical Genetics, Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh, India
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21
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Hoffmann A, Spengler D. Single-Cell Transcriptomics Supports a Role of CHD8 in Autism. Int J Mol Sci 2021; 22:3261. [PMID: 33806835 PMCID: PMC8004931 DOI: 10.3390/ijms22063261] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 03/16/2021] [Accepted: 03/20/2021] [Indexed: 12/16/2022] Open
Abstract
Chromodomain helicase domain 8 (CHD8) is one of the most frequently mutated and most penetrant genes in the autism spectrum disorder (ASD). Individuals with CHD8 mutations show leading symptoms of autism, macrocephaly, and facial dysmorphisms. The molecular and cellular mechanisms underpinning the early onset and development of these symptoms are still poorly understood and prevent timely and more efficient therapies of patients. Progress in this area will require an understanding of "when, why and how cells deviate from their normal trajectories". High-throughput single-cell RNA sequencing (sc-RNAseq) directly quantifies information-bearing RNA molecules that enact each cell's biological identity. Here, we discuss recent insights from sc-RNAseq of CRISPR/Cas9-editing of Chd8/CHD8 during mouse neocorticogenesis and human cerebral organoids. Given that the deregulation of the balance between excitation and inhibition (E/I balance) in cortical and subcortical circuits is thought to represent a major etiopathogenetic mechanism in ASD, we focus on the question of whether, and to what degree, results from current sc-RNAseq studies support this hypothesis. Beyond that, we discuss the pros and cons of these approaches and further steps to be taken to harvest the full potential of these transformative techniques.
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Affiliation(s)
| | - Dietmar Spengler
- Translational Research in Psychiatry, Max Planck Institute of Psychiatry, 80804 Munich, Germany;
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22
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Hoffmann A, Spengler D. Chromatin Remodeler CHD8 in Autism and Brain Development. J Clin Med 2021; 10:366. [PMID: 33477995 PMCID: PMC7835889 DOI: 10.3390/jcm10020366] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/14/2021] [Accepted: 01/14/2021] [Indexed: 12/14/2022] Open
Abstract
Chromodomain Helicase DNA-binding 8 (CHD8) is a high confidence risk factor for autism spectrum disorders (ASDs) and the genetic cause of a distinct neurodevelopmental syndrome with the core symptoms of autism, macrocephaly, and facial dysmorphism. The role of CHD8 is well-characterized at the structural, biochemical, and transcriptional level. By contrast, much less is understood regarding how mutations in CHD8 underpin altered brain function and mental disease. Studies on various model organisms have been proven critical to tackle this challenge. Here, we scrutinize recent advances in this field with a focus on phenotypes in transgenic animal models and highlight key findings on neurodevelopment, neuronal connectivity, neurotransmission, synaptic and homeostatic plasticity, and habituation. Against this backdrop, we further discuss how to improve future animal studies, both in terms of technical issues and with respect to the sex-specific effects of Chd8 mutations for neuronal and higher-systems level function. We also consider outstanding questions in the field including 'humanized' mice models, therapeutic interventions, and how the use of pluripotent stem cell-derived cerebral organoids might help to address differences in neurodevelopment trajectories between model organisms and humans.
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Affiliation(s)
| | - Dietmar Spengler
- Department of Translational Research in Psychiatry, Max-Planck Institute of Psychiatry, 80804 Munich, Germany;
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23
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Yamada M, Yamaguchi Y, Uehara T, Yagihashi T, Kosaki K. Heterozygous nonsense variant of CHD8 in a patient with forme-fruste Marfan syndrome and intellectual disability. Congenit Anom (Kyoto) 2021; 61:30-32. [PMID: 32951261 DOI: 10.1111/cga.12393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/06/2020] [Accepted: 09/13/2020] [Indexed: 11/27/2022]
Affiliation(s)
- Mamiko Yamada
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Yu Yamaguchi
- Department of Clinical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Tomoko Uehara
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Tatsuhiko Yagihashi
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
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24
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Vaisfeld A, Spartano S, Gobbi G, Vezzani A, Neri G. Chromosome 14 deletions, rings, and epilepsy genes: A riddle wrapped in a mystery inside an enigma. Epilepsia 2020; 62:25-40. [PMID: 33205446 DOI: 10.1111/epi.16754] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022]
Abstract
The ring 14 syndrome is a rare condition caused by the rearrangement of one chromosome 14 into a ring-like structure. The formation of the ring requires two breakpoints and loss of material from the short and long arms of the chromosome. Like many other chromosome syndromes, it is characterized by multiple congenital anomalies and developmental delays. Typical of the condition are retinal anomalies and drug-resistant epilepsy. These latter manifestations are not found in individuals who are carriers of comparable 14q deletions without formation of a ring (linear deletions). To find an explanation for this apparent discrepancy and gain insight into the mechanisms leading to seizures, we reviewed and compared literature cases of both ring and linear deletion syndrome with respect to both their clinical manifestations and the role and function of potentially epileptogenic genes. Knowledge of the epilepsy-related genes in chromosome 14 is an important premise for the search of new and effective drugs to combat seizures. Current clinical and molecular evidence is not sufficient to explain the known discrepancies between ring and linear deletions.
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Affiliation(s)
- Alessandro Vaisfeld
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Serena Spartano
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy
| | - Giuseppe Gobbi
- Residential Center for Rehabilitation Luce Sul Mare, Rimini, Italy
| | - Annamaria Vezzani
- Department of Neuroscience, IRCCS-Istituto di Ricerche Farmacologiche Mario Negri, Milano, Italy
| | - Giovanni Neri
- Institute of Genomic Medicine, Catholic University School of Medicine, Rome, Italy.,J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
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25
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Jiménez JA, Ptacek TS, Tuttle AH, Schmid RS, Moy SS, Simon JM, Zylka MJ. Chd8 haploinsufficiency impairs early brain development and protein homeostasis later in life. Mol Autism 2020; 11:74. [PMID: 33023670 PMCID: PMC7537101 DOI: 10.1186/s13229-020-00369-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022] Open
Abstract
Background Chromodomain helicase DNA-binding protein 8 (Chd8) is a high-confidence risk gene for autism spectrum disorder (ASD). However, how Chd8 haploinsufficiency impairs gene expression in the brain and impacts behavior at different stages of life is unknown. Methods We generated a mutant mouse line with an ASD-linked loss-of-function mutation in Chd8 (V986*; stop codon mutation). We examined the behavior of Chd8 mutant mice along with transcriptional changes in the cerebral cortex as a function of age, with a focus on one embryonic (E14.5) and three postnatal ages (1, 6, and 12 months). Results Chd8V986*/+ mutant mice displayed macrocephaly, reduced rearing responses and reduced center time in the open field, and enhanced social novelty preference. Behavioral phenotypes were more evident in Chd8V986*/+ mutant mice at 1 year of age. Pup survival was reduced in wild-type x Chd8V986*/+ crosses when the mutant parent was female. Transcriptomic analyses indicated that pathways associated with synaptic and neuronal projections and sodium channel activity were reduced in the cortex of embryonic Chd8V986*/+ mice and then equalized relative to wild-type mice in the postnatal period. At 12 months of age, expression of genes associated with endoplasmic reticulum (ER) stress, chaperone-mediated protein folding, and the unfolded protein response (UPR) were reduced in Chd8V986*/+ mice, whereas genes associated with the c-MET signaling pathway were increased in expression. Limitations It is unclear whether the transcriptional changes observed with age in Chd8V986*/+ mice reflect a direct effect of CHD8-regulated gene expression, or if CHD8 indirectly affects the expression of UPR/ER stress genes in adult mice as a consequence of neurodevelopmental abnormalities. Conclusions Collectively, these data suggest that UPR/ER stress pathways are reduced in the cerebral cortex of aged Chd8V986*/+ mice. Our study uncovers neurodevelopmental and age-related phenotypes in Chd8V986*/+ mice and highlights the importance of controlling for age when studying Chd8 haploinsufficient mice.
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Affiliation(s)
- Jessica A Jiménez
- Curriculum in Toxicology & Environmental Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Travis S Ptacek
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alex H Tuttle
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ralf S Schmid
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sheryl S Moy
- Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Psychiatry, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy M Simon
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.,Department of Genetics, The University of North Carolina at Chapel Hill, Campus Box #7264, Chapel Hill, NC, 27599, USA
| | - Mark J Zylka
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Carolina Institute for Developmental Disabilities, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA. .,Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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26
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Pierson TM, Otero MG, Grand K, Choi A, Graham JM, Young JI, Mackay JP. The NuRD complex and macrocephaly associated neurodevelopmental disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:548-556. [PMID: 31737996 DOI: 10.1002/ajmg.c.31752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.
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Affiliation(s)
- Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Maria G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew Choi
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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