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St John M, Tripathi T, Morgan AT, Amor DJ. To speak may draw on epigenetic writing and reading: Unravelling the complexity of speech and language outcomes across chromatin-related neurodevelopmental disorders. Neurosci Biobehav Rev 2023; 152:105293. [PMID: 37353048 DOI: 10.1016/j.neubiorev.2023.105293] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/11/2023] [Accepted: 06/20/2023] [Indexed: 06/25/2023]
Abstract
Speech and language development are complex neurodevelopmental processes that are incompletely understood, yet current evidence suggests that speech and language disorders are prominent in those with disorders of chromatin regulation. This review aimed to unravel what is known about speech and language outcomes for individuals with chromatin-related neurodevelopmental disorders. A systematic literature search following PRISMA guidelines was conducted on 70 chromatin genes, to identify reports of speech/language outcomes across studies, including clinical reports, formal subjective measures, and standardised/objective measures. 3932 studies were identified and screened and 112 were systematically reviewed. Communication impairment was core across chromatin disorders, and specifically, chromatin writers and readers appear to play an important role in motor speech development. Identification of these relationships is important because chromatin disorders show promise as therapeutic targets due to the capacity for epigenetic modification. Further research is required using standardised and formal assessments to understand the nuanced speech/language profiles associated with variants in each gene, and the influence of chromatin dysregulation on the neurobiology of speech and language development.
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Affiliation(s)
- Miya St John
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia.
| | - Tanya Tripathi
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia.
| | - Angela T Morgan
- Speech and Language, Murdoch Children's Research Institute, Parkville, VIC, Australia; Department of Audiology and Speech Pathology, University of Melbourne, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia.
| | - David J Amor
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Parkville, VIC, Australia; Speech Genomics Clinic, Royal Children's Hospital, Parkville, VIC, Australia; Department of Paediatrics, University of Melbourne, VIC, Australia.
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Li S, Li H, Liu D, Xing Q, Chen X, Zhang H, Wen J, Zhu H, Liang D, Li Z, Wu L. Identification of novel mendelian disorders of the epigenetic machinery (MDEMs) associated functional mutations and neurodevelopmental disorders. QJM 2023; 116:355-364. [PMID: 36625521 DOI: 10.1093/qjmed/hcad005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/01/2023] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Mendelian disorders of the epigenetic machinery (MDEMs) are a newly identified group of neurodevelopmental disorders (NDDs) and multiple congenital anoMalies caused by mutations in genes encoding components of the epigenetic machinery. Many studies have shown that MDEM-associated mutations may disrupt the balance between chromatin states and trigger dysplasia. AIM To help eight Chinese families with neurodevelopmental disorders acquire a definitive diagnosis. METHODS In this study, we used whole-exome sequencing (WES) to diagnose eight unrelated Chinese families with NDDs. We also verified the potential pathogenic variants by Sanger sequencing and analyzed the changes in gene expression along with histone methylation modifications. RESULTS Eight variants of six epigenetic machinery genes were identified, six of which were novel. Six variants were pathogenic (P) or likely pathogenic (LP), while two novel missense variants (c.5113T>C in CHD1 and c.10444C>T in KMT2D) were classified to be variants of uncertain significance (VUS). Further functional studies verified that c.5113T>C in CHD1 results in decreased protein levels and increased chromatin modifications (H3K27me3). In addition, c.10444C>T in KMT2D led to a significant decrease in mRNA transcription and chromatin modifications (H3K4me1). Based on experimental evidence, these two VUS variants could be classified as LP. CONCLUSION This study provided a definitive diagnosis of eight families with NDDs and expanded the mutation spectrum of MDEMs, enriching the pathogenesis study of variants in epigenetic machinery genes.
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Affiliation(s)
- Shun Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Huijuan Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Dihua Liu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Qin Xing
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Xin Chen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Hongyun Zhang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Juan Wen
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Huimin Zhu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Desheng Liang
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
- Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, 410078, China
| | - Zhuo Li
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
| | - Lingqian Wu
- Center for Medical Genetics, Hunan Key Laboratory of Medical Genetics & Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, 410078, China
- Laboratory of Molecular Genetics, Hunan Jiahui Genetics Hospital, Changsha, 410078, China
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Shen R, Li Y, Liang A, Li S, Yang C, Huang H. A female case with novel KDM5C heterozygous variation presenting with Claes-Jensen type-like phonotype. BMC Neurol 2022; 22:491. [PMID: 36536324 PMCID: PMC9762001 DOI: 10.1186/s12883-022-03023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 12/10/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Lysine(K)-specific demethylase 5C (KDM5C) dysfunction causes X-linked syndromic intellectual developmental disorder Claes-Jensen type in male patients. The clinical presentations of female individuals with heterozygous KDM5C variations vary widely and are only now beginning to be characterized in detail. CASE PRESENTATION Herein, we identified a novel de novo heterozygous nonsense variation of KDM5C (c.3533C > A, p.S1178X) in a sporadic 4-year-old Chinese girl, who presented with Claes-Jensen type-like phenotypes, such as moderate developmental delay, serious expressive language delay, short stature, microcephaly, and typical facial particularities. Moreover, X-chromosome inactivation (XCI) analysis showed no significant skewed X-inactivation. CONCLUSION The report expands the genotype of KDM5C variation in female patients, delineates the phenotype of affected females in this well-known X-linked disorder, and also reinforces the necessity to consider this X-linked gene, KDM5C, in sporadic female patients.
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Affiliation(s)
- Ruiyun Shen
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Yanyang Li
- grid.256922.80000 0000 9139 560XPediatric Department, Huaihe Hospital of Henan University, Kaifeng, 475000 China
| | - Aiming Liang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Shijie Li
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Chenlu Yang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
| | - Hongmei Huang
- grid.411609.b0000 0004 1758 4735Child Health Care Center, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, 100045 China
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Expanding the Spectrum of KDM5C Neurodevelopmental Disorder: A Novel De Novo Stop Variant in a Young Woman and Emerging Genotype-Phenotype Correlations. Genes (Basel) 2022; 13:genes13122266. [PMID: 36553533 PMCID: PMC9778367 DOI: 10.3390/genes13122266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/25/2022] [Accepted: 11/29/2022] [Indexed: 12/05/2022] Open
Abstract
As a consequence of the implementation of NGS technologies, the diagnostic yield of neurodevelopmental disorders has dramatically increased during the past two decades. Among neurodevelopmental genes, transcription-related genes and chromatin remodeling genes are the most represented category of disease-causing genes. Indeed, the term "chromatinopathies" is now widely used to describe epigenetic disorders caused by mutations in these genes. We hereby describe a twenty-seven-year-old female patient diagnosed with moderate intellectual disability comorbid with other neuropsychiatric and behavioral issues carrying a de novo heterozygous stop variant in the KDM5C gene (NM_004187.5: c. 3847G>T, p.Glu1283*), encoding a histone demethylase that specifically acts on the H3K4 lysines. The gene is located on the X chromosome and has been associated with Claes-Jensen-type intellectual disability, an X-linked syndromic disorder. We discuss our case in relation to previously reported affected females harboring pathogenic mutations in the KDM5C gene with the objective of delineating genotype-phenotype correlations and further defining a common recognizable phenotype. We also highlight the importance of reverse phenotyping in relation to whole-exome sequencing results.
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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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Wu PM, Yu WH, Chiang CW, Wu CY, Chen JS, Tu YF. Novel Variations in the KDM5C Gene Causing X-Linked Intellectual Disability. Neurol Genet 2021; 8:e646. [PMID: 34877407 PMCID: PMC8641966 DOI: 10.1212/nxg.0000000000000646] [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: 04/27/2021] [Accepted: 10/13/2021] [Indexed: 11/15/2022]
Abstract
Background and Objectives To investigate the pathogenicity of 2 novel KDM5C variations, report the clinical and neuroimaging findings, and review the available literature. Methods Physical examinations, structural neuroimaging studies, and exome sequence analysis were performed. KDM5C constructs were used to study the effect of the variations in transfected cells. Results We identified 2 novel variations c.2233C>G and c.3392_3393delAG in the KDM5C gene harboring from 2 Chinese families with X-linked intellectual disability (ID). The affected male patients exhibited severe ID, short stature, and facial dysmorphism. The 1 with c.3392_3393delAG additionally had epilepsy and autistic spectrum disorder (ASD). Transiently transfected mutant KDM5C constructs both reduced protein expression and stability and decreased histone demethylase activities in cells. Reviewing the available literature, we found that the associated ASD tended to occur in patients with variations near the C-terminus of KDM5C. Discussion We report the clinical, molecular genetic, and pathologic features in patients with novel variations of KDM5C. The variability of the clinical phenotype in addition to an ID may associate with altered particular parts of KDM5C.
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Affiliation(s)
- Po-Ming Wu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Hao Yu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chi-Wu Chiang
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Yu Wu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jia-Shing Chen
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Fang Tu
- Department of Pediatrics (P.-M.W., W.-H.Y., C.-Y.W., Y.-F.T.), National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan; School of Medicine for International Students (J.-S.C.), I-Shou University, Kaohsiung; Institute of Clinical Medicine (W.-H.Y., Y.-F.T.), College of Medicine, National Cheng Kung University, Tainan; Institute of Molecular Medicine (C.-W.C.), College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Aref-Eshghi E, Kerkhof J, Pedro VP, Barat-Houari M, Ruiz-Pallares N, Andrau JC, Lacombe D, Van-Gils J, Fergelot P, Dubourg C, Cormier-Daire V, Rondeau S, Lecoquierre F, Saugier-Veber P, Nicolas G, Lesca G, Chatron N, Sanlaville D, Vitobello A, Faivre L, Thauvin-Robinet C, Laumonnier F, Raynaud M, Alders M, Mannens M, Henneman P, Hennekam RC, Velasco G, Francastel C, Ulveling D, Ciolfi A, Pizzi S, Tartaglia M, Heide S, Héron D, Mignot C, Keren B, Whalen S, Afenjar A, Bienvenu T, Campeau PM, Rousseau J, Levy MA, Brick L, Kozenko M, Balci TB, Siu VM, Stuart A, Kadour M, Masters J, Takano K, Kleefstra T, de Leeuw N, Field M, Shaw M, Gecz J, Ainsworth PJ, Lin H, Rodenhiser DI, Friez MJ, Tedder M, Lee JA, DuPont BR, Stevenson RE, Skinner SA, Schwartz CE, Genevieve D, Sadikovic B, Sadikovic B. Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders. Am J Hum Genet 2020; 106:356-370. [PMID: 32109418 DOI: 10.1016/j.ajhg.2020.01.019] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/27/2020] [Indexed: 01/24/2023] Open
Abstract
Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called "episignatures"). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bekim Sadikovic
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada.
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