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Almansoori S, Alsters SI, Yiorkas AM, Nor Hashim NA, Walters RG, Chahal HS, Purkayastha S, Lessan N, Blakemore AIF. Oligogenic inheritance in severe adult obesity. Int J Obes (Lond) 2024; 48:815-820. [PMID: 38297031 PMCID: PMC11129943 DOI: 10.1038/s41366-024-01476-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 11/13/2023] [Accepted: 01/17/2024] [Indexed: 02/02/2024]
Abstract
BACKGROUND/OBJECTIVE The genetic architecture of extreme non-syndromic obesity in adults remains to be elucidated. A range of genes are known to cause monogenic obesity, but even when pathogenic mutations are present, there may be variable penetrance. METHODS Whole-exome sequencing (WES) was carried out on a 15-year-old male proband of Pakistani ancestry who had severe obesity. This was followed by family segregation analysis, using Sanger sequencing. We also undertook re-analysis of WES data from 91 unrelated adults with severe obesity (86% white European ancestry) from the Personalised Medicine for Morbid Obesity (PMMO) cohort, recruited from the UK National Health Service. RESULTS We identified an oligogenic mode of inheritance of obesity in the proband's family-this provided the impetus to reanalyze existing sequence data in a separate dataset. Analysis of PMMO participant data revealed two further patients who carried more than one rare, predicted-deleterious mutation in a known monogenic obesity gene. In all three cases, the genes involved had known autosomal dominant inheritance, with incomplete penetrance. CONCLUSION Oligogenic inheritance may explain some of the variable penetrance in Mendelian forms of obesity. We caution clinicians and researchers to avoid confining sequence analysis to individual genes and, in particular, not to stop looking when the first potentially-causative mutation is found.
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Affiliation(s)
- Sumaya Almansoori
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK.
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai Healthcare City, Dubai, United Arab Emirates.
- Genome Center, Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates.
| | - Suzanne I Alsters
- South West Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Andrianos M Yiorkas
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
| | - Nikman Adli Nor Hashim
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, Kuala Lumpur, 50603, Malaysia
- Centre for Drug Research in Systems Biology, Structural Bioinformatics and Human Digital Imaging (CRYSTAL), Universiti Malaya, Kuala Lumpur, 50603, Malaysia
| | - Robin G Walters
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, University of Oxford, Oxford, UK
| | - Harvinder S Chahal
- Imperial Weight Centre, Imperial College Healthcare NHS Trust, St Mary's Hospital, Praed Street, London, W2 1NY, UK
- Section of Investigative Medicine, Division of Diabetes, Endocrinology and Metabolism, Imperial College London, Hammersmith Campus, Hammersmith Hospital, 6th Floor Commonwealth Building, Du Cane Road, London, W12 0NN, UK
| | | | - Nader Lessan
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Imperial College London Diabetes Centre Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Alexandra I F Blakemore
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, London, UK
- College of Medicine, Nursing, and Health Science, University of Galway, Galway, Republic of Ireland
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Zhang Y, Ahsan MU, Wang K. Noncoding de novo mutations in SCN2A are associated with autism spectrum disorders. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.05.24306908. [PMID: 38766206 PMCID: PMC11100849 DOI: 10.1101/2024.05.05.24306908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Coding de novo mutations (DNMs) contribute to the risk for autism spectrum disorders (ASD), but the contribution of noncoding DNMs remains relatively unexplored. Here we use whole genome sequencing (WGS) data of 12,411 individuals (including 3,508 probands and 2,218 unaffected siblings) from 3,357 families collected in Simons Foundation Powering Autism Research for Knowledge (SPARK) to detect DNMs associated with ASD, while examining Simons Simplex Collection (SSC) with 6383 individuals from 2274 families to replicate the results. For coding DNMs, SCN2A reached exome-wide significance (p=2.06×10-11) in SPARK. The 618 known dominant ASD genes as a group are strongly enriched for coding DNMs in cases than sibling controls (fold change=1.51, p =1.13×10-5 for SPARK; fold change=1.86, p =2.06×10-9 for SSC). For noncoding DNMs, we used two methods to assess statistical significance: a point-based test that analyzes sites with a Combined Annotation Dependent Depletion (CADD) score ≥15, and a segment-based test that analyzes 1kb genomic segments with segment-specific background mutation rates (inferred from expected rare mutations in Gnocchi genome constraint scores). The point-based test identified SCN2A as marginally significant (p=6.12×10-4) in SPARK, yet segment-based test identified CSMD1, RBFOX1 and CHD13 as exome-wide significant. We did not identify significant enrichment of noncoding DNMs (in all 1kb segments or those with Gnocchi>4) in the 618 known ASD genes as a group in cases than sibling controls. When combining evidence from both coding and noncoding DNMs, we found that SCN2A with 11 coding and 5 noncoding DNMs exhibited the strongest significance (p=4.15×10-13). In summary, we identified both coding and noncoding DNMs in SCN2A associated with ASD, while nominating additional candidates for further examination in future studies.
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Affiliation(s)
- Yuan Zhang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mian Umair Ahsan
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kai Wang
- Raymond G. Perelman Center for Cellular and Molecular Therapeutics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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3
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Landis BJ, Helvaty LR, Geddes GC, Lin JI, Yatsenko SA, Lo CW, Border WL, Wechsler SB, Murali CN, Azamian MS, Lalani SR, Hinton RB, Garg V, McBride KL, Hodge JC, Ware SM. A Multicenter Analysis of Abnormal Chromosomal Microarray Findings in Congenital Heart Disease. J Am Heart Assoc 2023; 12:e029340. [PMID: 37681527 PMCID: PMC10547279 DOI: 10.1161/jaha.123.029340] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 05/24/2023] [Indexed: 09/09/2023]
Abstract
Background Chromosomal microarray analysis (CMA) provides an opportunity to understand genetic causes of congenital heart disease (CHD). The methods for describing cardiac phenotypes in patients with CMA abnormalities have been inconsistent, which may complicate clinical interpretation of abnormal testing results and hinder a more complete understanding of genotype-phenotype relationships. Methods and Results Patients with CHD and abnormal clinical CMA were accrued from 9 pediatric cardiac centers. Highly detailed cardiac phenotypes were systematically classified and analyzed for their association with CMA abnormality. Hierarchical classification of each patient into 1 CHD category facilitated broad analyses. Inclusive classification allowing multiple CHD types per patient provided sensitive descriptions. In 1363 registry patients, 28% had genomic disorders with well-recognized CHD association, 67% had clinically reported copy number variants (CNVs) with rare or no prior CHD association, and 5% had regions of homozygosity without CNV. Hierarchical classification identified expected CHD categories in genomic disorders, as well as uncharacteristic CHDs. Inclusive phenotyping provided sensitive descriptions of patients with multiple CHD types, which occurred commonly. Among CNVs with rare or no prior CHD association, submicroscopic CNVs were enriched for more complex types of CHD compared with large CNVs. The submicroscopic CNVs that contained a curated CHD gene were enriched for left ventricular obstruction or septal defects, whereas CNVs containing a single gene were enriched for conotruncal defects. Neuronal-related pathways were over-represented in single-gene CNVs, including top candidate causative genes NRXN3, ADCY2, and HCN1. Conclusions Intensive cardiac phenotyping in multisite registry data identifies genotype-phenotype associations in CHD patients with abnormal CMA.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chaya N. Murali
- Baylor College of MedicineHoustonTX
- Texas Children’s HospitalHoustonTX
| | | | - Seema R. Lalani
- Baylor College of MedicineHoustonTX
- Texas Children’s HospitalHoustonTX
| | | | - Vidu Garg
- Nationwide Children’s HospitalThe Ohio State UniversityColumbusOH
| | - Kim L. McBride
- Nationwide Children’s HospitalThe Ohio State UniversityColumbusOH
- University of CalgaryCalgaryCanada
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4
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Epstein RJ, Lin FPY, Brink RA, Blackburn J. Synonymous alterations of cancer-associated Trp53 CpG mutational hotspots cause fatal developmental jaw malocclusions but no tumors in knock-in mice. PLoS One 2023; 18:e0284327. [PMID: 37053216 PMCID: PMC10101519 DOI: 10.1371/journal.pone.0284327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 03/28/2023] [Indexed: 04/14/2023] Open
Abstract
Intragenic CpG dinucleotides are tightly conserved in evolution yet are also vulnerable to methylation-dependent mutation, raising the question as to why these functionally critical sites have not been deselected by more stable coding sequences. We previously showed in cell lines that altered exonic CpG methylation can modify promoter start sites, and hence protein isoform expression, for the human TP53 tumor suppressor gene. Here we extend this work to the in vivo setting by testing whether synonymous germline modifications of exonic CpG sites affect murine development, fertility, longevity, or cancer incidence. We substituted the DNA-binding exons 5-8 of Trp53, the mouse ortholog of human TP53, with variant-CpG (either CpG-depleted or -enriched) sequences predicted to encode the normal p53 amino acid sequence; a control construct was also created in which all non-CpG sites were synonymously substituted. Homozygous Trp53-null mice were the only genotype to develop tumors. Mice with variant-CpG Trp53 sequences remained tumor-free, but were uniquely prone to dental anomalies causing jaw malocclusion (p < .0001). Since the latter phenotype also characterises murine Rett syndrome due to dysfunction of the trans-repressive MeCP2 methyl-CpG-binding protein, we hypothesise that CpG sites may exert non-coding phenotypic effects via pre-translational cis-interactions of 5-methylcytosine with methyl-binding proteins which regulate mRNA transcript initiation, expression or splicing, although direct effects on mRNA structure or translation are also possible.
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Affiliation(s)
- Richard J Epstein
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - Frank P Y Lin
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Centre for Clinical Genomics, The Kinghorn Cancer Centre, Sydney, Australia
| | - Robert A Brink
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
| | - James Blackburn
- University of New South Wales, St Vincent's Hospital Campus, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
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5
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Bhatia M, Cavalleri GL, White M, Delanty N, Sweeney BJ, Costello DJ, Greally MT, Benson KA. Germline mosaicism in a family with MBD5 haploinsufficiency. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006253. [PMID: 36396431 PMCID: PMC9808559 DOI: 10.1101/mcs.a006253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 11/16/2022] [Indexed: 11/18/2022] Open
Abstract
Haploinsufficiency of the methyl-CpG-binding domain protein 5 (MBD5) gene causes a neurodevelopmental disorder that includes intellectual disability, developmental delay, speech impairment, seizures, sleep disturbances, and behavioral difficulties. Microdeletion of 2q23.1 is the most common cause of haploinsufficiency, although MBD5 haploinsufficiency may also cause this genetic disorder. We report a family harboring a heterozygous loss-of-function variant in MBD5 (NM_018328.5:c.728delC; p.Pro243Hisfs*26), which includes three affected siblings with varying phenotypic features. Both parents were phenotypically normal but deep coverage sequencing of the parents showed germline mosaicism in the mother.
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Affiliation(s)
- Mehak Bhatia
- School of Medicine, Royal College of Surgeons in Ireland, Dublin, DO2 VN51, Ireland
| | - Gianpiero L. Cavalleri
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, DO2 VN51, Ireland;,FutureNeuro Research Centre, Dublin, DO2 VN51, Ireland
| | - Máire White
- FutureNeuro Research Centre, Dublin, DO2 VN51, Ireland
| | - Norman Delanty
- School of Medicine, Royal College of Surgeons in Ireland, Dublin, DO2 VN51, Ireland;,FutureNeuro Research Centre, Dublin, DO2 VN51, Ireland;,Department of Neurology, Beaumont Hospital, Dublin, DO9 DK19, Ireland
| | - Brian J. Sweeney
- Epilepsy Service, Cork University Hospital and College of Medicine and Health, University Hospital Cork, Cork, T12 YE02, Ireland
| | - Daniel J. Costello
- Epilepsy Service, Cork University Hospital and College of Medicine and Health, University Hospital Cork, Cork, T12 YE02, Ireland
| | - Marie T. Greally
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, DO2 VN51, Ireland;,FutureNeuro Research Centre, Dublin, DO2 VN51, Ireland;,Department of Clinical Genetics, Children's Health Ireland at Crumlin, Dublin D12 N512, Ireland
| | - Katherine A. Benson
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, DO2 VN51, Ireland;,FutureNeuro Research Centre, Dublin, DO2 VN51, Ireland
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6
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Kushima I, Lo T, Aleksic B, Ozaki N. Case report of a female with bipolar disorder and MBD5 deletion. Psychiatry Clin Neurosci 2022; 76:127-128. [PMID: 35088487 DOI: 10.1111/pcn.13329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/13/2021] [Accepted: 12/29/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Tzuyao Lo
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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7
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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8
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Chen CH, Cheng MC, Hu TM, Ping LY. Chromosomal Microarray Analysis as First-Tier Genetic Test for Schizophrenia. Front Genet 2021; 12:620496. [PMID: 34659328 PMCID: PMC8517076 DOI: 10.3389/fgene.2021.620496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 09/20/2021] [Indexed: 01/07/2023] Open
Abstract
Schizophrenia is a chronic, devastating mental disorder with complex genetic components. Given the advancements in the molecular genetic research of schizophrenia in recent years, there is still a lack of genetic tests that can be used in clinical settings. Chromosomal microarray analysis (CMA) has been used as first-tier genetic testing for congenital abnormalities, developmental delay, and autism spectrum disorders. This study attempted to gain some experience in applying chromosomal microarray analysis as a first-tier genetic test for patients with schizophrenia. We consecutively enrolled patients with schizophrenia spectrum disorder from a clinical setting and conducted genome-wide copy number variation (CNV) analysis using a chromosomal microarray platform. We followed the 2020 “Technical Standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen)” to interpret the clinical significance of CNVs detected from patients. We recruited a total of 60 patients (36 females and 24 males) into this study. We detected three pathogenic CNVs and one likely pathogenic CNV in four patients, respectively. The detection rate was 6.7% (4/60, 95% CI: 0.004–0.13), comparable with previous studies in the literature. Also, we detected thirteen CNVs classified as uncertain clinical significance in nine patients. Detecting these CNVs can help establish the molecular genetic diagnosis of schizophrenia patients and provide helpful information for genetic counseling and clinical management. Also, it can increase our understanding of the pathogenesis of schizophrenia. Hence, we suggest CMA is a valuable genetic tool and considered first-tier genetic testing for schizophrenia spectrum disorders in clinical settings.
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Affiliation(s)
- Chia-Hsiang Chen
- Department of Psychiatry, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Min-Chih Cheng
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Tsung-Ming Hu
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Lieh-Yung Ping
- Department of Psychiatry, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
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9
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González-Ortega G, Llamas-Velasco S, Arteche-López A, Quesada-Espinosa JF, Puertas-Martín V, Gómez-Grande A, López-Álvarez J, Saiz Díaz RA, Lezana-Rosales JM, Villarejo-Galende A, González de la Aleja J. Early-Onset Dementia Associated with a Heterozygous, Nonsense, and de novo Variant in the MBD5 Gene. J Alzheimers Dis 2021; 84:73-78. [PMID: 34459404 DOI: 10.3233/jad-210648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The haploinsufficiency of the methyl-binding domain protein 5 (MBD5) gene has been identified as the determinant cause of the neuropsychiatric disorders grouped under the name MBD5-neurodevelopment disorders (MAND). MAND includes patients with intellectual disability, behavioral problems, and seizures with a static clinical course. However, a few reports have suggested regression. We describe a non-intellectually disabled female, with previous epilepsy and personality disorder, who developed early-onset dementia. The extensive etiologic study revealed a heterozygous nonsense de novo pathogenic variant in the MBD5 gene. This finding could support including the MBD5 gene in the study of patients with atypical early-onset dementia.
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Affiliation(s)
| | - Sara Llamas-Velasco
- Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain.,Biomedical Research Networking Center in Neurodegenerative diseases CIBERNED, Madrid, Spain
| | - Ana Arteche-López
- Department of Genetics, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Verónica Puertas-Martín
- Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Universidad Internacional de La Rioja (UNIR), Logroño, Spain
| | - Adolfo Gómez-Grande
- Department of Nuclear Medicine, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Jorge López-Álvarez
- Department of Psychiatry, Hospital Universitario 12 de Octubre, Madrid, Spain
| | - Rosa Ana Saiz Díaz
- Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Department of Medicine, School of Medicine, Complutense University, Madrid, Spain.,Epilepsy-EEG Unit, Hospital Universitario 12 de Octubre, Madrid, Spain
| | | | - Alberto Villarejo-Galende
- Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Group of Neurodegenerative Diseases, Instituto de Investigación Hospital 12 de Octubre (I+12), Madrid, Spain.,Biomedical Research Networking Center in Neurodegenerative diseases CIBERNED, Madrid, Spain.,Department of Medicine, School of Medicine, Complutense University, Madrid, Spain
| | - Jesús González de la Aleja
- Department of Neurology, Hospital Universitario 12 de Octubre, Madrid, Spain.,Epilepsy-EEG Unit, Hospital Universitario 12 de Octubre, Madrid, Spain
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10
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Parodi C, Di Fede E, Peron A, Viganò I, Grazioli P, Castiglioni S, Finnell RH, Gervasini C, Vignoli A, Massa V. Chromatin Imbalance as the Vertex Between Fetal Valproate Syndrome and Chromatinopathies. Front Cell Dev Biol 2021; 9:654467. [PMID: 33959609 PMCID: PMC8093873 DOI: 10.3389/fcell.2021.654467] [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: 01/16/2021] [Accepted: 04/01/2021] [Indexed: 12/12/2022] Open
Abstract
Prenatal exposure to valproate (VPA), an antiepileptic drug, has been associated with fetal valproate spectrum disorders (FVSD), a clinical condition including congenital malformations, developmental delay, intellectual disability as well as autism spectrum disorder, together with a distinctive facial appearance. VPA is a known inhibitor of histone deacetylase which regulates the chromatin state. Interestingly, perturbations of this epigenetic balance are associated with chromatinopathies, a heterogeneous group of Mendelian disorders arising from mutations in components of the epigenetic machinery. Patients affected from these disorders display a plethora of clinical signs, mainly neurological deficits and intellectual disability, together with distinctive craniofacial dysmorphisms. Remarkably, critically examining the phenotype of FVSD and chromatinopathies, they shared several overlapping features that can be observed despite the different etiologies of these disorders, suggesting the possible existence of a common perturbed mechanism(s) during embryonic development.
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Affiliation(s)
- Chiara Parodi
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Elisabetta Di Fede
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Angela Peron
- Human Pathology and Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy.,Child Neuropsychiatry Unit-Epilepsy Center, Department of Health Sciences, San Paolo Hospital, ASST Santi Paolo e Carlo, Università degli Studi di Milano, Milan, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Ilaria Viganò
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Paolo Grazioli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Silvia Castiglioni
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Richard H Finnell
- Departments of Molecular and Cellular Biology, Molecular and Human Genetics and Medicine, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, United States
| | - Cristina Gervasini
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
| | - Aglaia Vignoli
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy.,"Aldo Ravelli" Center for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy
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11
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Myers KA, Marini C, Carvill GL, McTague A, Panetta J, Stutterd C, Stanley T, Marin S, Nguyen J, Barba C, Rosati A, Scott RH, Mefford HC, Guerrini R, Scheffer IE. Phenotypic Spectrum of Seizure Disorders in MBD5-Associated Neurodevelopmental Disorder. NEUROLOGY-GENETICS 2021; 7:e579. [PMID: 33912662 PMCID: PMC8075573 DOI: 10.1212/nxg.0000000000000579] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 02/11/2021] [Indexed: 11/25/2022]
Abstract
Objective To describe the phenotypic spectrum in patients with MBD5-associated neurodevelopmental disorder (MAND) and seizures; features of MAND include intellectual disability, epilepsy, psychiatric features of aggression and hyperactivity, and dysmorphic features including short stature and microcephaly, sleep disturbance, and ataxia. Methods We performed phenotyping on patients with MBD5 deletions, duplications, or point mutations and a history of seizures. Results Twenty-three patients with MAND and seizures were included. Median seizure onset age was 2.9 years (range 3 days–13 years). The most common seizure type was generalized tonic-clonic; focal, atypical absence, tonic, drop attacks, and myoclonic seizures occurred frequently. Seven children had convulsive status epilepticus and 3 nonconvulsive status epilepticus. Fever, viral illnesses, and hot weather provoked seizures. EEG studies in 17/21 patients were abnormal, typically showing slow generalized spike-wave and background slowing. Nine had drug-resistant epilepsy, although 3 eventually became seizure-free. All but one had moderate-to-severe developmental impairment. Epilepsy syndromes included Lennox-Gastaut syndrome, myoclonic-atonic epilepsy, and infantile spasms syndrome. Behavioral problems in 20/23 included aggression, self-injurious behavior, and sleep disturbance. Conclusions MBD5 disruption may be associated with severe early childhood-onset developmental and epileptic encephalopathy. Because neuropsychiatric dysfunction is common and severe, it should be an important focus of clinical management.
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Affiliation(s)
- Kenneth A Myers
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Carla Marini
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Gemma L Carvill
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Amy McTague
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Julie Panetta
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Chloe Stutterd
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Thorsten Stanley
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Samantha Marin
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - John Nguyen
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Carmen Barba
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Anna Rosati
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Richard H Scott
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Heather C Mefford
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Renzo Guerrini
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
| | - Ingrid E Scheffer
- Research Institute of the McGill University Health Centre (K.M.), Montreal, PQ; Division of Child Neurology (K.M.), Department of Pediatrics, Montreal Children's Hospital, McGill University, Montreal, PQ; Department of Neurology & Neurosurgery (K.M.), Montreal Children's Hospital, McGill University, Montreal, PQ; Child Neurology and Psychiatry (C.M.), Salesi Pediatric Hospital, United Hospitals of Ancona, Ancona, Italy; Division of Genetic Medicine (G.L.C., J.N., H.C.M.), Department of Pediatrics, University of Washington, Seattle, WA; Department of Neurology (A.M.), Great Ormond Street Hospital for Children, London, UK; Developmental Neurosciences Programme (A.M.), UCL Great Ormond Street Institute of Child Health, London, UK; Neurology Network Melbourne (J.P.), Melbourne, Victoria, Australia; Murdoch Children's Research Institute (C.S., I.E.S.), Parkville, Victoria, Australia; Department of Paediatrics and Child Health (T.S.), School of Medicine and Health Sciences, University of Otago, Wellington, New Zealand; Division of Neurology (S.M.), Department of Pediatrics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada; Neurology Unit and Neurogenetic Laboratories (C.B., A.R., R.G.), Meyer Children's Hospital, Florence, Italy; Department of Clinical Genetics (R.H.S.), Great Ormond Street Hospital, London, UK; Epilepsy Research Centre (I.E.S.), Department of Medicine, The University of Melbourne, Austin Health, Heidelberg, Victoria, Australia; Department of Paediatrics (I.E.S.), Royal Children's Hospital, The University of Melbourne, Parkville, Victoria, Australia; and The Florey Institute of Neuroscience and Mental Health (I.E.S.), Heidelberg, Victoria, Australia
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Lee PH, Feng YCA, Smoller JW. Pleiotropy and Cross-Disorder Genetics Among Psychiatric Disorders. Biol Psychiatry 2021; 89:20-31. [PMID: 33131714 PMCID: PMC7898275 DOI: 10.1016/j.biopsych.2020.09.026] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/28/2020] [Accepted: 09/30/2020] [Indexed: 12/20/2022]
Abstract
Genome-wide analyses of common and rare genetic variations have documented the heritability of major psychiatric disorders, established their highly polygenic genetic architecture, and identified hundreds of contributing variants. In recent years, these studies have illuminated another key feature of the genetic basis of psychiatric disorders: the important role and pervasive nature of pleiotropy. It is now clear that a substantial fraction of genetic influences on psychopathology transcend clinical diagnostic boundaries. In this review, we summarize evidence in psychiatry for pleiotropy at multiple levels of analysis: from overall genome-wide correlation to biological pathways and down to the level of individual loci. We examine underlying mechanisms of observed pleiotropy, including genetic effects on neurodevelopment, diverse actions of regulatory elements, mediated effects, and spurious associations of genomic variation with multiple phenotypes. We conclude with an exploration of the implications of pleiotropy for understanding the genetic basis of psychiatric disorders, informing nosology, and advancing the aims of precision psychiatry and genomic medicine.
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Affiliation(s)
- Phil H Lee
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Psychiatry, Massachusetts General Hospital, Boston; and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Yen-Chen A Feng
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Psychiatry, Massachusetts General Hospital, Boston; and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Jordan W Smoller
- Psychiatric and Neurodevelopmental Genetics Unit, Center for Genomic Medicine, and Department of Psychiatry, Massachusetts General Hospital, Boston; and Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
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Composite Sleep Problems Observed Across Smith-Magenis Syndrome, MBD5-Associated Neurodevelopmental Disorder, Pitt-Hopkins Syndrome, and ASD. J Autism Dev Disord 2020; 51:1852-1865. [PMID: 32845423 DOI: 10.1007/s10803-020-04666-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Caregivers of preschool and elementary school age children with Smith-Magenis syndrome (SMS), MBD5-associated neurodevelopmental disorder (MAND), and Pitt-Hopkins syndrome (PTHS) were surveyed to assess sleep disturbance and to identify disorder-specific sleep problems. Because of overlapping features of these rare genetic neurodevelopmental syndromes, data were compared to reports of sleep disturbance in children with autism spectrum disorder (ASD). While similarities were observed with ASD, specific concerns between disorders differed, including mean nighttime sleep duration, daytime sleepiness, night wakings, parasomnias, restless sleep, and bedwetting. Overall, sleep disturbance in PTHS is significant but less severe than in SMS and MAND. The complexity of these conditions and the challenges of underlying sleep disturbance indicate the need for more support, education, and ongoing management of sleep for these individuals.
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Seabra CM, Aneichyk T, Erdin S, Tai DJC, De Esch CEF, Razaz P, An Y, Manavalan P, Ragavendran A, Stortchevoi A, Abad C, Young JI, Maciel P, Talkowski ME, Gusella JF. Transcriptional consequences of MBD5 disruption in mouse brain and CRISPR-derived neurons. Mol Autism 2020; 11:45. [PMID: 32503625 PMCID: PMC7275313 DOI: 10.1186/s13229-020-00354-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 05/25/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND MBD5, encoding the methyl-CpG-binding domain 5 protein, has been proposed as a necessary and sufficient driver of the 2q23.1 microdeletion syndrome. De novo missense and protein-truncating variants from exome sequencing studies have directly implicated MBD5 in the etiology of autism spectrum disorder (ASD) and related neurodevelopmental disorders (NDDs). However, little is known concerning the specific function(s) of MBD5. METHODS To gain insight into the complex interactions associated with alteration of MBD5 in individuals with ASD and related NDDs, we explored the transcriptional landscape of MBD5 haploinsufficiency across multiple mouse brain regions of a heterozygous hypomorphic Mbd5+/GT mouse model, and compared these results to CRISPR-mediated mutations of MBD5 in human iPSC-derived neuronal models. RESULTS Gene expression analyses across three brain regions from Mbd5+/GT mice showed subtle transcriptional changes, with cortex displaying the most widespread changes following Mbd5 reduction, indicating context-dependent effects. Comparison with MBD5 reduction in human neuronal cells reinforced the context-dependence of gene expression changes due to MBD5 deficiency. Gene co-expression network analyses revealed gene clusters that were associated with reduced MBD5 expression and enriched for terms related to ciliary function. LIMITATIONS These analyses included a limited number of mouse brain regions and neuronal models, and the effects of the gene knockdown are subtle. As such, these results will not reflect the full extent of MBD5 disruption across human brain regions during early neurodevelopment in ASD, or capture the diverse spectrum of cell-type-specific changes associated with MBD5 alterations. CONCLUSIONS Our study points to modest and context-dependent transcriptional consequences of Mbd5 disruption in the brain. It also suggests a possible link between MBD5 and perturbations in ciliary function, which is an established pathogenic mechanism in developmental disorders and syndromes.
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Affiliation(s)
- Catarina M Seabra
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,GABBA Program - Institute of Biomedical Sciences Abel Salazar of the University of Porto, Porto, Portugal
| | - Tatsiana Aneichyk
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Independent Data Lab UG, Munich, Germany
| | - Serkan Erdin
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA
| | - Derek J C Tai
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Celine E F De Esch
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Parisa Razaz
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Yu An
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Poornima Manavalan
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Ashok Ragavendran
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Center for Computational Biology of Human Disease & Center for Computation and Visualization, Brown University, Providence, Rhode Island, USA
| | - Alexei Stortchevoi
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Clemer Abad
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Juan I Young
- Dr. John T. Macdonald Foundation Department of Human Genetics, University of Miami, Miami, FL, USA
| | - Patricia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga, Guimarães, Portugal
| | - Michael E Talkowski
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - James F Gusella
- Molecular Neurogenetics Unit, Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA. .,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard Medical School, Boston, MA, USA. .,Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA. .,Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
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15
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Ross PJ, Mok RSF, Smith BS, Rodrigues DC, Mufteev M, Scherer SW, Ellis J. Modeling neuronal consequences of autism-associated gene regulatory variants with human induced pluripotent stem cells. Mol Autism 2020; 11:33. [PMID: 32398033 PMCID: PMC7218542 DOI: 10.1186/s13229-020-00333-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 04/03/2020] [Indexed: 12/27/2022] Open
Abstract
Genetic factors contribute to the development of autism spectrum disorder (ASD), and although non-protein-coding regions of the genome are being increasingly implicated in ASD, the functional consequences of these variants remain largely uncharacterized. Induced pluripotent stem cells (iPSCs) enable the production of personalized neurons that are genetically matched to people with ASD and can therefore be used to directly test the effects of genomic variation on neuronal gene expression, synapse function, and connectivity. The combined use of human pluripotent stem cells with genome editing to introduce or correct specific variants has proved to be a powerful approach for exploring the functional consequences of ASD-associated variants in protein-coding genes and, more recently, long non-coding RNAs (lncRNAs). Here, we review recent studies that implicate lncRNAs, other non-coding mutations, and regulatory variants in ASD susceptibility. We also discuss experimental design considerations for using iPSCs and genome editing to study the role of the non-protein-coding genome in ASD.
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Affiliation(s)
- P Joel Ross
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada.
| | - Rebecca S F Mok
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brandon S Smith
- Department of Biology, University of Prince Edward Island, Charlottetown, PE, Canada
| | - Deivid C Rodrigues
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marat Mufteev
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.,Genetics & Genome Biology Program and The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - James Ellis
- Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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16
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Nieto SJ, Grodin EN, Ray LA. On the path towards personalized medicine: Implications of pharmacogenetic studies of alcohol use disorder medications. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2020; 5:43-54. [PMID: 34291172 DOI: 10.1080/23808993.2020.1724510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Introduction The heritability of alcohol use disorder (AUD) is estimated to be ~50%; however, the genetic basis of the disease is still poorly understood. The genetic variants identified thus far only explain a small percentage of AUD phenotypic variability. While genome-wide association studies (GWAS) are impacted by technical and methodological limitations, genetic variants that have been identified independently of GWAS findings can moderate the efficacy of AUD medications. Areas Covered This review discusses findings from clinical pharmacogenetic studies of AUD medications. While the pharmacogenetic studies reviewed involve several genetic variants in the major neurotransmitter systems, genetic loci in the opioid system have garnered the most attention. Expert Opinion The clinical utility of pharmacogenetics in AUD populations is uncertain at this time. There are several ongoing prospective clinical trials that will enhance knowledge regarding the applicability of pharmacogenetics in clinical populations. We recommend that future work in this area consider reverse translating from genotype to phenotype, mapping genes to stages of the addiction cycle, mapping genes to neural circuits, and harnessing large population-based cohorts.
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Affiliation(s)
- Steven J Nieto
- University of California Los Angeles, Department of Psychology, Los Angeles, CA, USA
| | - Erica N Grodin
- University of California Los Angeles, Department of Psychology, Los Angeles, CA, USA
| | - Lara A Ray
- University of California Los Angeles, Department of Psychology, Los Angeles, CA, USA.,University of California, Los Angeles, Department of Psychiatry and Biobehavioral Sciences, Los Angeles, CA, USA.,University of California Los Angeles, Brain Research Institute, Los Angeles, CA, USA
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17
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Kolevzon A, Delaby E, Berry-Kravis E, Buxbaum JD, Betancur C. Neuropsychiatric decompensation in adolescents and adults with Phelan-McDermid syndrome: a systematic review of the literature. Mol Autism 2019; 10:50. [PMID: 31879555 PMCID: PMC6930682 DOI: 10.1186/s13229-019-0291-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 10/09/2019] [Indexed: 12/22/2022] Open
Abstract
Phelan-McDermid syndrome (PMS) is caused by haploinsufficiency of the SHANK3 gene on chromosome 22q13.33 and is characterized by intellectual disability, hypotonia, severe speech impairments, and autism spectrum disorder. Emerging evidence indicates that there are changes over time in the phenotype observed in individuals with PMS, including severe neuropsychiatric symptoms and loss of skills occurring in adolescence and adulthood. To gain further insight into these phenomena and to better understand the long-term course of the disorder, we conducted a systematic literature review and identified 56 PMS cases showing signs of behavioral and neurologic decompensation in adolescence or adulthood (30 females, 25 males, 1 gender unknown). Clinical presentations included features of bipolar disorder, catatonia, psychosis, and loss of skills, occurring at a mean age of 20 years. There were no apparent sex differences in the rates of these disorders except for catatonia, which appeared to be more frequent in females (13 females, 3 males). Reports of individuals with point mutations in SHANK3 exhibiting neuropsychiatric decompensation and loss of skills demonstrate that loss of one copy of SHANK3 is sufficient to cause these manifestations. In the majority of cases, no apparent cause could be identified; in others, symptoms appeared after acute events, such as infections, prolonged or particularly intense seizures, or changes in the individual's environment. Several individuals had a progressive neurological deterioration, including one with juvenile onset metachromatic leukodystrophy, a severe demyelinating disorder caused by recessive mutations in the ARSA gene in 22q13.33. These reports provide insights into treatment options that have proven helpful in some cases, and are reviewed herein. Our survey highlights how little is currently known about neuropsychiatric presentations and loss of skills in PMS and underscores the importance of studying the natural history in individuals with PMS, including both cross-sectional and long-term longitudinal analyses. Clearer delineation of these neuropsychiatric symptoms will contribute to their recognition and prompt management and will also help uncover the underlying biological mechanisms, potentially leading to improved interventions.
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Affiliation(s)
- Alexander Kolevzon
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Elsa Delaby
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
| | - Elizabeth Berry-Kravis
- Department of Pediatrics, Neurological Sciences, Biochemistry, Rush University Medical Center, Chicago, Illinois USA
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY USA
| | - Catalina Betancur
- Sorbonne Université, INSERM, CNRS, Neuroscience Paris Seine, Institut de Biologie Paris Seine, Paris, France
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18
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Verhoeven W, Egger J, Kipp J, Verheul‐ aan de Wiel J, Ockeloen C, Kleefstra T, Pfundt R. A novel MBD5 mutation in an intellectually disabled adult female patient with epilepsy: Suggestive of early onset dementia? Mol Genet Genomic Med 2019; 7:e849. [PMID: 31290275 PMCID: PMC6687664 DOI: 10.1002/mgg3.849] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 05/27/2019] [Accepted: 06/05/2019] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND The minimal critical region in 2q23.1 deletion syndrome comprises one gene only, that is, the methyl-CpG-binding domain protein 5 (MBD5) gene. Since the phenotypes of patients with deletions, duplications or pathogenic variants of MBD5 show considerable overlap, the term MBD5-associated neurodevelopmental disorder (MAND) was proposed. These syndromes are characterized by intellectual disability, seizures of any kind and symptoms from the autism spectrum. In a very limited number of patients, MAND may be associated with regression starting either at early infancy or at midlife. METHODS The present paper describes a severely intellectually disabled autistic female with therapy resistant complex partial epilepsy starting at her 16the with gradual cognitive and behavioral regression towards her sixth decade. RESULTS Cognitive and behavioral regression occurred towards the patient's sixth decade. Exome sequencing disclosed a novel heterozygous pathogenic frameshift mutation of MBD5 that was considered to be causative for the combination of intellectual disability, treatment-resistant epilepsy and autism. CONCLUSION The presented patient is the second with a pathogenic MBD5 mutation in whom the course of disease is suggestive of early onset dementia starting in her fifth decade. These findings stress the importance of exome sequencing, also in elderly intellectually disabled patients, particularly in those with autism.
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Affiliation(s)
- Willem Verhoeven
- Centre of Excellence for NeuropsychiatryVincent van Gogh Institute for PsychiatryVenraythe Netherlands
- Department of PsychiatryErasmus University Medical CentreRotterdamthe Netherlands
| | - Jos Egger
- Centre of Excellence for NeuropsychiatryVincent van Gogh Institute for PsychiatryVenraythe Netherlands
- Donders Institute for Brain, Cognition and BehaviourRadboud UniversityNijmegenthe Netherlands
- Stevig Specialized and Forensic Care for People with Intellectual Disabilities, DichterbijOostrumthe Netherlands
| | - Janneke Kipp
- ASVZ Institutes for Intellectual DisabilitiesLeerdamthe Netherlands
| | | | - Charlotte Ockeloen
- Department of Human GeneticsRadboud University Medical CenterNijmegenthe Netherlands
| | - Tjitske Kleefstra
- Department of Human GeneticsRadboud University Medical CenterNijmegenthe Netherlands
| | - Rolph Pfundt
- Department of Human GeneticsRadboud University Medical CenterNijmegenthe Netherlands
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19
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Currall BB, Antolik CW, Collins RL, Talkowski ME. Next Generation Sequencing of Prenatal Structural Chromosomal Rearrangements Using Large-Insert Libraries. Methods Mol Biol 2019; 1885:251-265. [PMID: 30506203 DOI: 10.1007/978-1-4939-8889-1_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Precise tests for genomic structural variation (SV) are essential for accurate diagnosis of prenatal genome abnormalities. The two most ubiquitous traditional methods for prenatal SV assessment, karyotyping and chromosomal microarrays, do not provide sufficient resolution for some clinically actionable SVs. Standard whole-genome sequencing (WGS) overcomes shortcomings of traditional techniques by providing base-pair resolution of the entire accessible genome. However, while sequencing costs have continued to decline in recent years, conventional WGS costs remain high for most routine clinical applications. Here, we describe a specialized WGS technique using large inserts (liWGS; also known as "jumping libraries") to resolve large (>5000-10,000 nucleotides) SVs at kilobase-resolution in prenatal samples, and at a fraction of the cost of standard WGS. We explicate the protocols for generating liWGS libraries and supplement with an overview for processing and analyzing liWGS data.
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Affiliation(s)
- Benjamin B Currall
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Caroline W Antolik
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Ryan L Collins
- Massachusetts General Hospital, Boston, MA, USA
- Broad Institute, Harvard Medical School, Cambridge, MA, USA
| | - Michael E Talkowski
- Massachusetts General Hospital, Boston, MA, USA.
- Broad Institute, Harvard Medical School, Cambridge, MA, USA.
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20
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Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, Stránecký V, Jiřička V, Preiss M, Příhodová K, Šaligová J, Wei J, Woodbury-Smith M, Bleyer AJ, Scherer SW, Kmoch S. Rare copy number variation in extremely impulsively violent males. GENES BRAIN AND BEHAVIOR 2018; 18:e12536. [DOI: 10.1111/gbb.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jan Vevera
- Department of Psychiatry; Faculty of Medicine and University Hospital in Pilsen, Charles University; Prague Czech Republic
- Department of Psychiatry, First Faculty of Medicine; Charles University and General University Hospital in Prague; Prague Czech Republic
- Institute for Postgraduate Medical Education; Prague Czech Republic
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Petra Oliveriusová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Václav Jiřička
- Prison Service of the Czech Republic, Directorate General; Department of Psychology; Prague Czech Republic
| | - Marek Preiss
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
- Psychology Department; University of New York in Prague; Prague Czech Republic
| | - Kateřina Příhodová
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Jana Šaligová
- Children's Faculty Hospital; Department of Pediatrics and Adolescent Medicine; Kosice Slovakia
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine of Pavel Jozef Šafárik University Kosice; Kosice Slovakia
| | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary; Newcastle upon Tyne UK
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
- Section on Nephrology, Wake Forest School of Medicine; Medical Center Blvd.; Winston-Salem North Carolina USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Ontario Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
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21
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Marco EJ, Aitken AB, Nair VP, da Gente G, Gerdes MR, Bologlu L, Thomas S, Sherr EH. Burden of de novo mutations and inherited rare single nucleotide variants in children with sensory processing dysfunction. BMC Med Genomics 2018; 11:50. [PMID: 29801487 PMCID: PMC5970458 DOI: 10.1186/s12920-018-0362-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/26/2018] [Indexed: 12/30/2022] Open
Abstract
Background In children with sensory processing dysfunction (SPD), who do not meet criteria for autism spectrum disorder (ASD) or intellectual disability, the contribution of de novo pathogenic mutation in neurodevelopmental genes is unknown and in need of investigation. We hypothesize that children with SPD may have pathogenic variants in genes that have been identified as causing other neurodevelopmental disorders including ASD. This genetic information may provide important insight into the etiology of sensory processing dysfunction and guide clinical evaluation and care. Methods Eleven community-recruited trios (children with isolated SPD and both biological parents) underwent WES to identify candidate de novo variants and inherited rare single nucleotide variants (rSNV) in genes previously associated with ASD. Gene enrichment in these children and their parents for transmitted and non-transmitted mutation burden was calculated. A comparison analysis to assess for enriched rSNV burden was then performed in 2377 children with ASD and their families from the Simons Simplex Collection. Results Of the children with SPD, 2/11 (18%), were identified as having a de novo loss of function or missense mutation in genes previously reported as causative for neurodevelopmental disorders (MBD5 and FMN2). We also found that the parents of children with SPD have significant enrichment of pathogenic rSNV burden in high-risk ASD candidate genes that are inherited by their affected children. Using the same approach, we confirmed enrichment of rSNV burden in a large cohort of children with autism and their parents but not unaffected siblings. Conclusions Our findings suggest that SPD, like autism, has a genetic basis that includes both de novo single gene mutations as well as an accumulated burden of rare inherited variants from their parents. Electronic supplementary material The online version of this article (10.1186/s12920-018-0362-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elysa Jill Marco
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA. .,Department of Psychiatry, University of California, San Francisco, 401 Parnassus Ave, San Francisco, CA, 94143, USA. .,Department of Pediatrics, University of California, San Francisco, 550 16th Street, Box 0110, San Francisco, CA, 94143, USA.
| | - Anne Brandes Aitken
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA
| | - Vishnu Prakas Nair
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA
| | - Gilberto da Gente
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA
| | - Molly Rae Gerdes
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA
| | | | - Sean Thomas
- Department of Biostatistics & Epidemiology, University of California, San Francisco, 550 16th Street, 2nd Floor, Box #0560, San Francisco, CA, 94158-2549, USA
| | - Elliott H Sherr
- Department of Neurology, University of California, San Francisco, 675 Nelson Rising Lane, San Francisco, CA, 9415, USA.,Department of Pediatrics, University of California, San Francisco, 550 16th Street, Box 0110, San Francisco, CA, 94143, USA.,Institute of Human Genetics, University of California, San Francisco, 513 Parnassus Avenue, S965, San Francisco, CA, 94143-0794, USA
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22
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Abstract
The role of DNA methylation in brain development is an intense area of research because the brain has particularly high levels of CpG and mutations in many of the proteins involved in the establishment, maintenance, interpretation, and removal of DNA methylation impact brain development and/or function. These include DNA methyltransferase (DNMT), Ten-Eleven Translocation (TET), and Methyl-CpG binding proteins (MBPs). Recent advances in sequencing breadth and depth as well the detection of different forms of methylation have greatly expanded our understanding of the diversity of DNA methylation in the brain. The contributions of DNA methylation and associated proteins to embryonic and adult neurogenesis will be examined. Particular attention will be given to the impact on adult hippocampal neurogenesis (AHN), which is a key mechanism contributing to brain plasticity, learning, memory and mood regulation. DNA methylation influences multiple aspects of neurogenesis from stem cell maintenance and proliferation, fate specification, neuronal differentiation and maturation, and synaptogenesis. In addition, DNA methylation during neurogenesis has been shown to be responsive to many extrinsic signals, both under normal conditions and during disease and injury. Finally, crosstalk between DNA methylation, Methyl-DNA binding domain (MBD) proteins such as MeCP2 and MBD1 and histone modifying complexes is used as an example to illustrate the extensive interconnection between these epigenetic regulatory systems.
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Affiliation(s)
- Emily M Jobe
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA
| | - Xinyu Zhao
- Cellular and Molecular Biology Graduate Program, University of Wisconsin-Madison, Madison, WI, USA.,Waisman Center, University of Wisconsin-Madison, Madison, WI, USA.,Department of Neuroscience, University of Wisconsin-Madison, Madison, WI, USA
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23
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Chaste P, Roeder K, Devlin B. The Yin and Yang of Autism Genetics: How Rare De Novo and Common Variations Affect Liability. Annu Rev Genomics Hum Genet 2017; 18:167-187. [DOI: 10.1146/annurev-genom-083115-022647] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pauline Chaste
- Centre de Psychiatrie et Neurosciences, 75014 Paris, France
- Centre hospitalier Sainte-Anne, 75674 Paris, France
| | - Kathryn Roeder
- Department of Statistics and Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Bernie Devlin
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15213
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24
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Diagnostic exome sequencing identifies a heterozygous MBD5 frameshift mutation in a family with intellectual disability and epilepsy. Eur J Med Genet 2017; 60:559-564. [PMID: 28807762 DOI: 10.1016/j.ejmg.2017.08.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 11/23/2022]
Abstract
Methyl-CpG-binding domain 5 (MBD5)-associated neurodevelopmental disorder caused by 2q23.1 or MBD5-specific mutation has been recently identified as a genetic disorder associated with autism spectrum disorders. Phenotypic features of 2q23.1 deletion or disruption of MBD5 gene include severe intellectual disability, seizure, significant speech impairment, sleep disturbance, and autistic-like behavioural problems. Here we report a 7-year-old girl with intellectual disability and epilepsy without previous clinical diagnosis. Diagnostic exome sequencing identified a novel frameshift mutation c.254_255delGA (p.Arg85Asnfs*6) in the MBD5 gene of the proband and her father. The proband's father with normal intelligence showed subclinical manifestations observed in subsequent investigations. Clinical manifestations, disease course, and molecular findings of the involvement of MBD5 gene in this family suggest an unusual MBD5-related neurodevelopmental disorder. Moreover, this report demonstrates the critical role of next-generation sequencing technique in characterizing such a rare disorder with variable or no clinical manifestation and providing opportunity to develop effective preventive measures such as pre-implantation genetic diagnosis.
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25
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Tadros S, Wang R, Waters JJ, Waterman C, Collins AL, Collinson MN, Ahn JW, Josifova D, Chetan R, Kumar A. Inherited 2q23.1 microdeletions involving the MBD5 locus. Mol Genet Genomic Med 2017; 5:608-613. [PMID: 28944244 PMCID: PMC5606852 DOI: 10.1002/mgg3.316] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/31/2017] [Accepted: 06/02/2017] [Indexed: 02/06/2023] Open
Abstract
Background Microdeletions of 2q23.1 disrupting MBD5 and loss of function mutations of MBD5 cause MBD5‐Associated Neurodevelopmental disorders (MAND). Nearly all reported patients have been isolated cases of de novo origin. Methods This study investigates three families with inherited MBD5 mutations from three different Regional Genetics Centres in the UK. Results Two of the parents in the study had MBD5 deletions in a mosaic form. The parent with an MBD5 deletion in an apparently nonmosaic form has a psychiatric disorder in the absence of developmental delay or dysmorphism. Conclusions Inherited forms of MBD5 deletions are rare, but do occur, especially in a mosaic form. The phenotypic spectrum of MAND may be wider than previously thought.
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Affiliation(s)
- Shereen Tadros
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Rubin Wang
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Jonathan J Waters
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
| | - Christine Waterman
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustOdstock RoadSalisburySP2 8BJUK
| | - Amanda L Collins
- Wessex Clinical Genetics ServicePrincess Anne HospitalMailpoint 627SouthamptonSO16 5YAUK
| | - Morag N Collinson
- Wessex Regional Genetics LaboratorySalisbury NHS Foundation TrustOdstock RoadSalisburySP2 8BJUK
| | - Joo W Ahn
- South East Thames Regional Genetics ServiceGuy's HospitalGreat Maze PondLondonSE1 9RTUK
| | - Dragana Josifova
- South East Thames Regional Genetics ServiceGuy's HospitalGreat Maze PondLondonSE1 9RTUK
| | - Ravi Chetan
- Department of PaediatricsSouthend University HospitalWestcliff on SeaSS0 0RYUK
| | - Ajith Kumar
- North East Thames Regional Genetics ServiceGreat Ormond Street HospitalLondonWC1N 3JHUK
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26
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Di Gregorio E, Riberi E, Belligni EF, Biamino E, Spielmann M, Ala U, Calcia A, Bagnasco I, Carli D, Gai G, Giordano M, Guala A, Keller R, Mandrile G, Arduino C, Maffè A, Naretto VG, Sirchia F, Sorasio L, Ungari S, Zonta A, Zacchetti G, Talarico F, Pappi P, Cavalieri S, Giorgio E, Mancini C, Ferrero M, Brussino A, Savin E, Gandione M, Pelle A, Giachino DF, De Marchi M, Restagno G, Provero P, Cirillo Silengo M, Grosso E, Buxbaum JD, Pasini B, De Rubeis S, Brusco A, Ferrero GB. Copy number variants analysis in a cohort of isolated and syndromic developmental delay/intellectual disability reveals novel genomic disorders, position effects and candidate disease genes. Clin Genet 2017; 92:415-422. [PMID: 28295210 DOI: 10.1111/cge.13009] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/14/2022]
Abstract
BACKGROUND Array-comparative genomic hybridization (array-CGH) is a widely used technique to detect copy number variants (CNVs) associated with developmental delay/intellectual disability (DD/ID). AIMS Identification of genomic disorders in DD/ID. MATERIALS AND METHODS We performed a comprehensive array-CGH investigation of 1,015 consecutive cases with DD/ID and combined literature mining, genetic evidence, evolutionary constraint scores, and functional information in order to assess the pathogenicity of the CNVs. RESULTS We identified non-benign CNVs in 29% of patients. Amongst the pathogenic variants (11%), detected with a yield consistent with the literature, we found rare genomic disorders and CNVs spanning known disease genes. We further identified and discussed 51 cases with likely pathogenic CNVs spanning novel candidate genes, including genes encoding synaptic components and/or proteins involved in corticogenesis. Additionally, we identified two deletions spanning potential Topological Associated Domain (TAD) boundaries probably affecting the regulatory landscape. DISCUSSION AND CONCLUSION We show how phenotypic and genetic analyses of array-CGH data allow unraveling complex cases, identifying rare disease genes, and revealing unexpected position effects.
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Affiliation(s)
- E Di Gregorio
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - E Riberi
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E F Belligni
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Biamino
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - M Spielmann
- Research Group Mundlos, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - U Ala
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - A Calcia
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - I Bagnasco
- Neuropsichiatria Infantile, Martini Hospital, ASL TO1, Turin, Italy
| | - D Carli
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - G Gai
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Giordano
- Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - A Guala
- SOC Pediatria, Castelli Hospital, Verbania, Italy
| | - R Keller
- Mental Health Department, ASL TO2, Adult Autism Center, Turin, Italy
| | - G Mandrile
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy
| | - C Arduino
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - A Maffè
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - V G Naretto
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - F Sirchia
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - L Sorasio
- Pediatrics, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S Ungari
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - A Zonta
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G Zacchetti
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy.,Department of Health Sciences, Laboratory of Genetics, University of Eastern Piedmont and Interdisciplinary Research Center of Autoimmune Diseases, Novara, Italy
| | - F Talarico
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Pappi
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - S Cavalieri
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Giorgio
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - C Mancini
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - M Ferrero
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - A Brussino
- University of Torino, Department of Medical Sciences, Turin, Italy
| | - E Savin
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - M Gandione
- Department of Neuropsychiatry, University of Torino, Turin, Italy
| | - A Pelle
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - D F Giachino
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - M De Marchi
- Medical Genetics, San Luigi Gonzaga University Hospital, Orbassano (TO), Italy.,Department of Clinical and Biological Sciences, University of Torino, Turin, Italy
| | - G Restagno
- Laboratory of Molecular Genetics, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - P Provero
- Computational Biology Unit, Molecular Biotechnology Center (MBC), Turin, Italy.,Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
| | - M Cirillo Silengo
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - E Grosso
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - J D Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York.,Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - B Pasini
- Molecular Biology and Genetics Unit, Santa Croce e Carle Hospital, Cuneo, Italy
| | - S De Rubeis
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York
| | - A Brusco
- University of Torino, Department of Medical Sciences, Turin, Italy.,Medical Genetics Unit, Città della Salute e della Scienza University Hospital, Turin, Italy
| | - G B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
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27
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Demkow U, Wolańczyk T. Genetic tests in major psychiatric disorders-integrating molecular medicine with clinical psychiatry-why is it so difficult? Transl Psychiatry 2017; 7:e1151. [PMID: 28608853 PMCID: PMC5537634 DOI: 10.1038/tp.2017.106] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 03/29/2017] [Indexed: 02/06/2023] Open
Abstract
With the advent of post-genomic era, new technologies create extraordinary possibilities for diagnostics and personalized therapy, transforming todays' medicine. Rooted in both medical genetics and clinical psychiatry, the paper is designed as an integrated source of information of the current and potential future application of emerging genomic technologies as diagnostic tools in psychiatry, moving beyond the classical concept of patient approach. Selected approaches are presented, starting from currently used technologies (next-generation sequencing (NGS) and microarrays), followed by newer options (reverse phenotyping). Next, we describe an old concept in a new light (endophenotypes), subsequently coming up with a sophisticated and complex approach (gene networks) ending by a nascent field (computational psychiatry). The challenges and barriers that exist to translate genomic research to real-world patient assessment are further discussed. We emphasize the view that only a paradigm shift can bring a fundamental change in psychiatric practice, allowing to disentangle the intricacies of mental diseases. All the diagnostic methods, as described, are directed at uncovering the integrity of the system including many types of relations within a complex structure. The integrative system approach offers new opportunity to connect genetic background with specific diseases entities, or concurrently, with symptoms regardless of a diagnosis. To advance the field, we propose concerted cross-disciplinary effort to provide a diagnostic platform operating at the general level of genetic pathogenesis of complex-trait psychiatric disorders rather than at the individual level of a specific disease.
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Affiliation(s)
- U Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Warsaw, Poland,Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Medical University of Warsaw, Zwirki i Wigury 63a, Warsaw 02-091, Poland. E-mail:
| | - T Wolańczyk
- Department of Child Psychiatry, Medical University of Warsaw, Warsaw, Poland
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28
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Woodbury-Smith M, Nicolson R, Zarrei M, Yuen RKC, Walker S, Howe J, Uddin M, Hoang N, Buchanan JA, Chrysler C, Thompson A, Szatmari P, Scherer SW. Variable phenotype expression in a family segregating microdeletions of the NRXN1 and MBD5 autism spectrum disorder susceptibility genes. NPJ Genom Med 2017. [PMID: 28649445 PMCID: PMC5482711 DOI: 10.1038/s41525-017-0020-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Autism spectrum disorder is a developmental condition of early childhood onset, which impacts socio-communicative functioning and is principally genetic in etiology. Currently, more than 50 genomic loci are deemed to be associated with susceptibility to autism spectrum disorder, showing de novo and inherited unbalanced copy number variants and smaller insertions and deletions (indels), more complex structural variants, as well as single-nucleotide variants deemed of pathological significance. However, the phenotypes associated with many of these genes are variable, and penetrance is largely unelaborated in clinical descriptions. This case report describes a family harboring two copy number variant microdeletions, which affect regions of NRXN1 and MBD5—each well-established in association with risk of autism spectrum disorder and other neurodevelopmental disorders. Although each copy number variant would likely be categorized as pathologically significant, both genomic alterations are transmitted in this family from an unaffected father to the proband, and shared by an unaffected sibling. This family case illustrates the importance of recognizing that phenotype can vary among exon overlapping variants of the same gene, and the need to evaluate penetrance of such variants in order to properly inform on risks.
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Affiliation(s)
- Marc Woodbury-Smith
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.,Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Mehdi Zarrei
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K C Yuen
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susan Walker
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohammed Uddin
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ny Hoang
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Janet A Buchanan
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christina Chrysler
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Peter Szatmari
- Centre for Addiction and Mental Health, The Hospital for Sick Children & University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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29
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Kushima I, Aleksic B, Nakatochi M, Shimamura T, Shiino T, Yoshimi A, Kimura H, Takasaki Y, Wang C, Xing J, Ishizuka K, Oya-Ito T, Nakamura Y, Arioka Y, Maeda T, Yamamoto M, Yoshida M, Noma H, Hamada S, Morikawa M, Uno Y, Okada T, Iidaka T, Iritani S, Yamamoto T, Miyashita M, Kobori A, Arai M, Itokawa M, Cheng MC, Chuang YA, Chen CH, Suzuki M, Takahashi T, Hashimoto R, Yamamori H, Yasuda Y, Watanabe Y, Nunokawa A, Someya T, Ikeda M, Toyota T, Yoshikawa T, Numata S, Ohmori T, Kunimoto S, Mori D, Iwata N, Ozaki N. High-resolution copy number variation analysis of schizophrenia in Japan. Mol Psychiatry 2017; 22:430-440. [PMID: 27240532 DOI: 10.1038/mp.2016.88] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2015] [Revised: 04/18/2016] [Accepted: 04/20/2016] [Indexed: 12/30/2022]
Abstract
Recent schizophrenia (SCZ) studies have reported an increased burden of de novo copy number variants (CNVs) and identified specific high-risk CNVs, although with variable phenotype expressivity. However, the pathogenesis of SCZ has not been fully elucidated. Using array comparative genomic hybridization, we performed a high-resolution genome-wide CNV analysis on a mainly (92%) Japanese population (1699 SCZ cases and 824 controls) and identified 7066 rare CNVs, 70.0% of which were small (<100 kb). Clinically significant CNVs were significantly more frequent in cases than in controls (odds ratio=3.04, P=9.3 × 10-9, 9.0% of cases). We confirmed a significant association of X-chromosome aneuploidies with SCZ and identified 11 de novo CNVs (e.g., MBD5 deletion) in cases. In patients with clinically significant CNVs, 41.7% had a history of congenital/developmental phenotypes, and the rate of treatment resistance was significantly higher (odds ratio=2.79, P=0.0036). We found more severe clinical manifestations in patients with two clinically significant CNVs. Gene set analysis replicated previous findings (e.g., synapse, calcium signaling) and identified novel biological pathways including oxidative stress response, genomic integrity, kinase and small GTPase signaling. Furthermore, involvement of multiple SCZ candidate genes and biological pathways in the pathogenesis of SCZ was suggested in established SCZ-associated CNV loci. Our study shows the high genetic heterogeneity of SCZ and its clinical features and raises the possibility that genomic instability is involved in its pathogenesis, which may be related to the increased burden of de novo CNVs and variable expressivity of CNVs.
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Affiliation(s)
- I Kushima
- Institute for Advanced Research, Nagoya University, Nagoya, Japan.,Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Nakatochi
- Bioinformatics Section, Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Shimamura
- Division of Systems Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Shiino
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - A Yoshimi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Takasaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - C Wang
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - J Xing
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - K Ishizuka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Oya-Ito
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Nakamura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - T Maeda
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yamamoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Yoshida
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - H Noma
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Hamada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Morikawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Y Uno
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Okada
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Iidaka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - S Iritani
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - T Yamamoto
- Department of Legal Medicine and Bioethics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - M Miyashita
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - A Kobori
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Arai
- Department of Psychiatry and Behavioral Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M Itokawa
- Center for Medical Cooperation, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - M-C Cheng
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - Y-A Chuang
- Department of Psychiatry, Yuli Mental Health Research Center, Yuli Branch, Taipei Veterans General Hospital, Hualien, Taiwan
| | - C-H Chen
- Department of Psychiatry, Chang Gung Memorial Hospital-Linkou, Taoyuan, Taiwan.,Department and Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - M Suzuki
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - T Takahashi
- Department of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan
| | - R Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - H Yamamori
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Yasuda
- Department of Psychiatry, Osaka University Graduate School of Medicine, Suita, Japan
| | - Y Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - A Nunokawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - T Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - M Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - T Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - T Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Japan
| | - S Numata
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - T Ohmori
- Department of Psychiatry, Institute of Biomedical Sciences, Tokushima University Graduate School, Tokushima, Japan
| | - S Kunimoto
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - D Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - N Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - N Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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30
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Yuen RKC, Merico D, Cao H, Pellecchia G, Alipanahi B, Thiruvahindrapuram B, Tong X, Sun Y, Cao D, Zhang T, Wu X, Jin X, Zhou Z, Liu X, Nalpathamkalam T, Walker S, Howe JL, Wang Z, MacDonald JR, Chan A, D'Abate L, Deneault E, Siu MT, Tammimies K, Uddin M, Zarrei M, Wang M, Li Y, Wang J, Wang J, Yang H, Bookman M, Bingham J, Gross SS, Loy D, Pletcher M, Marshall CR, Anagnostou E, Zwaigenbaum L, Weksberg R, Fernandez BA, Roberts W, Szatmari P, Glazer D, Frey BJ, Ring RH, Xu X, Scherer SW. Genome-wide characteristics of de novo mutations in autism. NPJ Genom Med 2016; 1:160271-1602710. [PMID: 27525107 PMCID: PMC4980121 DOI: 10.1038/npjgenmed.2016.27] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
De novo mutations (DNMs) are important in Autism Spectrum Disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole genome sequencing (WGS) of 200 ASD parent-child trios and characterized germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (p=4.2×10-10). However, when clustered DNMs (those within 20kb) were found in ASD, not only did they mostly originate from the mother (p=7.7×10-13), but they could also be found adjacent to de novo copy number variations (CNVs) where the mutation rate was significantly elevated (p=2.4×10-24). By comparing DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (p=8.0×10-9; OR=1.84), of which 15.6% (p=4.3×10-3) and 22.5% (p=7.0×10-5) were in the non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, boundaries involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD risk- and epigenetic- genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the etiology of ASD.
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Affiliation(s)
- Ryan K C Yuen
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Daniele Merico
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Giovanna Pellecchia
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Babak Alipanahi
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Xin Tong
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Yuhui Sun
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | - Tao Zhang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Xueli Wu
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Xin Jin
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Ze Zhou
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | - Thomas Nalpathamkalam
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Susan Walker
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jennifer L Howe
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeffrey R MacDonald
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ada Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lia D'Abate
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Eric Deneault
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle T Siu
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Kristiina Tammimies
- Center of Neurodevelopmental Disorders (KIND), Pediatric Neuropsychiatry Unit, Karolinska Institutet, Stockholm, Sweden
| | - Mohammed Uddin
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Jun Wang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Jian Wang
- BGI-Shenzhen, Yantian, Shenzhen, China
| | | | | | | | | | - Dion Loy
- Google, Mountain View, California, USA
| | | | - Christian R Marshall
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Evdokia Anagnostou
- Bloorview Research Institute, University of Toronto, Toronto, Ontario, Canada
| | - Lonnie Zwaigenbaum
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Bridget A Fernandez
- Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada; Provincial Medical Genetic Program, Eastern Health, St. John's, Newfoundland, Canada
| | - Wendy Roberts
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Szatmari
- Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada; Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, Ontario, Canada; Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada
| | - David Glazer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brendan J Frey
- Department of Electrical and Computer Engineering, University of Toronto, Toronto, Ontario, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | | | - Xun Xu
- BGI-Shenzhen, Yantian, Shenzhen, China
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada; Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada; McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
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Rosenfeld JA, Patel A. Chromosomal Microarrays: Understanding Genetics of Neurodevelopmental Disorders and Congenital Anomalies. J Pediatr Genet 2016; 6:42-50. [PMID: 28180026 DOI: 10.1055/s-0036-1584306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 04/23/2016] [Indexed: 01/09/2023]
Abstract
Chromosomal microarray (CMA) testing, used to identify DNA copy number variations (CNVs), has helped advance knowledge about genetics of human neurodevelopmental disease and congenital anomalies. It has aided in discovering new CNV syndromes and uncovering disease genes. It has discovered CNVs that are not fully penetrant and/or cause a spectrum of phenotypes, including intellectual disability, autism, schizophrenia, and dysmorphisms. Such CNVs can pose challenges to genetic counseling. They also have helped increase knowledge of genetic risk factors for neurodevelopmental disease and raised awareness of possible shared etiologies among these variable phenotypes. Advances in CMA technology allow CNV identification at increasingly finer scales, improving detection of pathogenic changes, although these sometimes are difficult to distinguish from normal population variation. This paper confronts some of the challenges uncovered by CMA testing while reviewing advances in genetics and the clinical use of this test that has replaced standard karyotyping in most genetic evaluations.
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Affiliation(s)
- Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States; Baylor Miraca Genetics Laboratories, Baylor College of Medicine, Houston, Texas, United States
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Clinical and Molecular Aspects of MBD5-Associated Neurodevelopmental Disorder (MAND). Eur J Hum Genet 2016; 24:1235-43. [PMID: 27222293 DOI: 10.1038/ejhg.2016.35] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Revised: 03/03/2016] [Accepted: 03/08/2016] [Indexed: 11/08/2022] Open
Abstract
MBD5-associated neurodevelopmental disorder (MAND) is an umbrella term that describes a group of disorders, 2q23.1 deletion syndrome, 2q23.1 duplication syndrome, and MBD5 variants, that affect the function of methyl-binding domain 5 (MBD5) and share a common set of neurodevelopmental, cognitive, and behavioral impairments. This review provides a comprehensive clinical and molecular synopsis of 2q23.1 deletion syndrome. Approaches to diagnosis, genetic counseling, and up-to-date management are summarized, followed by a discussion of the molecular and functional role of MBD5. Finally, we also include a brief summary of MBD5 variants that affect function of MBD5 and 2q23.1 duplication syndrome.
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Fry AE, Rees E, Thompson R, Mantripragada K, Blake P, Jones G, Morgan S, Jose S, Mugalaasi H, Archer H, McCann E, Clarke A, Taylor C, Davies S, Gibbon F, Te Water Naude J, Hartley L, Thomas G, White C, Natarajan J, Thomas RH, Drew C, Chung SK, Rees MI, Holmans P, Owen MJ, Kirov G, Pilz DT, Kerr MP. Pathogenic copy number variants and SCN1A mutations in patients with intellectual disability and childhood-onset epilepsy. BMC MEDICAL GENETICS 2016; 17:34. [PMID: 27113213 PMCID: PMC4845474 DOI: 10.1186/s12881-016-0294-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 04/14/2016] [Indexed: 11/10/2022]
Abstract
Background Copy number variants (CNVs) have been linked to neurodevelopmental disorders such as intellectual disability (ID), autism, epilepsy and psychiatric disease. There are few studies of CNVs in patients with both ID and epilepsy. Methods We evaluated the range of rare CNVs found in 80 Welsh patients with ID or developmental delay (DD), and childhood-onset epilepsy. We performed molecular cytogenetic testing by single nucleotide polymorphism array or microarray-based comparative genome hybridisation. Results 8.8 % (7/80) of the patients had at least one rare CNVs that was considered to be pathogenic or likely pathogenic. The CNVs involved known disease genes (EHMT1, MBD5 and SCN1A) and imbalances in genomic regions associated with neurodevelopmental disorders (16p11.2, 16p13.11 and 2q13). Prompted by the observation of two deletions disrupting SCN1A we undertook further testing of this gene in selected patients. This led to the identification of four pathogenic SCN1A mutations in our cohort. Conclusions We identified five rare de novo deletions and confirmed the clinical utility of array analysis in patients with ID/DD and childhood-onset epilepsy. This report adds to our clinical understanding of these rare genomic disorders and highlights SCN1A mutations as a cause of ID and epilepsy, which can easily be overlooked in adults. Electronic supplementary material The online version of this article (doi:10.1186/s12881-016-0294-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andrew E Fry
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK. .,Institute of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Rose Thompson
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Kiran Mantripragada
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Penny Blake
- Llwyneryr Unit, Learning Disability Services, Clasemont Road, Morriston, Swansea, SA6 6AH, UK
| | - Glyn Jones
- Learning Disabilities Directorate, Abertawe Bro Morgannwg University NHS Trust, Treseder Way, Caerau, Cardiff, CF5 5WF, UK
| | - Sian Morgan
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Sian Jose
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Hood Mugalaasi
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Hayley Archer
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Emma McCann
- Department of Clinical Genetics, Glan Clwyd Hospital, Betsi Cadwaladr University Health Board, Rhyl, Denbighshire, LL18 5UJ, UK
| | - Angus Clarke
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK.,Institute of Cancer and Genetics, Cardiff University, Cardiff, CF14 4XN, UK
| | - Clare Taylor
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Sally Davies
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Frances Gibbon
- Department of Paediatric Neurology, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Johann Te Water Naude
- Department of Paediatric Neurology, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Louise Hartley
- Department of Paediatric Neurology, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Gareth Thomas
- Department of Paediatric Neurology, Morriston Hospital, Abertawe Bro Morgannwg University Health Board, Swansea, SA6 6NL, UK
| | - Catharine White
- Department of Paediatric Neurology, Morriston Hospital, Abertawe Bro Morgannwg University Health Board, Swansea, SA6 6NL, UK
| | - Jaya Natarajan
- Department of Paediatrics, Royal Glamorgan Hospital, Cwm Taf University Health Board, Pontyclun, Mid Glamorgan, CF72 8XR, UK
| | - Rhys H Thomas
- Welsh Epilepsy Centre, Neurosciences Directorate, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Cheney Drew
- Neurology and Molecular Neuroscience Research, Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP, UK
| | - Seo-Kyung Chung
- Neurology and Molecular Neuroscience Research, Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP, UK
| | - Mark I Rees
- Neurology and Molecular Neuroscience Research, Institute of Life Science, College of Medicine, Swansea University, Swansea, SA2 8PP, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK
| | - Daniela T Pilz
- Institute of Medial Genetics, University Hospital of Wales, Cardiff, CF14 4XW, UK
| | - Michael P Kerr
- MRC Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, CF24 4HQ, UK.,Learning Disabilities Directorate, Abertawe Bro Morgannwg University NHS Trust, Treseder Way, Caerau, Cardiff, CF5 5WF, UK
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Turner T, Hormozdiari F, Duyzend M, McClymont S, Hook P, Iossifov I, Raja A, Baker C, Hoekzema K, Stessman H, Zody M, Nelson B, Huddleston J, Sandstrom R, Smith J, Hanna D, Swanson J, Faustman E, Bamshad M, Stamatoyannopoulos J, Nickerson D, McCallion A, Darnell R, Eichler E. Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA. Am J Hum Genet 2016; 98:58-74. [PMID: 26749308 DOI: 10.1016/j.ajhg.2015.11.023] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Accepted: 11/25/2015] [Indexed: 12/17/2022] Open
Abstract
We performed whole-genome sequencing (WGS) of 208 genomes from 53 families affected by simplex autism. For the majority of these families, no copy-number variant (CNV) or candidate de novo gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequencing (WES). We integrated multiple CNV and SNV analyses and extensive experimental validation to identify additional candidate mutations in eight families. We report that compared to control individuals, probands showed a significant (p = 0.03) enrichment of de novo and private disruptive mutations within fetal CNS DNase I hypersensitive sites (i.e., putative regulatory regions). This effect was only observed within 50 kb of genes that have been previously associated with autism risk, including genes where dosage sensitivity has already been established by recurrent disruptive de novo protein-coding mutations (ARID1B, SCN2A, NR3C2, PRKCA, and DSCAM). In addition, we provide evidence of gene-disruptive CNVs (in DISC1, WNT7A, RBFOX1, and MBD5), as well as smaller de novo CNVs and exon-specific SNVs missed by exome sequencing in neurodevelopmental genes (e.g., CANX, SAE1, and PIK3CA). Our results suggest that the detection of smaller, often multiple CNVs affecting putative regulatory elements might help explain additional risk of simplex autism.
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36
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Insights into Autism Spectrum Disorder Genomic Architecture and Biology from 71 Risk Loci. Neuron 2015; 87:1215-1233. [PMID: 26402605 DOI: 10.1016/j.neuron.2015.09.016] [Citation(s) in RCA: 915] [Impact Index Per Article: 101.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/05/2015] [Accepted: 09/09/2015] [Indexed: 11/22/2022]
Abstract
Analysis of de novo CNVs (dnCNVs) from the full Simons Simplex Collection (SSC) (N = 2,591 families) replicates prior findings of strong association with autism spectrum disorders (ASDs) and confirms six risk loci (1q21.1, 3q29, 7q11.23, 16p11.2, 15q11.2-13, and 22q11.2). The addition of published CNV data from the Autism Genome Project (AGP) and exome sequencing data from the SSC and the Autism Sequencing Consortium (ASC) shows that genes within small de novo deletions, but not within large dnCNVs, significantly overlap the high-effect risk genes identified by sequencing. Alternatively, large dnCNVs are found likely to contain multiple modest-effect risk genes. Overall, we find strong evidence that de novo mutations are associated with ASD apart from the risk for intellectual disability. Extending the transmission and de novo association test (TADA) to include small de novo deletions reveals 71 ASD risk loci, including 6 CNV regions (noted above) and 65 risk genes (FDR ≤ 0.1).
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Du Q, Luu PL, Stirzaker C, Clark SJ. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics 2015; 7:1051-73. [DOI: 10.2217/epi.15.39] [Citation(s) in RCA: 265] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
How DNA methylation is interpreted and influences genome regulation remains largely unknown. Proteins of the methyl-CpG-binding domain (MBD) family are primary candidates for the readout of DNA methylation as they recruit chromatin remodelers, histone deacetylases and methylases to methylated DNA associated with gene repression. MBD protein binding requires both functional MBD domains and methyl-CpGs; however, some MBD proteins also bind unmethylated DNA and active regulatory regions via alternative regulatory domains or interaction with the nucleosome remodeling deacetylase (NuRD/Mi-2) complex members. Mutations within MBD domains occur in many diseases, including neurological disorders and cancers, leading to loss of MBD binding specificity to methylated sites and gene deregulation. Here, we summarize the current state of knowledge about MBD proteins and their role as readers of the epigenome.
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Affiliation(s)
- Qian Du
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Phuc-Loi Luu
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Clare Stirzaker
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
| | - Susan J Clark
- Epigenetics Research Laboratory, Genomics & Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
- St Vincent's Clinical School, University of NSW, Darlinghurst, NSW 2010, Australia
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Fahrner JA, Bjornsson HT. Mendelian disorders of the epigenetic machinery: tipping the balance of chromatin states. Annu Rev Genomics Hum Genet 2015; 15:269-93. [PMID: 25184531 DOI: 10.1146/annurev-genom-090613-094245] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mendelian disorders of the epigenetic machinery are a newly delineated group of multiple congenital anomaly and intellectual disability syndromes resulting from mutations in genes encoding components of the epigenetic machinery. The gene products affected in these inherited conditions act in trans and are expected to have widespread epigenetic consequences. Many of these syndromes demonstrate phenotypic overlap with classical imprinting disorders and with one another. The various writer and eraser systems involve opposing players, which we propose must maintain a balance between open and closed chromatin states in any given cell. An imbalance might lead to disrupted expression of disease-relevant target genes. We suggest that classifying disorders based on predicted effects on this balance would be informative regarding pathogenesis. Furthermore, strategies targeted at restoring this balance might offer novel therapeutic avenues, taking advantage of available agents such as histone deacetylase inhibitors and histone acetylation antagonists.
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Affiliation(s)
- Jill A Fahrner
- McKusick-Nathans Institute of Genetic Medicine and Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205; ,
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39
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Phenotypic and molecular convergence of 2q23.1 deletion syndrome with other neurodevelopmental syndromes associated with autism spectrum disorder. Int J Mol Sci 2015; 16:7627-43. [PMID: 25853262 PMCID: PMC4425039 DOI: 10.3390/ijms16047627] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/19/2015] [Accepted: 03/19/2015] [Indexed: 12/21/2022] Open
Abstract
Roughly 20% of autism spectrum disorders (ASD) are syndromic with a well-established genetic cause. Studying the genes involved can provide insight into the molecular and cellular mechanisms of ASD. 2q23.1 deletion syndrome (causative gene, MBD5) is a recently identified genetic neurodevelopmental disorder associated with ASD. Mutations in MBD5 have been found in ASD cohorts. In this study, we provide a phenotypic update on the prevalent features of 2q23.1 deletion syndrome, which include severe intellectual disability, seizures, significant speech impairment, sleep disturbance, and autistic-like behavioral problems. Next, we examined the phenotypic, molecular, and network/pathway relationships between nine neurodevelopmental disorders associated with ASD: 2q23.1 deletion Rett, Angelman, Pitt-Hopkins, 2q23.1 duplication, 5q14.3 deletion, Kleefstra, Kabuki make-up, and Smith-Magenis syndromes. We show phenotypic overlaps consisting of intellectual disability, speech delay, seizures, sleep disturbance, hypotonia, and autistic-like behaviors. Molecularly, MBD5 possibly regulates the expression of UBE3A, TCF4, MEF2C, EHMT1 and RAI1. Network analysis reveals that there could be indirect protein interactions, further implicating function for these genes in common pathways. Further, we show that when MBD5 and RAI1 are haploinsufficient, they perturb several common pathways that are linked to neuronal and behavioral development. These findings support further investigations into the molecular and pathway relationships among genes linked to neurodevelopmental disorders and ASD, which will hopefully lead to common points of regulation that may be targeted toward therapeutic intervention.
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40
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Kato T. Whole genome/exome sequencing in mood and psychotic disorders. Psychiatry Clin Neurosci 2015; 69:65-76. [PMID: 25319632 DOI: 10.1111/pcn.12247] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/09/2014] [Indexed: 02/06/2023]
Abstract
Recent developments in DNA sequencing technologies have allowed for genetic studies using whole genome or exome analysis, and these have been applied in the study of mood and psychotic disorders, including bipolar disorder, depression, schizophrenia, and schizoaffective disorder. In this review, the current situation, recent findings, methodological problems, and future directions of whole genome/exome analysis studies of these disorders are summarized. Whole genome/exome studies of bipolar disorder have included pedigree analysis and case-control studies, demonstrating the role of previously implicated pathways, such as calcium signaling, cyclic adenosine monophosphate response element binding protein (CREB) signaling, and potassium channels. Extensive analysis of trio families and case-control studies showed that de novo mutations play a role in the genetic architecture of schizophrenia and indicated that mutations in several molecular pathways, including chromatin regulation, activity-regulated cytoskeleton, post-synaptic density, N-methyl-D-aspartate receptor, and targets of fragile X mental retardation protein, are associated with this disorder. Depression is a heterogeneous group of diseases and studies using exome analysis have been conducted to identify rare mutations causing Mendelian diseases that accompany depression. In the near future, clarification of the genetic architecture of bipolar disorder and schizophrenia is expected. Identification of causative mutations using these new technologies will facilitate neurobiological studies of these disorders.
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Affiliation(s)
- Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN Brain Science Institute, Wako, Japan
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41
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Kloosterman WP, Hochstenbach R. Deciphering the pathogenic consequences of chromosomal aberrations in human genetic disease. Mol Cytogenet 2014; 7:100. [PMID: 25606056 PMCID: PMC4299681 DOI: 10.1186/s13039-014-0100-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Accepted: 12/08/2014] [Indexed: 01/14/2023] Open
Abstract
Chromosomal aberrations include translocations, deletions, duplications, inversions, aneuploidies and complex rearrangements. They underlie genetic disease in roughly 15% of patients with multiple congenital abnormalities and/or mental retardation (MCA/MR). In genetic diagnostics, the pathogenicity of chromosomal aberrations in these patients is typically assessed based on criteria such as phenotypic similarity to other patients with the same or overlapping aberration, absence in healthy individuals, de novo occurrence, and protein coding gene content. However, a thorough understanding of the molecular mechanisms that lead to MCA/MR as a result of chromosome aberrations is often lacking. Chromosome aberrations can affect one or more genes in a complex manner, such as by changing the regulation of gene expression, by disrupting exons, and by creating fusion genes. The precise delineation of breakpoints by whole-genome sequencing enables the construction of local genomic architecture and facilitates the prediction of the molecular determinants of the patient's phenotype. Here, we review current methods for breakpoint identification and their impact on the interpretation of chromosome aberrations in patients with MCA/MR. In addition, we discuss opportunities to dissect disease mechanisms based on large-scale genomic technologies and studies in model organisms.
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Affiliation(s)
- Wigard P Kloosterman
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, P.O. Box 85060, 3508 AB Utrecht, The Netherlands
| | - Ron Hochstenbach
- Department of Medical Genetics, Genome Diagnostics, P.O. Box 85090, 3508 AB Utrecht, The Netherlands
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Mullegama SV, Elsea SH. Intragenic MBD5 familial deletion variant does not negatively impact MBD5 mRNA expression. Mol Cytogenet 2014; 7:80. [PMID: 25426169 PMCID: PMC4243375 DOI: 10.1186/s13039-014-0080-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 10/25/2014] [Indexed: 12/19/2022] Open
Abstract
2q23.1 deletion syndrome is characterized by intellectual disability, speech impairment, seizures, disturbed sleep pattern, behavioral problems, and hypotonia. Core features of this syndrome are due to haploinsufficiency of MBD5. Deletions that include coding and noncoding exons show reduced MBD5 mRNA expression. We report a patient with a neurological and behavioral phenotype similar to 2q23.1 deletion syndrome with an inherited intronic deletion in the 5-prime untranslated region of MBD5. Our data show that this patient has normal MBD5 mRNA expression; therefore, this deletion is likely not causative for 2q23.1 deletion syndrome. Overall, it is important to validate intronic deletions for pathogenicity.
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Affiliation(s)
- Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
| | - Sarah H Elsea
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, NAB2015, Houston, TX 77030 USA
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Mullegama SV, Pugliesi L, Burns B, Shah Z, Tahir R, Gu Y, Nelson DL, Elsea SH. MBD5 haploinsufficiency is associated with sleep disturbance and disrupts circadian pathways common to Smith-Magenis and fragile X syndromes. Eur J Hum Genet 2014; 23:781-9. [PMID: 25271084 DOI: 10.1038/ejhg.2014.200] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 07/23/2014] [Accepted: 08/26/2014] [Indexed: 11/09/2022] Open
Abstract
Individuals with autism spectrum disorders (ASD) who have an identifiable single-gene neurodevelopmental disorder (NDD), such as fragile X syndrome (FXS, FMR1), Smith-Magenis syndrome (SMS, RAI1), or 2q23.1 deletion syndrome (del 2q23.1, MBD5) share phenotypic features, including a high prevalence of sleep disturbance. We describe the circadian deficits in del 2q23.1 through caregiver surveys in which we identify several frequent sleep anomalies, including night/early awakenings, coughing/snoring loudly, and difficulty falling asleep. We couple these findings with studies on the molecular analysis of the circadian deficits associated with haploinsufficiency of MBD5 in which circadian gene mRNA levels of NR1D2, PER1, PER2, and PER3 were altered in del 2q23.1 lymphoblastoid cell lines (LCLs), signifying that haploinsufficiency of MBD5 can result in dysregulation of circadian rhythm gene expression. These findings were further supported by expression microarrays of MBD5 siRNA knockdown cells that showed significantly altered expression of additional circadian rhythm signaling pathway genes. Based on the common sleep phenotypes observed in del 2q23.1, SMS, and FXS patients, we explored the possibility that MBD5, RAI1, and FMR1 function in overlapping circadian rhythm pathways. Bioinformatic analysis identified conserved putative E boxes in MBD5 and RAI1, and expression levels of NR1D2 and CRY2 were significantly reduced in patient LCLs. Circadian and mTOR signaling pathways, both associated with sleep disturbance, were altered in both MBD5 and RAI1 knockdown microarray data, overlapping with findings associated with FMR1. These data support phenotypic and molecular overlaps across these syndromes that may be exploited to provide therapeutic intervention for multiple disorders.
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Affiliation(s)
- Sureni V Mullegama
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Loren Pugliesi
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Brooke Burns
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Zalak Shah
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Raiha Tahir
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Yanghong Gu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - David L Nelson
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Sarah H Elsea
- 1] Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA [2] Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
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Weissman J, Naidu S, Bjornsson HT. Abnormalities of the DNA methylation mark and its machinery: an emerging cause of neurologic dysfunction. Semin Neurol 2014; 34:249-57. [PMID: 25192503 PMCID: PMC4512289 DOI: 10.1055/s-0034-1386763] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, Mendelian disorders of the DNA methylation machinery have been described which demonstrate the complex roles of epigenetics in neurodevelopment and disease. For example, defects of DNMT1, the maintenance methyltransferase, lead to adult-onset progressive neurologic disorders, whereas defects of the de novo methyltransferases DNMT3A and DNMT3B lead to nonprogressive neurodevelopmental conditions. Furthermore, patients with DNMT3A deficiency demonstrate overgrowth, a feature common to disorders of histone machinery and imprinting disorders, highlighting the interconnectedness of the many epigenetic layers. Disorders of the DNA methylation machinery include both the aforementioned "writers" and also the "readers" of the methyl mark, such as MeCP2, the cause of Rett syndrome. Any dosage disruption, either haploinsufficiency or overexpression of DNA methylation machinery leads to widespread gene expression changes in trans, disrupting expression of a subset of target genes that contribute to individual disease phenotypes. In contrast, classical imprinting disorders such as Angelman syndrome have been thought generally to cause epigenetic dysregulation in cis. However, the recent description of multilocus methylation disorders challenges this generalization. Here, in addition to summarizing recent developments in identifying the pathogenesis of these diseases, we highlight clinical considerations and some unexpected therapeutic opportunities, such as topoisomerase inhibitors for classical imprinting disorders.
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Affiliation(s)
- Jacqueline Weissman
- Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sakkubai Naidu
- Kennedy Krieger Institute, Baltimore, Maryland
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hans T. Bjornsson
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland
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Blumenthal I, Ragavendran A, Erdin S, Klei L, Sugathan A, Guide J, Manavalan P, Zhou J, Wheeler V, Levin J, Ernst C, Roeder K, Devlin B, Gusella J, Talkowski M. Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. Am J Hum Genet 2014; 94:870-83. [PMID: 24906019 DOI: 10.1016/j.ajhg.2014.05.004] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 05/12/2014] [Indexed: 12/18/2022] Open
Abstract
Reciprocal copy-number variation (CNV) of a 593 kb region of 16p11.2 is a common genetic cause of autism spectrum disorder (ASD), yet it is not completely penetrant and can manifest in a wide array of phenotypes. To explore its molecular consequences, we performed RNA sequencing of cerebral cortex from mouse models with CNV of the syntenic 7qF3 region and lymphoblast lines from 34 members of 7 multiplex ASD-affected families harboring the 16p11.2 CNV. Expression of all genes in the CNV region correlated well with their DNA copy number, with no evidence of dosage compensation. We observed effects on gene expression outside the CNV region, including apparent positional effects in cis and in trans at genomic segments with evidence of physical interaction in Hi-C chromosome conformation data. One of the most significant positional effects was telomeric to the 16p11.2 CNV and includes the previously described "distal" 16p11.2 microdeletion. Overall, 16p11.2 CNV was associated with altered expression of genes and networks that converge on multiple hypotheses of ASD pathogenesis, including synaptic function (e.g., NRXN1, NRXN3), chromatin modification (e.g., CHD8, EHMT1, MECP2), transcriptional regulation (e.g., TCF4, SATB2), and intellectual disability (e.g., FMR1, CEP290). However, there were differences between tissues and species, with the strongest effects being consistently within the CNV region itself. Our analyses suggest that through a combination of indirect regulatory effects and direct effects on nuclear architecture, alteration of 16p11.2 genes disrupts expression networks that involve other genes and pathways known to contribute to ASD, suggesting an overlap in mechanisms of pathogenesis.
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Du X, An Y, Yu L, Liu R, Qin Y, Guo X, Sun D, Zhou S, Wu B, Jiang YH, Wang Y. A genomic copy number variant analysis implicates the MBD5 and HNRNPU genes in Chinese children with infantile spasms and expands the clinical spectrum of 2q23.1 deletion. BMC MEDICAL GENETICS 2014; 15:62. [PMID: 24885232 PMCID: PMC4061518 DOI: 10.1186/1471-2350-15-62] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 05/13/2014] [Indexed: 02/06/2023]
Abstract
Background Infantile spasms (IS) is a specific type of epileptic encephalopathy associated with severe developmental disabilities. Genetic factors are strongly implicated in IS, however, the exact genetic defects remain unknown in the majority of cases. Rare mutations in a single gene or in copy number variants (CNVs) have been implicated in IS of children in Western countries. The objective of this study was to dissect the role of copy number variations in Chinese children with infantile spasms. Methods We used the Agilent Human Genome CGH microarray 180 K for genome-wide detection of CNVs. Real-time qPCR was used to validate the CNVs. We performed genomic and medical annotations for individual CNVs to determine the pathogenicity of CNVs related to IS. Results We report herein the first genome-wide CNV analysis in children with IS, detecting a total of 14 CNVs in a cohort of 47 Chinese children with IS. Four CNVs (4/47 = 8.5%) (1q21.1 gain; 1q44, 2q31.1, and 17p13 loss) are considered to be pathogenic. The CNV loss at 17p13.3 contains PAFAH1B1 (LIS1), a causative gene for lissencephaly. Although the CNVs at 1q21.1, 1q44, and 2q23.1 have been previously implicated in a wide spectrum of clinical features including autism spectrum disorders (ASD) and generalized seizure, our study is the first report identifying them in individuals with a primary diagnosis of IS. The CNV loss in the 1q44 region contains HNRNPU, a strong candidate gene recently suggested in IS by the whole exome sequencing of children with IS. The CNV loss at 2q23.1 includes MBD5, a methyl-DNA binding protein that is a causative gene of ASD and a candidate gene for epileptic encephalopathy. We also report a distinct clinical presentation of IS, microcephaly, intellectual disability, and absent hallux in a case with the 2q23.1 deletion. Conclusion Our findings strongly support the role of CNVs in infantile spasms and expand the clinical spectrum associate with 2q23.1 deletion. In particular, our study implicates the HNRNPU and MBD5 genes in Chinese children with IS. Our study also supports that the molecular mechanisms of infantile spasms appear conserved among different ethnic backgrounds.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Yong-Hui Jiang
- Division of Neurology, Children's Hospital of Fudan University, 399 Wan Yuan Road, Shanghai 201102, China.
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Tao Y, Wu Q, Guo X, Zhang Z, Shen Y, Wang F. MBD5 regulates iron metabolism via methylation-independent genomic targeting of Fth1 through KAT2A in mice. Br J Haematol 2014; 166:279-91. [PMID: 24750026 DOI: 10.1111/bjh.12863] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 02/25/2014] [Indexed: 12/19/2022]
Abstract
Ferritin plays important roles in iron metabolism and controls iron absorption in the intestine. The ferritin subunits ferritin heavy chain (Fth1) and ferritin light chain (Ftl1) are tightly regulated at both the transcriptional and post-transcriptional levels. However, mechanisms of maintaining stable, basal expression of Fth1 are poorly understood. Here, we show that global deletion of Mbd5 in mice induces an iron overload phenotype. Liver and serum iron levels in Mbd5(-/-) mice were 3·2-fold and 1·5-fold higher respectively, than wild-type littermates; moreover, serum ferritin was increased >5-fold in the Mbd5(-/-) mice. Mbd5 encodes a member of the methyl-CpG binding domain family; however, the precise function of this gene is poorly understood. Here, we found that intestinal Fth1 mRNA levels were decreased in Mbd5(-/-) mice. Loss of Fth1 expression in the intestine could lead to iron over-absorption. Furthermore, deleting Mbd5 specifically in the intestine resulted in a phenotype similar to that of conditional deletion of Fth1 mice. An Fth1 promoter-report luciferase assay indicated that overexpression of Mbd5 enhanced Fth1 transcription in a dose-dependent manner. Histone H4 acetylation of the Fth1 promoter was reduced in the intestine of Mbd5(-/-) mice and further analysis showed that histone acetyltransferase KAT2A was essential for MBD5-induced Fth1 transcription.
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Affiliation(s)
- Yunlong Tao
- Key Laboratory of Nutrition and Metabolism, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Graduate School of the Chinese Academy of Sciences, Shanghai, China; Department of Nutrition, School of Public Health, Institute of Nutrition and Food Safety, Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, Zhejiang, China
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Suliman R, Ben-David E, Shifman S. Chromatin regulators, phenotypic robustness, and autism risk. Front Genet 2014; 5:81. [PMID: 24782891 PMCID: PMC3989700 DOI: 10.3389/fgene.2014.00081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 03/25/2014] [Indexed: 12/14/2022] Open
Abstract
Though extensively characterized clinically, the causes of autism spectrum disorder (ASD) remain a mystery. ASD is known to have a strong genetic basis, but it is genetically very heterogeneous. Recent studies have estimated that de novo disruptive mutations in hundreds of genes may contribute to ASD. However, it is unclear how it is possible for mutations in so many different genes to contribute to ASD. Recent findings suggest that many of the mutations disrupt genes involved in transcription regulation that are expressed prenatally in the developing brain. De novo disruptive mutations are also more frequent in girls with ASD, despite the fact that ASD is more prevalent in boys. In this paper, we hypothesize that loss of robustness may contribute to ASD. Loss of phenotypic robustness may be caused by mutations that disrupt capacitors that operate in the developing brain. This may lead to the release of cryptic genetic variation that contributes to ASD. Reduced robustness is consistent with the observed variability in expressivity and incomplete penetrance. It is also consistent with the hypothesis that the development of the female brain is more robust, and it may explain the higher rate and severity of disruptive de novo mutations in girls with ASD.
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Affiliation(s)
- Reut Suliman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Eyal Ben-David
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
| | - Sagiv Shifman
- Department of Genetics, The Institute of Life Sciences, The Hebrew University of Jerusalem Jerusalem, Israel
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Hanscom C, Talkowski M. Design of large-insert jumping libraries for structural variant detection using Illumina sequencing. CURRENT PROTOCOLS IN HUMAN GENETICS 2014; 80:7.22.1-7.22.9. [PMID: 24789519 PMCID: PMC4009510 DOI: 10.1002/0471142905.hg0722s80] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Next-generation sequencing is an important and efficient tool for the identification of structural variation, particularly balanced chromosomal rearrangements, because such events are not routinely detected by microarray and localization of altered regions by karyotype is imprecise. Indeed, the degree of resolution that can be obtained through next-generation technologies enables elucidation of precise breakpoints and has facilitated the discovery of numerous pathogenic loci in human disease and congenital anomalies. The protocol described here explains one type of large-insert "jumping library" and the steps required to generate such a library for multiplexed sequencing using Illumina sequencing technology. This approach allows for cost-efficient multiplexing of samples and provides a very high yield of fragments with large inserts, or "jumping" fragments.
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Affiliation(s)
- C Hanscom
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
| | - M Talkowski
- Molecular Neurogenetics Unit, Psychiatric and Neurodevelopmental Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts
- Department of Neurology, Harvard Medical School, Boston, Massachusetts
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Lionel AC, Tammimies K, Vaags AK, Rosenfeld JA, Ahn JW, Merico D, Noor A, Runke CK, Pillalamarri VK, Carter MT, Gazzellone MJ, Thiruvahindrapuram B, Fagerberg C, Laulund LW, Pellecchia G, Lamoureux S, Deshpande C, Clayton-Smith J, White AC, Leather S, Trounce J, Melanie Bedford H, Hatchwell E, Eis PS, Yuen RKC, Walker S, Uddin M, Geraghty MT, Nikkel SM, Tomiak EM, Fernandez BA, Soreni N, Crosbie J, Arnold PD, Schachar RJ, Roberts W, Paterson AD, So J, Szatmari P, Chrysler C, Woodbury-Smith M, Brian Lowry R, Zwaigenbaum L, Mandyam D, Wei J, Macdonald JR, Howe JL, Nalpathamkalam T, Wang Z, Tolson D, Cobb DS, Wilks TM, Sorensen MJ, Bader PI, An Y, Wu BL, Musumeci SA, Romano C, Postorivo D, Nardone AM, Monica MD, Scarano G, Zoccante L, Novara F, Zuffardi O, Ciccone R, Antona V, Carella M, Zelante L, Cavalli P, Poggiani C, Cavallari U, Argiropoulos B, Chernos J, Brasch-Andersen C, Speevak M, Fichera M, Ogilvie CM, Shen Y, Hodge JC, Talkowski ME, Stavropoulos DJ, Marshall CR, Scherer SW. Disruption of the ASTN2/TRIM32 locus at 9q33.1 is a risk factor in males for autism spectrum disorders, ADHD and other neurodevelopmental phenotypes. Hum Mol Genet 2013; 23:2752-68. [PMID: 24381304 DOI: 10.1093/hmg/ddt669] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Rare copy number variants (CNVs) disrupting ASTN2 or both ASTN2 and TRIM32 have been reported at 9q33.1 by genome-wide studies in a few individuals with neurodevelopmental disorders (NDDs). The vertebrate-specific astrotactins, ASTN2 and its paralog ASTN1, have key roles in glial-guided neuronal migration during brain development. To determine the prevalence of astrotactin mutations and delineate their associated phenotypic spectrum, we screened ASTN2/TRIM32 and ASTN1 (1q25.2) for exonic CNVs in clinical microarray data from 89 985 individuals across 10 sites, including 64 114 NDD subjects. In this clinical dataset, we identified 46 deletions and 12 duplications affecting ASTN2. Deletions of ASTN1 were much rarer. Deletions near the 3' terminus of ASTN2, which would disrupt all transcript isoforms (a subset of these deletions also included TRIM32), were significantly enriched in the NDD subjects (P = 0.002) compared with 44 085 population-based controls. Frequent phenotypes observed in individuals with such deletions include autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), speech delay, anxiety and obsessive compulsive disorder (OCD). The 3'-terminal ASTN2 deletions were significantly enriched compared with controls in males with NDDs, but not in females. Upon quantifying ASTN2 human brain RNA, we observed shorter isoforms expressed from an alternative transcription start site of recent evolutionary origin near the 3' end. Spatiotemporal expression profiling in the human brain revealed consistently high ASTN1 expression while ASTN2 expression peaked in the early embryonic neocortex and postnatal cerebellar cortex. Our findings shed new light on the role of the astrotactins in psychopathology and their interplay in human neurodevelopment.
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