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Dasgupta A, Nandi S, Gupta S, Roy S, Das C. To Ub or not to Ub: The epic dilemma of histones that regulate gene expression and epigenetic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195033. [PMID: 38750882 DOI: 10.1016/j.bbagrm.2024.195033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
A dynamic array of histone post-translational modifications (PTMs) regulate diverse cellular processes in the eukaryotic chromatin. Among them, histone ubiquitination is particularly complex as it alters nucleosome surface area fostering intricate cross-talk with other chromatin modifications. Ubiquitin signaling profoundly impacts DNA replication, repair, and transcription. Histones can undergo varied extent of ubiquitination such as mono, multi-mono, and polyubiquitination, which brings about distinct cellular fates. Mechanistic studies of the ubiquitin landscape in chromatin have unveiled a fascinating tapestry of events that orchestrate gene regulation. In this review, we summarize the key contributors involved in mediating different histone ubiquitination and deubiquitination events, and discuss their mechanism which impacts cell transcriptional identity and DNA damage response. We also focus on the proteins bearing epigenetic reader modules critical in discerning site-specific histone ubiquitination, pivotal for establishing complex epigenetic crosstalk. Moreover, we highlight the role of histone ubiquitination in different human diseases including neurodevelopmental disorders and cancer. Overall the review elucidates the intricate orchestration of histone ubiquitination impacting diverse cellular functions and disease pathogenesis, and provides insights into the current challenges of targeting them for therapeutic interventions.
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Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sayan Gupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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2
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Woods E, Holmes N, Albaba S, Evans IR, Balasubramanian M. ASXL3-related disorder: Molecular phenotyping and comprehensive review providing insights into disease mechanism. Clin Genet 2024; 105:470-487. [PMID: 38420660 DOI: 10.1111/cge.14506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/06/2024] [Accepted: 02/07/2024] [Indexed: 03/02/2024]
Abstract
ASXL3-related disorder, sometimes referred to as Bainbridge-Ropers syndrome, was first identified as a distinct neurodevelopmental disorder by Bainbridge et al. in 2013. Since then, there have been a number of case series and single case reports published worldwide. A comprehensive review of the literature was carried out. Abstracts were screened, relevant literature was analysed, and descriptions of common phenotypic features were quantified. ASXL3 variants were collated and categorised. Common phenotypic features comprised global developmental delay or intellectual disability (97%), feeding problems (76%), hypotonia (88%) and characteristic facial features (93%). The majority of genetic variants were de novo truncating variants in exon 11 or 12 of the ASXL3 gene. Several gaps in our knowledge of this disorder were identified, namely, underlying pathophysiology and disease mechanism, disease contribution of missense variants, relevance of variant location, prevalence and penetrance data. Clinical information is currently limited by patient numbers and lack of longitudinal data, which this review aims to address.
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Affiliation(s)
- Emily Woods
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, UK
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
| | - Nicola Holmes
- Sheffield Diagnostic Genetics Service, Sheffield Children's Hospital, Sheffield, UK
| | - Shadi Albaba
- Sheffield Diagnostic Genetics Service, Sheffield Children's Hospital, Sheffield, UK
| | - Iwan R Evans
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
- The Bateson Centre, University of Sheffield, Sheffield, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's Hospital, Sheffield, UK
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK
- The Bateson Centre, University of Sheffield, Sheffield, UK
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3
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Ryan CW, Peirent ER, Regan SL, Guxholli A, Bielas SL. H2A monoubiquitination: insights from human genetics and animal models. Hum Genet 2024; 143:511-527. [PMID: 37086328 DOI: 10.1007/s00439-023-02557-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023]
Abstract
Metazoan development arises from spatiotemporal control of gene expression, which depends on epigenetic regulators like the polycomb group proteins (PcG) that govern the chromatin landscape. PcG proteins facilitate the addition and removal of histone 2A monoubiquitination at lysine 119 (H2AK119ub1), which regulates gene expression, cell fate decisions, cell cycle progression, and DNA damage repair. Regulation of these processes by PcG proteins is necessary for proper development, as pathogenic variants in these genes are increasingly recognized to underly developmental disorders. Overlapping features of developmental syndromes associated with pathogenic variants in specific PcG genes suggest disruption of central developmental mechanisms; however, unique clinical features observed in each syndrome suggest additional non-redundant functions for each PcG gene. In this review, we describe the clinical manifestations of pathogenic PcG gene variants, review what is known about the molecular functions of these gene products during development, and interpret the clinical data to summarize the current evidence toward an understanding of the genetic and molecular mechanism.
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Affiliation(s)
- Charles W Ryan
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Medical Science Training Program, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Emily R Peirent
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Samantha L Regan
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
| | - Alba Guxholli
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48199-5618, USA
| | - Stephanie L Bielas
- Cellular and Molecular Biology Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
- Neuroscience Graduate Program, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA.
- Department of Human Genetics, University of Michigan Medical School, 3703 Med Sci II, 1241 E. Catherine St., Ann Arbor, MI, 48109-5618, USA.
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI, 48199-5618, USA.
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4
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Lomeli C. S, Kristin B. A. Epigenetic regulation of craniofacial development and disease. Birth Defects Res 2024; 116:e2271. [PMID: 37964651 PMCID: PMC10872612 DOI: 10.1002/bdr2.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/13/2023] [Accepted: 10/24/2023] [Indexed: 11/16/2023]
Abstract
BACKGROUND The formation of the craniofacial complex relies on proper neural crest development. The gene regulatory networks (GRNs) and signaling pathways orchestrating this process have been extensively studied. These GRNs and signaling cascades are tightly regulated as alterations to any stage of neural crest development can lead to common congenital birth defects, including multiple syndromes affecting facial morphology as well as nonsyndromic facial defects, such as cleft lip with or without cleft palate. Epigenetic factors add a hierarchy to the regulation of transcriptional networks and influence the spatiotemporal activation or repression of specific gene regulatory cascades; however less is known about their exact mechanisms in controlling precise gene regulation. AIMS In this review, we discuss the role of epigenetic factors during neural crest development, specifically during craniofacial development and how compromised activities of these regulators contribute to congenital defects that affect the craniofacial complex.
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Affiliation(s)
- Shull Lomeli C.
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Artinger Kristin B.
- Department of Diagnostic and Biological Sciences, University of Minnesota School of Dentistry, Minneapolis, MN, USA
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Zheng Y, Yang L, Niu M, Zhao S, Liang L, Wu Y, Li T, Yang F, Yang Z, Wang Y, Wang D. Identification of a de novo variant in the ASXL2 gene related to Shashi-Pena syndrome. Mol Genet Genomic Med 2023; 11:e2251. [PMID: 37493007 PMCID: PMC10655504 DOI: 10.1002/mgg3.2251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/06/2023] [Accepted: 07/13/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND ASXL2 encodes proteins involved in epigenetic regulation and the assembly of transcription factors at specific genomic loci. Germline de novo truncating variants in ASXL2 have been implicated in Shashi-Pena syndrome, which results in features of developmental delay (DD), glabellar nevus flammeus, hypotonia, and cardiac disorders. However, the variants are rare, and the clinical spectrum may be incomplete. METHODS The clinical data such as brain MRI were collect. The whole exome sequencing was performed for genetic etiology analysis. RESULTS Here, we report a patient with DD, hypotonia, early atrial septal defect, and abnormal white matter signal. She presented with Shashi-Pena syndrome with a truncated variant in ASXL2 (NM_018263.6, c.2142_2152del, p.Ser714Argfs*5). She died of a digestive tract infection when she was 1 year and 6 months old. CONCLUSIONS Our study further expanded the spectrum of phenotypes and genetic variations of the syndrome, and we believe that it is necessary to screen the ASXL2 gene in patients with DD and cardiac and bone disorders.
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Affiliation(s)
- Yanyan Zheng
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Le Yang
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Mengmeng Niu
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Siyu Zhao
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Lili Liang
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Yan Wu
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Taoli Li
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | | | | | - Yan Wang
- Department of NeurologyXi'an Children's HospitalXi'anChina
| | - Dong Wang
- Department of NeurologyXi'an Children's HospitalXi'anChina
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Lin I, Wei A, Awamleh Z, Singh M, Ning A, Herrera A, Russell BE, Weksberg R, Arboleda VA. Multiomics of Bohring-Opitz syndrome truncating ASXL1 mutations identify canonical and noncanonical Wnt signaling dysregulation. JCI Insight 2023; 8:e167744. [PMID: 37053013 PMCID: PMC10322691 DOI: 10.1172/jci.insight.167744] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/07/2023] [Indexed: 04/14/2023] Open
Abstract
ASXL1 (additional sex combs-like 1) plays key roles in epigenetic regulation of early developmental gene expression. De novo protein-truncating mutations in ASXL1 cause Bohring-Opitz syndrome (BOS; OMIM #605039), a rare neurodevelopmental condition characterized by severe intellectual disabilities, distinctive facial features, hypertrichosis, increased risk of Wilms tumor, and variable congenital anomalies, including heart defects and severe skeletal defects giving rise to a typical BOS posture. These BOS-causing ASXL1 variants are also high-prevalence somatic driver mutations in acute myeloid leukemia. We used primary cells from individuals with BOS (n = 18) and controls (n = 49) to dissect gene regulatory changes caused by ASXL1 mutations using comprehensive multiomics assays for chromatin accessibility (ATAC-seq), DNA methylation, histone methylation binding, and transcriptome in peripheral blood and skin fibroblasts. Our data show that regardless of cell type, ASXL1 mutations drive strong cross-tissue effects that disrupt multiple layers of the epigenome. The data showed a broad activation of canonical Wnt signaling at the transcriptional and protein levels and upregulation of VANGL2, which encodes a planar cell polarity pathway protein that acts through noncanonical Wnt signaling to direct tissue patterning and cell migration. This multiomics approach identifies the core impact of ASXL1 mutations and therapeutic targets for BOS and myeloid leukemias.
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Affiliation(s)
- Isabella Lin
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Angela Wei
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, California, USA
| | - Zain Awamleh
- Department of Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Meghna Singh
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Aileen Ning
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | - Analeyla Herrera
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
| | | | - Bianca E. Russell
- Division of Genetics, Department of Pediatrics, UCLA, Los Angeles, California, USA
| | - Rosanna Weksberg
- Department of Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Sciences and Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Valerie A. Arboleda
- Department of Human Genetics
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, UCLA, Los Angeles, California, USA
- Department of Computational Medicine, UCLA, Los Angeles, California, USA
- Interdepartmental BioInformatics Program, UCLA, Los Angeles, California, USA
- Molecular Biology Institute, UCLA, Los Angeles, California, USA
- Jonsson Comprehensive Cancer Center, UCLA, Los Angeles, California, USA
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7
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Yuan M, Shan Y, Xu F, Yang L, Sun C, Cheng R, Wu B, Zhang Z, Cao Y, Zhang R, Zhou W, Cheng G, Hu L. A newborn with a pathogenic variant in ASXL2 expanding the phenotype of SHAPNS: a case report and literature review. Transl Pediatr 2023; 12:86-96. [PMID: 36798937 PMCID: PMC9926125 DOI: 10.21037/tp-22-220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/02/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Shashi-Pena syndrome (SHAPNS) is a developmental disorder caused by mutations in additional sex combs-like Protein 2 (ASXL2). Since 2016, only 12 cases from 10 families have been reported. However, neonatal period characteristics remain largely unknown. Herein, we report a case with a pathogenic variant in ASXL2 in a newborn. CASE DESCRIPTION A newborn was diagnosed with a previously unreported de novo truncating mutation in ASXL2 (NM_018263.6) at 21 days and the clinical characteristics of all probands with ASXL2-related SHAPNS was reported in the literature. He had persistent hypoglycemia caused by inappropriate insulin levels and achieved stable glucose levels after octreotide treatment. Magnetic resonance imaging (MRI) revealed a small cerebellum, and fundoscopy showed bilateral retinal paving-stone-like white lesions. The results of trio-based whole exome sequencing (WES) were returned on the 21st day of life, and a heterozygous de novo truncating pathogenic c.1792C>T (p.Gln598*) variant in exon 11 of the ASXL2 gene was identified. The clinical features of our patient and another 10 probands with ASXL2-related SHAPNS reported in the literature were included in this review. More than half shared recognizable clinical features, including hypertelorism (11/11), broad nasal tip (10/11), arched eyebrows (9/11), a large V-shaped glabellar nevus flammeus on the forehead (9/11), low-set ears (8/11), posteriorly rotated ears (7/11), proptosis (6/11) and deep palm creases (6/11). Major clinical issues included feeding difficulties (10/11), developmental delay (10/11), skeletal and/or extremity abnormalities (8/11), progressive macrocephaly (8/11), hypotonia (8/11), hypoglycemia (6/11) and seizures (6/11). Neurodevelopmental regression was possible in patients (2/11) with normal MRI findings who later developed nonfebrile seizures. CONCLUSIONS We present a newborn diagnosing the SHAPNS by trio-WES, which is the earliest age of diagnosis. The application of octreotide for hypoglycemia, the small cerebellum and bilateral paving-stone-like white lesions of the retinas are described for the first time in an individual with ASXL2-related SHAPNS. Additional clinical reports of neonates with damaging ASXL2 variants are necessary to verify the mechanism and optimal treatment of ASXL2-related hypoglycemia, neurological damage and optic impairment. Neurological, endocrinological, ophthalmological, and rehabilitative follow-ups of these patients are necessary and important.
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Affiliation(s)
- Meng Yuan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yuanyuan Shan
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Fanshu Xu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Lin Yang
- Department of Endocrinology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Chengjun Sun
- Department of Endocrinology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Ruoqian Cheng
- Department of Endocrinology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Bingbing Wu
- Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Zhehuan Zhang
- Department of Ophthalmology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Yun Cao
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Key Laboratory of Neonatal Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Rong Zhang
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Wenhao Zhou
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Clinical Genetic Center, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Shanghai Key Laboratory of Birth Defects, The Translational Medicine Center of Children Development and Disease of Fudan University, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China.,Key Laboratory of Neonatal Diseases, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Guoqiang Cheng
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
| | - Liyuan Hu
- Department of Neonatology, Children's Hospital of Fudan University, National Children's Medical Center, Shanghai, China
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8
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Copy number variations on chromosome 2: impact on human phenotype, a cross-sectional study. Porto Biomed J 2023; 8:e198. [DOI: 10.1097/j.pbj.0000000000000198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 10/22/2022] [Indexed: 02/10/2023] Open
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Zhou Y, Liu J, Wu S, Li W, Zheng Y. Case report: A heterozygous mutation in ZNF462 leads to growth hormone deficiency. Front Genet 2022; 13:1015021. [PMID: 36568367 PMCID: PMC9770794 DOI: 10.3389/fgene.2022.1015021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/16/2022] [Indexed: 12/13/2022] Open
Abstract
Weiss-Kruszka syndrome (WSKA) is a rare disease most often caused by mutations in the ZNF462 gene. To screen for hereditary diseases, exons from the patient's genome were sequenced. Genomic PCR experiments followed by Sanger sequencing were used to confirm the mutated genomic regions in the patient and his parents. We report a new mutation site, a heterozygous mutation (NM_021224.6:c.6311dup) in ZNF462 in a male patient of 8 years old. The mutation in the ZNF462 gene caused WSKA. This patient is the first case with WSKA characterized by attention-deficit hyperactivity disorder and complete growth hormone deficiency without pituitary lesions. Our results suggest that the heterozygous mutation in ZNF462 is the direct cause of WSKA in this patient. Mutations in other genes interacting with ZNF462 result in similar symptoms of WSKA. Furthermore, ZNF462 and its interacting proteins ASXL2 and VPS13B may form a protein complex that is important for normal development but awaits more studies to reveal its detailed functions.
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Affiliation(s)
- Yikun Zhou
- Department of Endocrinology and Metabolism, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China,*Correspondence: Yikun Zhou, ; Yun Zheng,
| | - Jianmei Liu
- Department of Endocrinology and Metabolism, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Shuai Wu
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Wanran Li
- State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China
| | - Yun Zheng
- Department of Endocrinology and Metabolism, The First People’s Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China,State Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, China,College of Horticulture and Landscape, Yunnan Agricultural University, Kunming, China,*Correspondence: Yikun Zhou, ; Yun Zheng,
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10
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RINGs, DUBs and Abnormal Brain Growth-Histone H2A Ubiquitination in Brain Development and Disease. EPIGENOMES 2022; 6:epigenomes6040042. [PMID: 36547251 PMCID: PMC9778336 DOI: 10.3390/epigenomes6040042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/03/2022] Open
Abstract
During mammalian neurodevelopment, signaling pathways converge upon transcription factors (TFs) to establish appropriate gene expression programmes leading to the production of distinct neural and glial cell types. This process is partially regulated by the dynamic modulation of chromatin states by epigenetic systems, including the polycomb group (PcG) family of co-repressors. PcG proteins form multi-subunit assemblies that sub-divide into distinct, yet functionally related families. Polycomb repressive complexes 1 and 2 (PRC1 and 2) modify the chemical properties of chromatin by covalently modifying histone tails via H2A ubiquitination (H2AK119ub1) and H3 methylation, respectively. In contrast to the PRCs, the Polycomb repressive deubiquitinase (PR-DUB) complex removes H2AK119ub1 from chromatin through the action of the C-terminal hydrolase BAP1. Genetic screening has identified several PcG mutations that are causally associated with a range of congenital neuropathologies associated with both localised and/or systemic growth abnormalities. As PRC1 and PR-DUB hold opposing functions to control H2AK119ub1 levels across the genome, it is plausible that such neurodevelopmental disorders arise through a common mechanism. In this review, we will focus on advancements regarding the composition and opposing molecular functions of mammalian PRC1 and PR-DUB, and explore how their dysfunction contributes to the emergence of neurodevelopmental disorders.
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11
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Spedicati B, Morgan A, Pianigiani G, Musante L, Rubinato E, Santin A, Nardone GG, Faletra F, Girotto G. Challenging Occam’s Razor: Dual Molecular Diagnoses Explain Entangled Clinical Pictures. Genes (Basel) 2022; 13:genes13112023. [PMID: 36360260 PMCID: PMC9690221 DOI: 10.3390/genes13112023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 10/31/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022] Open
Abstract
Dual molecular diagnoses are defined as the presence of pathogenic variants at two distinct and independently segregating loci that cause two different Mendelian conditions. In this study, we report the identification of double genetic disorders in a series of patients with complex clinical features. In the last 24 months, 342 syndromic patients have been recruited and clinically characterised. Whole Exome Sequencing analysis has been performed on the proband and on both parents and identified seven patients affected by a dual molecular diagnosis. Upon a detailed evaluation of both their clinical and molecular features, subjects are able to be divided into two groups: (A) five patients who present distinct phenotypes, due to each of the two different underlying genetic diseases; (B) two patients with overlapping clinical features that may be underpinned by both the identified genetic variations. Notably, only in one case a multilocus genomic variation was already suspected during the clinical evaluation. Overall, our findings highlight how dual molecular diagnoses represent a challenging model of complex inheritance that should always be considered whenever a patient shows atypical clinical features. Indeed, an accurate genetic characterisation is of the utmost importance to provide patients with a personalised and safe clinical management.
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Affiliation(s)
- Beatrice Spedicati
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | - Anna Morgan
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giulia Pianigiani
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
- Correspondence: ; Tel.: +39-040-3785539
| | - Luciana Musante
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Elisa Rubinato
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Aurora Santin
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
| | | | - Flavio Faletra
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
| | - Giorgia Girotto
- Department of Medicine, Surgery and Health Sciences, University of Trieste, 34149 Trieste, Italy
- Institute for Maternal and Child Health-I.R.C.C.S. “Burlo Garofolo”, 34137 Trieste, Italy
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12
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Jones ER, Griffitt RJ. Oil and hypoxia alter DNA methylation and transcription of genes related to neurological function in larval Cyprinodon variegatus. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2022; 251:106267. [PMID: 36058102 DOI: 10.1016/j.aquatox.2022.106267] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 06/15/2023]
Abstract
DNA methylation is an important epigenetic mark involved in modulating transcription. While multiple studies document the ability of environmental stressors to alter methylation patterns, there is little information regarding the effects of oil and hypoxia on the methylome. Oil and hypoxic stress are threats in coastal ecosystems, which act as nursery habitats for developing fish. To explore the methylation altering effects of oil and hypoxia on developing fish, we exposed larval Cyprinodon variegatus to oil, hypoxia, or both for 48 h followed by 48 h of depuration in clean, normoxic conditions. We then used immunoprecipitation coupled with high-throughput sequencing (MeDIP seq) to evaluate genome-wide methylation changes. We also performed RNA seq to associate methylation and altered transcription. Oil and hypoxia together elicited greater impacts to methylation than either stressor individually. Additionally, the oil+hypoxia treatment exhibited an overlap between differentially methylated regions and differential gene expression at 20 loci. Functional analyses of these loci revealed enrichment of processes related to neurological function and development. Two neurological genes (slc1a2, asxl2) showed altered methylation of promoter CpG islands and transcriptional changes, suggesting epigenetic modulation of gene expression. Our results suggest a possible mechanism explaining altered behavior patterns noted in fish following oil exposure.
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Affiliation(s)
- Elizabeth R Jones
- School of Ocean Science and Engineering, The University of Southern Mississippi, 112 McIlwain Drive, Ocean Springs, MS 39564, USA; Department of Biology, Francis Marion University, 4822 Palmetto Street, Florence, South Carolina, 29506, USA.
| | - Robert J Griffitt
- School of Ocean Science and Engineering, The University of Southern Mississippi, 112 McIlwain Drive, Ocean Springs, MS 39564, USA
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13
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Murphy SA, O'Rourke NE, O'Grady MJ. Prepubertal onset of type 2 diabetes in Shashi-Pena syndrome due to ASXL2 mutation. Am J Med Genet A 2022; 188:2803-2807. [PMID: 35716351 DOI: 10.1002/ajmg.a.62876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/22/2022] [Accepted: 06/07/2022] [Indexed: 01/25/2023]
Abstract
Type 2 diabetes remains rare in the pediatric population and the majority of cases occur during puberty. A combination of genetic and environmental factors leads to the development of insulin resistance and β-cell failure. An increased prevalence is recognized in a number of rare genetic disorders such as Alström and Bardet-Biedl syndromes. Recently, a rare neurodevelopmental disorder, Shashi-Pena syndrome due to the dominant negative effect of heterozygous mutations in additional Sex-Combs-Like Genes 2 (ASXL2) has been reported. ASXL2 null mice exhibit glucose intolerance, insulin resistance and lipodystrophy. The regulatory role of ASXL2 in glucose and lipid homeostasis occurs through its interaction with peroxisome proliferator-activated receptor gamma (PPARγ), a gene implicated in the pathogenesis of type 2 diabetes on genome-wide association studies. Thiazolidinediones, used for the treatment of type 2 diabetes, exert their effects as direct agonists of PPARγ. We report the first case of type 2 diabetes in Shashi-Pena syndrome, occurring in an 8-year-old prepubertal boy with no family history. In addition, the proband had dyslipidemia, and fatty infiltration of the liver with elevated transaminases. Mutation of ASXL2 in humans, through its interaction with PPARγ appears to cause a phenotype of insulin resistance, type 2 diabetes, and dyslipidemia. Further reported cases will assist in confirming this association.
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Affiliation(s)
- Siobhan A Murphy
- Department of Paediatric Diabetes, Regional Hospital Mullingar, County Westmeath, Ireland
| | - Niamh E O'Rourke
- Department of Paediatric Diabetes, Regional Hospital Mullingar, County Westmeath, Ireland
| | - Michael Joseph O'Grady
- Department of Paediatric Diabetes, Regional Hospital Mullingar, County Westmeath, Ireland.,Women's and Children's Health, School of Medicine, University College Dublin, Dublin 4, Ireland
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14
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Barish S, Senturk M, Schoch K, Minogue AL, Lopergolo D, Fallerini C, Harland J, Seemann JH, Stong N, Kranz PG, Kansagra S, Mikati MA, Jasien J, El-Dairi M, Galluzzi P, Ariani F, Renieri A, Mari F, Wangler MF, Arur S, Jiang YH, Yamamoto S, Shashi V, Bellen HJ. The microRNA processor DROSHA is a candidate gene for a severe progressive neurological disorder. Hum Mol Genet 2022; 31:2934-2950. [PMID: 35405010 PMCID: PMC9433733 DOI: 10.1093/hmg/ddac085] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 03/14/2022] [Accepted: 04/05/2022] [Indexed: 11/15/2022] Open
Abstract
DROSHA encodes a ribonuclease that is a subunit of the Microprocessor complex and is involved in the first step of microRNA (miRNA) biogenesis. To date, DROSHA has not yet been associated with a Mendelian disease. Here, we describe two individuals with profound intellectual disability, epilepsy, white matter atrophy, microcephaly and dysmorphic features, who carry damaging de novo heterozygous variants in DROSHA. DROSHA is constrained for missense variants and moderately intolerant to loss-of-function (o/e = 0.24). The loss of the fruit fly ortholog drosha causes developmental arrest and death in third instar larvae, a severe reduction in brain size and loss of imaginal discs in the larva. Loss of drosha in eye clones causes small and rough eyes in adult flies. One of the identified DROSHA variants (p.Asp1219Gly) behaves as a strong loss-of-function allele in flies, while another variant (p.Arg1342Trp) is less damaging in our assays. In worms, a knock-in that mimics the p.Asp1219Gly variant at a worm equivalent residue causes loss of miRNA expression and heterochronicity, a phenotype characteristic of the loss of miRNA. Together, our data show that the DROSHA variants found in the individuals presented here are damaging based on functional studies in model organisms and likely underlie the severe phenotype involving the nervous system.
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Affiliation(s)
- Scott Barish
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Mumine Senturk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda L Minogue
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Diego Lopergolo
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Chiara Fallerini
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
| | - Jake Harland
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Jacob H Seemann
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mohamad A Mikati
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke Health, Durham, NC 27710, USA
| | - Paolo Galluzzi
- Department of Medical Genetics, NeuroImaging and NeuroInterventional Unit, Azienda Ospedaliera e Universitaria, Senese, Siena 53100, Italy
| | - Francesca Ariani
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Alessandra Renieri
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Francesca Mari
- Med Biotech Hub and Competence Center, Department of Medical Biotechnologies, University of Siena, Siena 53100, Italy
- Medical Genetics, University of Siena, Siena 53100, Italy
- Genetica Medica, Azienda Ospedaliera Universitaria Senese, Siena 53100, Italy
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Swathi Arur
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yong-Hui Jiang
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
- Yale School of Medicine, New Haven, CT 06510, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Howard Hughes Medical Institute, BCM, Houston, TX 77030, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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15
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Germline Abnormalities in DNA Methylation and Histone Modification and Associated Cancer Risk. Curr Hematol Malig Rep 2022; 17:82-93. [PMID: 35653077 DOI: 10.1007/s11899-022-00665-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2022] [Indexed: 11/03/2022]
Abstract
PURPOSE OF REVIEW Somatic mutations in DNA methyltransferases and other DNA methylation associated genes have been found in a wide variety of cancers. Germline mutations in these genes have been associated with several rare hereditary disorders. Among the described germline/congenital disorders, neurological dysfunction and/or growth abnormalities appear to be a common phenotype. Here, we outline known germline abnormalities and examine the cancer risks associated with these mutations. RECENT FINDINGS The increased use and availability of sequencing techniques in the clinical setting has expanded the identification of germline abnormalities involving DNA methylation machinery. This has provided additional cases to study these rare hereditary disorders and their predisposition to cancer. Studying these syndromes may offer an opportunity to better understand the contribution of these genes in cancer development.
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16
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Awamleh Z, Chater-Diehl E, Choufani S, Wei E, Kianmahd RR, Yu A, Chad L, Costain G, Tan WH, Scherer SW, Arboleda VA, Russell BE, Weksberg R. DNA methylation signature associated with Bohring-Opitz syndrome: a new tool for functional classification of variants in ASXL genes. Eur J Hum Genet 2022; 30:695-702. [PMID: 35361921 PMCID: PMC9177544 DOI: 10.1038/s41431-022-01083-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/20/2022] [Accepted: 03/01/2022] [Indexed: 01/01/2023] Open
Abstract
The additional sex combs-like (ASXL) gene family-encoded by ASXL1, ASXL2, and ASXL3-is crucial for mammalian development. Pathogenic variants in the ASXL gene family are associated with three phenotypically distinct neurodevelopmental syndromes. Our previous work has shown that syndromic conditions caused by pathogenic variants in epigenetic regulatory genes show consistent patterns of genome-wide DNA methylation (DNAm) alterations, i.e., DNAm signatures in peripheral blood. Given the role of ASXL1 in chromatin modification, we hypothesized that pathogenic ASXL1 variants underlying Bohring-Opitz syndrome (BOS) have a unique DNAm signature. We profiled whole-blood DNAm for 17 ASXL1 variants, and 35 sex- and age-matched typically developing individuals, using Illumina's Infinium EPIC array. We identified 763 differentially methylated CpG sites in individuals with BOS. Differentially methylated sites overlapped 323 unique genes, including HOXA5 and HOXB4, supporting the functional relevance of DNAm signatures. We used a machine-learning classification model based on the BOS DNAm signature to classify variants of uncertain significance in ASXL1, as well as pathogenic ASXL2 and ASXL3 variants. The DNAm profile of one individual with the ASXL2 variant was BOS-like, whereas the DNAm profiles of three individuals with ASXL3 variants were control-like. We also used Horvath's epigenetic clock, which showed acceleration in DNAm age in individuals with pathogenic ASXL1 variants, and the individual with the pathogenic ASXL2 variant, but not in individuals with ASXL3 variants. These studies enhance our understanding of the epigenetic dysregulation underpinning ASXL gene family-associated syndromes.
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Affiliation(s)
- Zain Awamleh
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Eric Chater-Diehl
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elizabeth Wei
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rebecca R Kianmahd
- Department of Pediatrics, Division of Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Anna Yu
- Department of Pediatrics, Division of Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Lauren Chad
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Paediatrics, University of Toronto, Toronto, ON, Canada
| | - Gregory Costain
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, ON, Canada
| | - Wen-Hann Tan
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Stephen W Scherer
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Ontario, ON, Canada
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada
| | - Valerie A Arboleda
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Pathology & Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Department of Computational Medicine, University of California, Los Angeles, CA, USA
| | - Bianca E Russell
- Department of Pediatrics, Division of Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Clinical & Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Ontario, ON, Canada.
- Institute of Medical Sciences, University of Toronto, Toronto, ON, Canada.
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17
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Wang Q, Zhang J, Jiang N, Xie J, Yang J, Zhao X. De novo nonsense variant in ASXL3 in a Chinese girl causing Bainbridge-Ropers syndrome: A case report and review of literature. Mol Genet Genomic Med 2022; 10:e1924. [PMID: 35276034 PMCID: PMC9034677 DOI: 10.1002/mgg3.1924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/18/2022] [Accepted: 02/28/2022] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Bainbridge-Ropers syndrome (BRPS, OMIM #615485) was first identified in 2013 by Bainbridge et al. and is a neurodevelopment disorder characterized by failure to thrive, facial dysmorphism and severe developmental delay. BRPS is caused by heterozygous loss-of-function (LOF) variants in the additional sex combs-like 3 (ASXL3) gene. Due to the limited specific recognizable features and overlapping symptoms with Bohring-Opitz syndrome (BOS, OMIM #612990), clinical diagnosis of BRPS is challenging. METHODS In this study, a 2-year-8-month-old Chinese girl was referred for genetic evaluation of severe developmental delay. The reduced fetal movement was found during the antenatal period and bilateral varus deformity of feet was observed at birth. Whole-exome sequencing and Sanger sequencing were used to detect and confirm the variant. RESULTS A novel nonsense variant c.1063G>T (p.E355*) in the ASXL3 gene (NM_030632.3) was identified in the proband and the clinical symptoms were compatible with BRPS. The parents were physical and genetic normal and prenatal diagnosis was requested for her pregnant mother with a negative Sanger sequencing result. CONCLUSION The study revealed a de novo LOF variant in the ASXL3 gene and expanded the mutation spectrum for this clinical condition. By performing a literature review, we summarized genetic results and the clinical phenotypes of all BPRSs reported so far. More cases study may help to elucidate the function of the ASXL3 gene may be critical to understand the genetic aetiology of this syndrome and assist in accurate genetic counselling, informed decision making and prenatal diagnosis.
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Affiliation(s)
- Qin Wang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Jianming Zhang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Nan Jiang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Jiansheng Xie
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
- The University of Hong Kong‐Shenzhen Hospital ShenzhenShenzhenChina
| | - Jingxin Yang
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
| | - Xiaoshan Zhao
- Affiliated Shenzhen Maternity & Child Healthcare HospitalSouthern Medical UniversityShenzhenChina
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18
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Carvalho J, Rolim S, Novo A, Proença E, Mota C, Carvalho C. Preterm Infant with Craniofacial Dysmorphic Features and Posture. Neoreviews 2022; 23:e208-e211. [PMID: 35229138 DOI: 10.1542/neo.23-3-e208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Joana Carvalho
- Pediatrics Department, Hospital Pedro Hispano, Matosinhos, Portugal
| | - Sara Rolim
- Pediatrics Department, Centro Hospitalar do Médio Ave, Famalicão, Portugal
| | - Ana Novo
- Neonatal Intensive Care Unit, Centro Materno Infantil do Norte, Porto, Portugal
| | - Elisa Proença
- Neonatal Intensive Care Unit, Centro Materno Infantil do Norte, Porto, Portugal
| | - Céu Mota
- Neonatal Intensive Care Unit, Centro Materno Infantil do Norte, Porto, Portugal
| | - Carmen Carvalho
- Neonatal Intensive Care Unit, Centro Materno Infantil do Norte, Porto, Portugal
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19
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Jiao Z, Zhao X, Wang Y, Wei E, Mei S, Liu N, Kong X, Shi H. A de novo and novel nonsense variants in ASXL2 gene is associated with Shashi-Pena syndrome. Eur J Med Genet 2022; 65:104454. [PMID: 35182806 DOI: 10.1016/j.ejmg.2022.104454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/18/2022] [Accepted: 02/14/2022] [Indexed: 11/03/2022]
Abstract
This ASXL2 gene encodes a member of a family of epigenetic regulators that bind various histone-modifying enzymes and are involved in the assembly of transcription factors at specific genomic loci. Recent research has found that pathogenic variants in ASXL2 gene can lead to Shashi-Pena syndrome. However, clinical reports of individuals with damaging ASXL2 variants were limited and clinical phenotypic information may also be incomplete at present. Here, we reported a patient from Chinese family presenting with Shashi-Pena syndrome duo to a nonsense variant c.2485C > T; p. (Gln829*) in ASXL2 and analyzed the clinical phenotypes of the patient. In addition to the typical facial appearance, feeding difficulty, cardiac dysfunction and developmental delay, the patient also demonstrated multiple clinical problems not reported in other published cases, including granulocytopenia, thrombocytopenia and "simian line". Additionally, this is also the first case of premature death associated to Shashi-Pena syndrome induced by ASXL2 variants in a Chinese population. Our results provided important information for genetic counseling of the family and broaden the spectrum of phenotypes and genetic variations of the syndrome.
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Affiliation(s)
- Zhihui Jiao
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, China; The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, China.
| | - Xuechao Zhao
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, China.
| | - Yanhong Wang
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, He Nan Province, China, No-33, Longhu Waihuan East Road, Zhengzhou, 450018, China.
| | - Erhu Wei
- Department of Pediatrics, First Affiliated Hospital of Zhengzhou University, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, China.
| | - Shiyue Mei
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, He Nan Province, China, No-33, Longhu Waihuan East Road, Zhengzhou, 450018, China.
| | - Ning Liu
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, China.
| | - Xiangdong Kong
- Genetics and Prenatal Diagnosis Center, The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, Jianshe Rd, Erqi District, Zhengzhou, Henan, 450052, China.
| | - Huirong Shi
- The Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, China.
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20
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Küry S, Ebstein F, Mollé A, Besnard T, Lee MK, Vignard V, Hery T, Nizon M, Mancini GM, Giltay JC, Cogné B, McWalter K, Deb W, Mor-Shaked H, Li H, Schnur RE, Wentzensen IM, Denommé-Pichon AS, Fourgeux C, Verheijen FW, Faurie E, Schot R, Stevens CA, Smits DJ, Barr E, Sheffer R, Bernstein JA, Stimach CL, Kovitch E, Shashi V, Schoch K, Smith W, van Jaarsveld RH, Hurst AC, Smith K, Baugh EH, Bohm SG, Vyhnálková E, Ryba L, Delnatte C, Neira J, Bonneau D, Toutain A, Rosenfeld JA, Audebert-Bellanger S, Gilbert-Dussardier B, Odent S, Laumonnier F, Berger SI, Smith AC, Bourdeaut F, Stern MH, Redon R, Krüger E, Margueron R, Bézieau S, Poschmann J, Isidor B, Isidor B. Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder. Am J Hum Genet 2022; 109:361-372. [PMID: 35051358 DOI: 10.1016/j.ajhg.2021.12.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bertrand Isidor
- Service de Génétique Médicale, CHU Nantes, 44093 Nantes, France; Université de Nantes, CHU Nantes, CNRS, INSERM, l'Institut du Thorax, 44007 Nantes, France.
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21
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Alqaisi D, Hassona Y. Oral findings and healthcare management in Shashi-Pena syndrome. SPECIAL CARE IN DENTISTRY 2021; 42:432-436. [PMID: 34902171 DOI: 10.1111/scd.12689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/30/2022]
Abstract
Shashi Pena syndrome (SHAPNS) is a newly recognized and rare neurodevelopmental disorder with unique phenotypic features. The syndrome is caused by truncating variants in ASXL2 gene. To date, there are only seven documented cases in scientific literature, but oral and dental findings are sparsely reported. Here, we present a new case of SHAPNS and describe the oro-dental findings and oral healthcare management of affected patients.
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Affiliation(s)
- Dua'a Alqaisi
- School of Dentistry, the University of Jordan, Amman, Jordan
| | - Yazan Hassona
- School of Dentistry, the University of Jordan, Amman, Jordan.,Oral Medicine and Special Care Dentistry, the University of Jordan, Amman, Jordan
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22
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Wang Y, Tan J, Wang Y, Liu A, Qiao F, Huang M, Zhang C, Zhou J, Hu P, Xu Z. Diagnosis of Shashi-Pena Syndrome Caused by Chromosomal Rearrangement Using Nanopore Sequencing. Neurol Genet 2021; 7:e635. [PMID: 34841066 PMCID: PMC8611502 DOI: 10.1212/nxg.0000000000000635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 09/14/2021] [Indexed: 12/02/2022]
Abstract
Background and Objectives The aim of this study was to uncover the genetic cause of delayed psychomotor development and variable intellectual disability in a proband whose previous genetic analyses, including chromosome microarray and whole exome sequencing, had been negative. Methods Long-read sequencing Oxford Nanopore Technology and RNA-seq analysis were performed on peripheral blood mononuclear cells. Genes with a fold change ≥ 1.5 and p ≤ 0.05 were identified as differentially expressed. Results Clinical examinations showed that the proband's features were similar to a rare autosomal-dominant neurodevelopmental syndrome, Shashi-Pena syndrome (MIM #617190). Karyotyping showed that a chromosomal balanced translocation t(2; 11) (p23; q23) was detected in the proband, her father, and her grandmother. Meanwhile, long-read sequencing identified 102 balanced translocations and 145 inversions affecting ASXL2 at an average of 15×. Combined with the family's RNA-seq results, the average mRNA expression of ASXL2 decreased in the patients. Discussion We identified a complex chromosomal rearrangement affecting ASXL2 as a pathogenic mechanism of Shashi-Pena syndrome in a Chinese family. This case study suggests that nanopore sequencing is suitable for pathogenic analysis of complex rearrangements, providing new avenues for the diagnosis of genetic diseases.
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Affiliation(s)
- Ya Wang
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jianxin Tan
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Yan Wang
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - An Liu
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Fengchang Qiao
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Mingtao Huang
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Cuiping Zhang
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Jing Zhou
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ping Hu
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Zhengfeng Xu
- Department of Prenatal Diagnosis, State Key Laboratory of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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23
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Oncogenic Truncations of ASXL1 Enhance a Motif for BRD4 ET-Domain Binding. J Mol Biol 2021; 433:167242. [PMID: 34536441 DOI: 10.1016/j.jmb.2021.167242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 11/23/2022]
Abstract
Proper regulation of gene-expression relies on specific protein-protein interactions between a myriad of epigenetic regulators. As such, mutation of genes encoding epigenetic regulators often drive cancer and developmental disorders. Additional sex combs-like protein 1 (ASXL1) is a key example, where mutations frequently drive haematological cancers and can cause developmental disorders. It has been reported that nonsense mutations in ASXL1 promote an interaction with BRD4, another central epigenetic regulator. Here we provide a molecular mechanism for the BRD4-ASXL1 interaction, demonstrating that a motif near to common truncation breakpoints of ASXL1 contains an epitope that binds the ET domain within BRD4. Binding-studies show that this interaction is analogous to common ET-binding modes of BRD4-interactors, and that all three ASX-like protein orthologs (ASXL1-3) contain a functional ET domain-binding epitope. Crucially, we observe that BRD4-ASXL1 binding is markedly increased in the prevalent ASXL1Y591X truncation that maintains the BRD4-binding epitope, relative to full-length ASXL1 or truncated proteins that delete the epitope. Together, these results show that ASXL1 truncation enhances BRD4 recruitment to transcriptional complexes via its ET domain, which could misdirect regulatory activity of either BRD4 or ASXL1 and may inform potential therapeutic interventions.
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24
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Rees E, Creeth HDJ, Hwu HG, Chen WJ, Tsuang M, Glatt SJ, Rey R, Kirov G, Walters JTR, Holmans P, Owen MJ, O'Donovan MC. Schizophrenia, autism spectrum disorders and developmental disorders share specific disruptive coding mutations. Nat Commun 2021; 12:5353. [PMID: 34504065 PMCID: PMC8429694 DOI: 10.1038/s41467-021-25532-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 08/16/2021] [Indexed: 12/24/2022] Open
Abstract
People with schizophrenia are enriched for rare coding variants in genes associated with neurodevelopmental disorders, particularly autism spectrum disorders and intellectual disability. However, it is unclear if the same changes to gene function that increase risk to neurodevelopmental disorders also do so for schizophrenia. Using data from 3444 schizophrenia trios and 37,488 neurodevelopmental disorder trios, we show that within shared risk genes, de novo variants in schizophrenia and neurodevelopmental disorders are generally of the same functional category, and that specific de novo variants observed in neurodevelopmental disorders are enriched in schizophrenia (P = 5.0 × 10-6). The latter includes variants known to be pathogenic for syndromic disorders, suggesting that schizophrenia be included as a characteristic of those syndromes. Our findings imply that, in part, neurodevelopmental disorders and schizophrenia have shared molecular aetiology, and therefore likely overlapping pathophysiology, and support the hypothesis that at least some forms of schizophrenia lie on a continuum of neurodevelopmental disorders.
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Affiliation(s)
- Elliott Rees
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Hugo D J Creeth
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | | | - Wei J Chen
- National Taiwan University, Taipei, Taiwan
| | - Ming Tsuang
- University of California, San Diego, La Jolla, CA, USA
| | | | - Romain Rey
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
- INSERM, U1028; CNRS, UMR5292; Lyon Neuroscience Research Center, Psychiatric Disorders: from Resistance to Response Team, Lyon, F-69000, France
| | - George Kirov
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - James T R Walters
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Peter Holmans
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK
| | - Michael J Owen
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
| | - Michael C O'Donovan
- MRC Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, School of Medicine, Cardiff University, Cardiff, UK.
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25
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Tamburri S, Conway E, Pasini D. Polycomb-dependent histone H2A ubiquitination links developmental disorders with cancer. Trends Genet 2021; 38:333-352. [PMID: 34426021 DOI: 10.1016/j.tig.2021.07.011] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/21/2021] [Accepted: 07/26/2021] [Indexed: 12/18/2022]
Abstract
Cell identity is tightly controlled by specific transcriptional programs which require post-translational modifications of histones. These histone modifications allow the establishment and maintenance of active and repressed chromatin domains. Histone H2A lysine 119 ubiquitination (H2AK119ub1) has an essential role in building repressive chromatin domains during development. It is regulated by the counteracting activities of the Polycomb repressive complex 1 (PRC1) and the Polycomb repressive-deubiquitinase (PR-DUB) complexes, two multi-subunit ensembles that write and erase this modification, respectively. We have catalogued the recurrent genetic alterations in subunits of the PRC1 and PR-DUB complexes in both neurodevelopmental disorders and cancer. These genetic lesions are often shared across disorders, and we highlight common mechanisms of H2AK119ub1 dysregulation and how they affect development in multiple disease contexts.
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Affiliation(s)
- Simone Tamburri
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
| | - Eric Conway
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- European Institute of Oncology (IEO), Istituto Di Ricovero e Cura a Carattere Scientifico (IRCCS), Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via Antonio di Rudinì 8, 20142 Milan, Italy.
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26
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Luo X, Schoch K, Jangam SV, Bhavana VH, Graves HK, Kansagra S, Jasien JM, Stong N, Keren B, Mignot C, Ravelli C, Bellen HJ, Wangler MF, Shashi V, Yamamoto S. Rare deleterious de novo missense variants in Rnf2/Ring2 are associated with a neurodevelopmental disorder with unique clinical features. Hum Mol Genet 2021; 30:1283-1292. [PMID: 33864376 PMCID: PMC8255132 DOI: 10.1093/hmg/ddab110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 04/09/2021] [Accepted: 04/14/2021] [Indexed: 01/16/2023] Open
Abstract
The Polycomb group (PcG) gene RNF2 (RING2) encodes a catalytic subunit of the Polycomb repressive complex 1 (PRC1), an evolutionarily conserved machinery that post-translationally modifies chromatin to maintain epigenetic transcriptional repressive states of target genes including Hox genes. Here, we describe two individuals, each with rare de novo missense variants in RNF2. Their phenotypes include intrauterine growth retardation, severe intellectual disabilities, behavioral problems, seizures, feeding difficulties and dysmorphic features. Population genomics data suggest that RNF2 is highly constrained for loss-of-function (LoF) and missense variants, and both p.R70H and p.S82R variants have not been reported to date. Structural analyses of the two alleles indicate that these changes likely impact the interaction between RNF2 and BMI1, another PRC1 subunit or its substrate Histone H2A, respectively. Finally, we provide functional data in Drosophila that these two missense variants behave as LoF alleles in vivo. The evidence provide support for deleterious alleles in RNF2 being associated with a new and recognizable genetic disorder. This tentative gene-disease association in addition to the 12 previously identified disorders caused by PcG genes attests to the importance of these chromatin regulators in Mendelian disorders.
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Affiliation(s)
- Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Sharayu V Jangam
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Venkata Hemanjani Bhavana
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Hillary K Graves
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Sujay Kansagra
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Joan M Jasien
- Division of Pediatric Neurology, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY 10032, USA
| | - Boris Keren
- Département de Génétique, Hospitalier Pitié-Salpêtrière, APHP, Paris 75013, France
- Sorbonne Université, Paris 75006, France
| | - Cyril Mignot
- Sorbonne Université, Paris 75006, France
- APHP, Sorbonne Université, Département de Génétique et Centre de Référence Déficiences Intellectuelles de Causes Rares, Groupe Hospitalier Pitié-Salpêtrière et Hôpital Trousseau, Paris 75013, France
| | - Claudia Ravelli
- Sorbonne Université, Paris 75006, France
- Département de Neuropédiatrie, Hôpital Armand Trousseau, APHP, Paris 75012, France
| | | | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
- Howard Hughes Medical Institute, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC 27710, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine (BCM), Houston, TX 77030, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX 77030, USA
- Department of Neuroscience, BCM, Houston, TX 77030, USA
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27
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Cuddapah VA, Dubbs HA, Adang L, Kugler SL, McCormick EM, Zolkipli-Cunningham Z, Ortiz-González XR, McCormack S, Zackai E, Licht DJ, Falk MJ, Marsh ED. Understanding the phenotypic spectrum of ASXL-related disease: Ten cases and a review of the literature. Am J Med Genet A 2021; 185:1700-1711. [PMID: 33751773 DOI: 10.1002/ajmg.a.62156] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 02/10/2021] [Accepted: 02/22/2021] [Indexed: 01/11/2023]
Abstract
Over the past decade, pathogenic variants in all members of the ASXL family of genes, ASXL1, ASXL2, and ASXL3, have been found to lead to clinically distinct but overlapping syndromes. Bohring-Opitz syndrome (BOPS) was first described as a clinical syndrome and later found to be associated with pathogenic variants in ASXL1. This syndrome is characterized by developmental delay, microcephaly, characteristic facies, hypotonia, and feeding difficulties. Subsequently, pathogenic variants in ASXL2 were found to lead to Shashi-Pena syndrome (SHAPNS) and in ASXL3 to lead to Bainbridge-Ropers syndrome (BRPS). While SHAPNS and BRPS share many core features with BOPS, there also seem to be emerging clear differences. Here, we present five cases of BOPS, one case of SHAPNS, and four cases of BRPS. By adding our cohort to the limited number of previously published patients, we review the overlapping features of ASXL-related diseases that bind them together, while focusing on the characteristics that make each neurodevelopmental syndrome unique. This will assist in diagnosis of these overlapping conditions and allow clinicians to more comprehensively counsel affected families.
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Affiliation(s)
- Vishnu Anand Cuddapah
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Holly A Dubbs
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Laura Adang
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Steven L Kugler
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Zarazuela Zolkipli-Cunningham
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xilma R Ortiz-González
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Shana McCormack
- Division of Endocrinology and Diabetes, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Elaine Zackai
- Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Daniel J Licht
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eric D Marsh
- Division of Neurology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Departments of Neurology and Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,The Epilepsy Neurogenetics Initiative, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
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28
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Lyu B, Dong Y, Kang J. A New Case of de novo Variant c.892C>T (p.Arg298Trp) in NACC1: A First Case Report From China. Front Pediatr 2021; 9:754261. [PMID: 34869110 PMCID: PMC8634650 DOI: 10.3389/fped.2021.754261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The nucleus accumbens associated 1 (NACC1) gene is a transcription factor member of the BTB/POZ family. A de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 may define a syndrome characterized by intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. Case Presentation: We report a new case with a neurodevelopmental disorder characterized by severe intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. Brain MRI reveals brain dysplasia. We observe a de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 gene in this case. Now, the child regularly goes to the hospital for rehabilitation training (once a month). Sodium Valproate (10 mg/kg/day) and Clobazam (10 mg/kg/day) are used in the treatment of epilepsy. A total of three articles were screened, and two papers were excluded. The search revealed one article related to a syndrome caused by a de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1; they screened the main clinical features of eight cases of a syndrome, which were summarized and analyzed. Conclusions: The NACC1 gene is a member of the BTB/POZ family of transcription factors. A de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 may define a syndrome characterized by intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. At present, there is no effective cure. In the future, we need more cases to determine the phenotype-genotype correlation of NACC1 variants. Many questions remain to be answered, and many challenges remain to be faced. Future transcriptional studies may further clarify this rare, recurrent variant, and could potentially lead to targeted therapies.
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Affiliation(s)
- Baiyu Lyu
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan Dong
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Kang
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
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29
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Li JR, Huang Z, Lu Y, Ji QY, Jiang MY, Yang F. Novel mutation in the ASXL3 gene in a Chinese boy with microcephaly and speech impairment: A case report. World J Clin Cases 2020; 8:6465-6472. [PMID: 33392332 PMCID: PMC7760454 DOI: 10.12998/wjcc.v8.i24.6465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/08/2020] [Accepted: 10/26/2020] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Bainbridge-Ropers syndrome (BRPS) is a severe disorder characterized by failure to thrive, facial dysmorphism, and severe developmental delay. BRPS is caused by a heterozygous loss-of-function mutation in the ASXL3 gene. Due to limited knowledge of the disease and lack of specific features, clinical diagnosis of this syndrome is challenging. With the use of trio-based whole exome sequencing, we identified a novel ASXL3 mutation in a Chinese boy with BRPS and performed a literature review.
CASE SUMMARY A 3-year-old Chinese boy was referred to our hospital due to progressive postnatal microcephaly and intellectual disability with severe speech impairment for 2 years. His other remarkable clinical features were shown as follows: Facial dysmorphism, feeding difficulties, poor growth, motor delay, and abnormal behavior. For the proband, regular laboratory tests, blood tandem mass spectrometry, urine gas chromatographic mass spectrometry, karyotype, hearing screening, and brain magnetic resonance imaging were performed, with negative results. Therefore, for the proband and his unaffected parents, trio-based whole exome sequencing and subsequent validation by Sanger sequencing were performed. A novel nonsense variant in exon 11 of the ASXL3 gene (c.1795G>T; p.E599*) was detected, present in the patient but absent from his parents. Taking into account the concordant phenotypic features of our patient with reported BRPS patients and the detected truncated variant located in the known mutational cluster region, we confirmed a diagnosis of BRPS for this proband. The rehabilitation treatment seemed to have a mild effect.
CONCLUSION In this case, a novel nonsense mutation (c.1795G>T, p.E599*) in ASXL3 gene was identified in a Chinese boy with BRPS. This finding not only contributed to better genetic counseling and prenatal diagnosis for this family but also expanded the pathogenic mutation spectrum of ASXL3 gene and provided key information for clinical diagnosis of BRPS.
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Affiliation(s)
- Jin-Rong Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Department of Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu 610041, Sichuan Province, China
| | - Zhuo Huang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - You Lu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Qiao-Yun Ji
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
| | - Ming-Yan Jiang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Department of Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu 610041, Sichuan Province, China
| | - Fan Yang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu 610041, Sichuan Province, China
- Department of Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Chengdu 610041, Sichuan Province, China
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30
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Yu KPT, Luk HM, Fung JLF, Chung BHY, Lo IFM. Further expanding the clinical phenotype in Bainbridge-Ropers syndrome and dissecting genotype-phenotype correlation in the ASXL3 mutational cluster regions. Eur J Med Genet 2020; 64:104107. [PMID: 33242595 DOI: 10.1016/j.ejmg.2020.104107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/22/2020] [Accepted: 11/15/2020] [Indexed: 11/30/2022]
Abstract
Bainbridge-Ropers syndrome (BRPS) [OMIM#615485] is a neurodevelopmental disorder, characterized by delayed psychomotor development with generalized hypotonia, intellectual disability with poor or absent speech, feeding difficulties, growth failure, specific craniofacial and minor skeletal features. It was firstly reported in 2013 by Bainbridge et al., who observed a group of individuals sharing overlapping features with Bohring-Opitz syndrome which were caused by pathogenic variant in ASXL1, who indeed carried truncating mutations in ASXL3. To date, 33 cases were described in the literature. BRPS is caused by loss-of-function mutations in ASXL3 which are mostly located in two mutational cluster regions (MCR). The exact molecular mechanism of these mutations resulting in the disease phenotype is still uncertain due to the observation of LOF mutations in healthy population. Here, we report four individuals with BRPS carrying de novo LOF mutations in ASXL3, comparing and summarizing the clinical phenotype of all BRPS reported so far. Furthermore, we try to dissect the genotype-phenotype correlation among the two well reported MCRs in all BRPS from the literature.
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Affiliation(s)
- Kris Pui-Tak Yu
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong.
| | - Ho-Ming Luk
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong
| | - Jasmine L F Fung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, HKSAR, Hong Kong
| | - Brian Hon-Yin Chung
- Department of Paediatrics and Adolescent Medicine, University of Hong Kong, HKSAR, Hong Kong
| | - Ivan Fai-Man Lo
- Clinical Genetic Service, Department of Health, University of Hong Kong, HKSAR, Hong Kong
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Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes. Nat Commun 2020; 11:5947. [PMID: 33230107 PMCID: PMC7683540 DOI: 10.1038/s41467-020-19722-9] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Accepted: 10/12/2020] [Indexed: 12/19/2022] Open
Abstract
Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed. Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
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Reddington CJ, Fellner M, Burgess AE, Mace PD. Molecular Regulation of the Polycomb Repressive-Deubiquitinase. Int J Mol Sci 2020; 21:ijms21217837. [PMID: 33105797 PMCID: PMC7660087 DOI: 10.3390/ijms21217837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/20/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022] Open
Abstract
Post-translational modification of histone proteins plays a major role in histone–DNA packaging and ultimately gene expression. Attachment of ubiquitin to the C-terminal tail of histone H2A (H2AK119Ub in mammals) is particularly relevant to the repression of gene transcription, and is removed by the Polycomb Repressive-Deubiquitinase (PR-DUB) complex. Here, we outline recent advances in the understanding of PR-DUB regulation, which have come through structural studies of the Drosophila melanogaster PR-DUB, biochemical investigation of the human PR-DUB, and functional studies of proteins that associate with the PR-DUB. In humans, mutations in components of the PR-DUB frequently give rise to malignant mesothelioma, melanomas, and renal cell carcinoma, and increase disease risk from carcinogens. Diverse mechanisms may underlie disruption of the PR-DUB across this spectrum of disease. Comparing and contrasting the PR-DUB in mammals and Drosophila reiterates the importance of H2AK119Ub through evolution, provides clues as to how the PR-DUB is dysregulated in disease, and may enable new treatment approaches in cancers where the PR-DUB is disrupted.
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Do Antibiotics Reduce the Incidence of Infections After Percutaneous Endoscopic Gastrostomy Placement in Children? J Pediatr Gastroenterol Nutr 2020; 71:23-28. [PMID: 32205769 DOI: 10.1097/mpg.0000000000002709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVE Percutaneous endoscopic gastrostomy (PEG) provides a long-term solution for tube dependency. Pediatric guidelines recommend prophylactic antibiotic treatment (ABT) based on adult studies. AIM To compare wound infection and other complications in children receiving a PEG with and without prophylactic ABT. METHODS Retrospective study including children 0 to 18 years undergoing PEG placement. Patients with (2010-2013) and without (2000-2010) ABT were compared with respect to the occurrence of wound infection and other complications. RESULTS In total, 297 patients were included (median age 2.9 years, 53% boys). Patients receiving ABT per PEG protocol (n = 78) had a similar wound infection rate (17.9% vs 21%, P = 0.625), significantly less fever (3.8% vs 14.6%, P = 0.013), leakage (0% vs 9.1%, P = 0.003) and shorter hospital admission (2 vs 4 days, P = 0.000), but more overgranulation (28.2% vs 8.7%, P = 0.000) compared with those without (n = 219). Patients receiving any ABT, per PEG protocol or clinical indication (n = 115), had similar occurrence of wound infection (19.1% vs 20.9%, P = 0.768), fever (7.8% vs 14.3%, P = 0.100) and leakage (3.5% vs 8.8%, P = 0.096), a significantly shorter hospital admission (3 vs 4 days, P = 0.000), but more overgranulation (21.7% vs 8.8%, P =0.003) compared with those without (n = 182). CONCLUSIONS Prophylactic ABT does not seem to reduce the occurrence of wound infection but it might be beneficial with respect to fever, leakage and duration of hospital admission, but not overgranulation. A randomized controlled trial is needed to confirm our results.
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Identification of Differentially Methylated CpG Sites in Fibroblasts from Keloid Scars. Biomedicines 2020; 8:biomedicines8070181. [PMID: 32605309 PMCID: PMC7400180 DOI: 10.3390/biomedicines8070181] [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: 05/31/2020] [Revised: 06/20/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022] Open
Abstract
As a part of an abnormal healing process of dermal injuries and irritation, keloid scars arise on the skin as benign fibroproliferative tumors. Although the etiology of keloid scarring remains unsettled, considerable recent evidence suggested that keloidogenesis may be driven by epigenetic changes, particularly, DNA methylation. Therefore, genome-wide scanning of methylated cytosine-phosphoguanine (CpG) sites in extracted DNA from 12 keloid scar fibroblasts (KF) and 12 control skin fibroblasts (CF) (six normal skin fibroblasts and six normotrophic fibroblasts) was conducted using the Illumina Human Methylation 450K BeadChip in two replicates for each sample. Comparing KF and CF used a Linear Models for Microarray Data (Limma) model revealed 100,000 differentially methylated (DM) CpG sites, 20,695 of which were found to be hypomethylated and 79,305 were hypermethylated. The top DM CpG sites were associated with TNKS2, FAM45B, LOC723972, GAS7, RHBDD2 and CAMKK1. Subsequently, the most functionally enriched genes with the top 100 DM CpG sites were significantly (p ≤ 0.05) associated with SH2 domain binding, regulation of transcription, DNA-templated, nucleus, positive regulation of protein targeting to mitochondrion, nucleoplasm, Swr1 complex, histone exchange, and cellular response to organic substance. In addition, NLK, CAMKK1, LPAR2, CASP1, and NHS showed to be the most common regulators in the signaling network analysis. Taken together, these findings shed light on the methylation status of keloids that could be implicated in the underlying mechanism of keloid scars formation and remission.
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35
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Zou W, Rohatgi N, Brestoff JR, Moley JR, Li Y, Williams JW, Alippe Y, Pan H, Pietka TA, Mbalaviele G, Newberry EP, Davidson NO, Dey A, Shoghi KI, Head RD, Wickline SA, Randolph GJ, Abumrad NA, Teitelbaum SL. Myeloid-specific Asxl2 deletion limits diet-induced obesity by regulating energy expenditure. J Clin Invest 2020; 130:2644-2656. [PMID: 32310225 PMCID: PMC7190927 DOI: 10.1172/jci128687] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 02/04/2020] [Indexed: 01/13/2023] Open
Abstract
We previously established that global deletion of the enhancer of trithorax and polycomb (ETP) gene, Asxl2, prevents weight gain. Because proinflammatory macrophages recruited to adipose tissue are central to the metabolic complications of obesity, we explored the role of ASXL2 in myeloid lineage cells. Unexpectedly, mice without Asxl2 only in myeloid cells (Asxl2ΔLysM) were completely resistant to diet-induced weight gain and metabolically normal despite increased food intake, comparable activity, and equivalent fecal fat. Asxl2ΔLysM mice resisted HFD-induced adipose tissue macrophage infiltration and inflammatory cytokine gene expression. Energy expenditure and brown adipose tissue metabolism in Asxl2ΔLysM mice were protected from the suppressive effects of HFD, a phenomenon associated with relatively increased catecholamines likely due to their suppressed degradation by macrophages. White adipose tissue of HFD-fed Asxl2ΔLysM mice also exhibited none of the pathological remodeling extant in their control counterparts. Suppression of macrophage Asxl2 expression, via nanoparticle-based siRNA delivery, prevented HFD-induced obesity. Thus, ASXL2 controlled the response of macrophages to dietary factors to regulate metabolic homeostasis, suggesting modulation of the cells' inflammatory phenotype may impact obesity and its complications.
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Affiliation(s)
- Wei Zou
- Department of Pathology and Immunology and
| | | | | | | | - Yongjia Li
- Department of Pathology and Immunology and
| | | | - Yael Alippe
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Hua Pan
- Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Terri A. Pietka
- Division of Geriatrics and Nutritional Science, Department of Medicine, and
| | - Gabriel Mbalaviele
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Elizabeth P. Newberry
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Nicholas O. Davidson
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Anwesha Dey
- Department of Discovery Oncology, Genentech Inc., South San Francisco, California, USA
| | - Kooresh I. Shoghi
- Department of Radiology
- Department of Biomedical Engineering
- Division of Biology and Biomedical Sciences and
| | - Richard D. Head
- Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Samuel A. Wickline
- Department of Cardiovascular Sciences, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | | | - Nada A. Abumrad
- Division of Geriatrics and Nutritional Science, Department of Medicine, and
| | - Steven L. Teitelbaum
- Department of Pathology and Immunology and
- Division of Bone and Mineral Diseases, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
- Shriners Hospitals for Children, St. Louis, Missouri, USA
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Lichtig H, Artamonov A, Polevoy H, Reid CD, Bielas SL, Frank D. Modeling Bainbridge-Ropers Syndrome in Xenopus laevis Embryos. Front Physiol 2020; 11:75. [PMID: 32132929 PMCID: PMC7040374 DOI: 10.3389/fphys.2020.00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 01/23/2020] [Indexed: 12/14/2022] Open
Abstract
The Additional sex combs-like (ASXL1-3) genes are linked to human neurodevelopmental disorders. The de novo truncating variants in ASXL1-3 proteins serve as the genetic basis for severe neurodevelopmental diseases such as Bohring-Opitz, Shashi-Pena, and Bainbridge-Ropers syndromes, respectively. The phenotypes of these syndromes are similar but not identical, and include dramatic craniofacial defects, microcephaly, developmental delay, and severe intellectual disability, with a loss of speech and language. Bainbridge-Ropers syndrome resulting from ASXL3 gene mutations also includes features of autism spectrum disorder. Human genomic studies also identified missense ASXL3 variants associated with autism spectrum disorder, but lacking more severe Bainbridge-Ropers syndromic features. While these findings strongly implicate ASXL3 in mammalian brain development, its functions are not clearly understood. ASXL3 protein is a component of the polycomb deubiquitinase complex that removes mono-ubiquitin from Histone H2A. Dynamic chromatin modifications play important roles in the specification of cell fates during early neural patterning and development. In this study, we utilize the frog, Xenopus laevis as a simpler and more accessible vertebrate neurodevelopmental model system to understand the embryological cause of Bainbridge-Ropers syndrome. We have found that ASXL3 protein knockdown during early embryo development highly perturbs neural cell fate specification, potentially resembling the Bainbridge-Ropers syndrome phenotype in humans. Thus, the frog embryo is a powerful tool for understanding the etiology of Bainbridge-Ropers syndrome in humans.
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Affiliation(s)
- Hava Lichtig
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Artyom Artamonov
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hanna Polevoy
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
| | - Christine D Reid
- Department of Genetics, Stanford University, Stanford, CA, United States
| | - Stephanie L Bielas
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, United States
| | - Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion - Israel Institute of Technology, Haifa, Israel
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37
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Karaca E, Posey JE, Bostwick B, Liu P, Gezdirici A, Yesil G, Coban Akdemir Z, Bayram Y, Harms FL, Meinecke P, Alawi M, Bacino CA, Sutton VR, Kortüm F, Lupski JR. Biallelic and De Novo Variants in DONSON Reveal a Clinical Spectrum of Cell Cycle-opathies with Microcephaly, Dwarfism and Skeletal Abnormalities. Am J Med Genet A 2019; 179:2056-2066. [PMID: 31407851 DOI: 10.1002/ajmg.a.61315] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/10/2019] [Accepted: 07/14/2019] [Indexed: 01/30/2023]
Abstract
Co-occurrence of primordial dwarfism and microcephaly together with particular skeletal findings are seen in a wide range of Mendelian syndromes including microcephaly micromelia syndrome (MMS, OMIM 251230), microcephaly, short stature, and limb abnormalities (MISSLA, OMIM 617604), and microcephalic primordial dwarfisms (MPDs). Genes associated with these syndromes encode proteins that have crucial roles in DNA replication or in other critical steps of the cell cycle that link DNA replication to cell division. We identified four unrelated families with five affected individuals having biallelic or de novo variants in DONSON presenting with a core phenotype of severe short stature (z score < -3 SD), additional skeletal abnormalities, and microcephaly. Two apparently unrelated families with identical homozygous c.631C > T p.(Arg211Cys) variant had clinical features typical of Meier-Gorlin syndrome (MGS), while two siblings with compound heterozygous c.346delG p.(Asp116Ile*62) and c.1349A > G p.(Lys450Arg) variants presented with Seckel-like phenotype. We also identified a de novo c.683G > T p.(Trp228Leu) variant in DONSON in a patient with prominent micrognathia, short stature and hypoplastic femur and tibia, clinically diagnosed with Femoral-Facial syndrome (FFS, OMIM 134780). Biallelic variants in DONSON have been recently described in individuals with microcephalic dwarfism. These studies also demonstrated that DONSON has an essential conserved role in the cell cycle. Here we describe novel biallelic and de novo variants that are associated with MGS, Seckel-like phenotype and FFS, the last of which has not been associated with any disease gene to date.
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Affiliation(s)
- Ender Karaca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Bret Bostwick
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Alper Gezdirici
- Department of Medical Genetics, Kanuni Sultan Suleyman Training and Research Hospital, Istanbul, Turkey
| | - Gozde Yesil
- Department of Medical Genetics, Bezmialem University, Istanbul, Turkey
| | - Zeynep Coban Akdemir
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Yavuz Bayram
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Frederike L Harms
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Peter Meinecke
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Service Facility, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Center for Bioinformatics, University of Hamburg, Hamburg, Germany.,Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Virus Genomics, Hamburg, Germany
| | - Carlos A Bacino
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Fanny Kortüm
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Baylor College of Medicine, Houston, Texas.,Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, 1 Baylor Plaza, Houston, Texas
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38
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Kruszka P, Hu T, Hong S, Signer R, Cogné B, Isidor B, Mazzola SE, Giltay JC, van Gassen KLI, England EM, Pais L, Ockeloen CW, Sanchez-Lara PA, Kinning E, Adams DJ, Treat K, Torres-Martinez W, Bedeschi MF, Iascone M, Blaney S, Bell O, Tan TY, Delrue MA, Jurgens J, Barry BJ, Engle EC, Savage SK, Fleischer N, Martinez-Agosto JA, Boycott K, Zackai EH, Muenke M. Phenotype delineation of ZNF462 related syndrome. Am J Med Genet A 2019; 179:2075-2082. [PMID: 31361404 DOI: 10.1002/ajmg.a.61306] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/30/2019] [Accepted: 07/09/2019] [Indexed: 12/20/2022]
Abstract
Zinc finger protein 462 (ZNF462) is a relatively newly discovered vertebrate specific protein with known critical roles in embryonic development in animal models. Two case reports and a case series study have described the phenotype of 10 individuals with ZNF462 loss of function variants. Herein, we present 14 new individuals with loss of function variants to the previous studies to delineate the syndrome of loss of function in ZNF462. Collectively, these 24 individuals present with recurring phenotypes that define a multiple congenital anomaly syndrome. Most have some form of developmental delay (79%) and a minority has autism spectrum disorder (33%). Characteristic facial features include ptosis (83%), down slanting palpebral fissures (58%), exaggerated Cupid's bow/wide philtrum (54%), and arched eyebrows (50%). Metopic ridging or craniosynostosis was found in a third of study participants and feeding problems in half. Other phenotype characteristics include dysgenesis of the corpus callosum in 25% of individuals, hypotonia in half, and structural heart defects in 21%. Using facial analysis technology, a computer algorithm applying deep learning was able to accurately differentiate individuals with ZNF462 loss of function variants from individuals with Noonan syndrome and healthy controls. In summary, we describe a multiple congenital anomaly syndrome associated with haploinsufficiency of ZNF462 that has distinct clinical characteristics and facial features.
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Affiliation(s)
- Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Tommy Hu
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Sungkook Hong
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Rebecca Signer
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Benjamin Cogné
- Service de génétique médicale, Hôtel-Dieu, Nantes, France
| | - Betrand Isidor
- Service de génétique médicale, Hôtel-Dieu, Nantes, France
| | - Sarah E Mazzola
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jacques C Giltay
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Eleina M England
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Lynn Pais
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Charlotte W Ockeloen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pedro A Sanchez-Lara
- Keck School of Medicine, University of Southern California, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Esther Kinning
- West of Scotland Genetics Service, Queen Elizabeth Hospitals, Glasgow, Scotland
| | - Darius J Adams
- Personalized Genomic Medicine and Pediatric Genetics, Atlantic Health System, Morristown, New Jersey
| | - Kayla Treat
- Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | | | - Maria F Bedeschi
- Medical Genetic Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Maria Iascone
- Laboratorio di Genetica Medica, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Stephanie Blaney
- Genetics, Vaccine Preventable Diseases, and Sexual Health, Algoma Public Health, Sault Ste. Marie, Ontario, Canada
| | - Oliver Bell
- Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Tiong Y Tan
- Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia.,Victorian Clinical Genetics Services, Melbourne, Victoria, Australia
| | - Marie-Ange Delrue
- Département de pédiatrie, Service de génétique médicale, Centre Hospitalier Universitaire Ste-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Julie Jurgens
- Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Brenda J Barry
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Elizabeth C Engle
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts.,Howard Hughes Medical Institute, Chevy Chase, Maryland.,Department of Ophthalmology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | | | | | - Julian A Martinez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California
| | - Kym Boycott
- Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario, Canada
| | - Elaine H Zackai
- Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
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Sharma M, Hu X, Geddes GC, Acharya K. Microcephalic Newborn with Forehead Nevus Flammeus, Bulging Eyes, and Clenched Fists. Neoreviews 2019; 20:e170-e173. [PMID: 31261057 DOI: 10.1542/neo.20-3-e170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Megha Sharma
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Xiangxin Hu
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | | | - Krishna Acharya
- Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
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40
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Asada S, Fujino T, Goyama S, Kitamura T. The role of ASXL1 in hematopoiesis and myeloid malignancies. Cell Mol Life Sci 2019; 76:2511-2523. [PMID: 30927018 PMCID: PMC11105736 DOI: 10.1007/s00018-019-03084-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 12/19/2022]
Abstract
Recent high-throughput genome-wide sequencing studies have identified recurrent somatic mutations in myeloid neoplasms. An epigenetic regulator, Additional sex combs-like 1 (ASXL1), is one of the most frequently mutated genes in all subtypes of myeloid malignancies. ASXL1 mutations are also frequently detected in clonal hematopoiesis, which is associated with an increased risk of mortality. Therefore, it is important to understand how ASXL1 mutations contribute to clonal expansion and myeloid transformation in hematopoietic cells. Studies using ASXL1-depleted human hematopoietic cells and Asxl1 knockout mice have shown that deletion of wild-type ASXL1 protein leads to impaired hematopoiesis and accelerates myeloid malignancies via loss of interaction with polycomb repressive complex 2 proteins. On the other hand, ASXL1 mutations in myeloid neoplasms typically occur near the last exon and result in the expression of C-terminally truncated mutant ASXL1 protein. Biological studies and biochemical analyses of this variant have shed light on its dominant-negative and gain-of-function features in myeloid transformation via a variety of epigenetic changes. Based on these results, it would be possible to establish novel promising therapeutic strategies for myeloid malignancies harboring ASXL1 mutations by blocking interactions between ASXL1 and associating epigenetic regulators. Here, we summarize the clinical implications of ASXL1 mutations, the role of wild-type ASXL1 in normal hematopoiesis, and oncogenic functions of mutant ASXL1 in myeloid neoplasms.
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Affiliation(s)
- Shuhei Asada
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Susumu Goyama
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan.
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41
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Wayhelova M, Oppelt J, Smetana J, Hladilkova E, Filkova H, Makaturova E, Nikolova P, Beharka R, Gaillyova R, Kuglik P. Novel de novo frameshift variant in the ASXL3 gene in a child with microcephaly and global developmental delay. Mol Med Rep 2019; 20:505-512. [PMID: 31180560 PMCID: PMC6579994 DOI: 10.3892/mmr.2019.10303] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 04/09/2019] [Indexed: 01/11/2023] Open
Abstract
De novo sequence variants, including truncating and splicing variants, in the additional sex-combs like 3 gene (ASXL3) have been described as the cause of Bainbridge-Ropers syndrome (BRS). This pathology is characterized by delayed psychomotor development, severe intellectual disability, growth delay, hypotonia and facial dimorphism. The present study reports a case of a girl (born in 2013) with severe global developmental delay, central hypotonia, microcephaly and poor speech. The proband was examined using a multi-step molecular diagnostics algorithm, including karyotype and array-comparative genomic hybridization analysis, with negative results. Therefore, the proband and her unaffected parents were enrolled for a pilot study using targeted next-generation sequencing technology (NGS) with gene panel ClearSeq Inherited DiseaseXT and subsequent validation by Sanger sequencing. A novel de novo heterozygous frameshift variant in the ASXL3 gene (c.3006delT, p.R1004Efs*21), predicted to result in a premature termination codon, was identified. In conclusion, the present study demonstrated that targeted NGS using a suitable, gene-rich panel may provide a conclusive molecular genetics diagnosis in children with severe global developmental delays.
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Affiliation(s)
- Marketa Wayhelova
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Jan Oppelt
- CEITEC‑Central European Institute of Technology, Masaryk University, 625 00 Brno, Czech Republic
| | - Jan Smetana
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
| | - Eva Hladilkova
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Hana Filkova
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Eva Makaturova
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Petra Nikolova
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Rastislav Beharka
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Renata Gaillyova
- Department of Medical Genetics, University Hospital Brno, 625 00 Brno, Czech Republic
| | - Petr Kuglik
- Institute of Experimental Biology, Faculty of Science, Masaryk University, 611 37 Brno, Czech Republic
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Kweon SM, Chen Y, Moon E, Kvederaviciutė K, Klimasauskas S, Feldman DE. An Adversarial DNA N 6-Methyladenine-Sensor Network Preserves Polycomb Silencing. Mol Cell 2019; 74:1138-1147.e6. [PMID: 30982744 PMCID: PMC6591016 DOI: 10.1016/j.molcel.2019.03.018] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 11/12/2018] [Accepted: 03/18/2019] [Indexed: 02/07/2023]
Abstract
Adenine N6 methylation in DNA (6mA) is widespread among bacteria and phage and is detected in mammalian genomes, where its function is largely unexplored. Here we show that 6mA deposition and removal are catalyzed by the Mettl4 methyltransferase and Alkbh4 dioxygenase, respectively, and that 6mA accumulation in genic elements corresponds with transcriptional silencing. Inactivation of murine Mettl4 depletes 6mA and causes sublethality and craniofacial dysmorphism in incross progeny. We identify distinct 6mA sensor domains of prokaryotic origin within the MPND deubiquitinase and ASXL1, a component of the Polycomb repressive deubiquitinase (PR-DUB) complex, both of which act to remove monoubiquitin from histone H2A (H2A-K119Ub), a repressive mark. Deposition of 6mA by Mettl4 triggers the proteolytic destruction of both sensor proteins, preserving genome-wide H2A-K119Ub levels. Expression of the bacterial 6mA methyltransferase Dam, in contrast, fails to destroy either sensor. These findings uncover a native, adversarial 6mA network architecture that preserves Polycomb silencing. 6mA deposition and erasure by mammalian Mettl4 and Alkbh4, respectively Mettl4-deficient mice display craniofacial dysmorphism 6mA triggers proteolysis of its cognate sensor proteins ASXL1 and MPND Adversarial 6mA network architecture preserves Polycomb silencing
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Affiliation(s)
- Soo-Mi Kweon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Yibu Chen
- Bioinformatics Service, Department of Health Sciences Libraries, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Eugene Moon
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA
| | - Kotryna Kvederaviciutė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Saulius Klimasauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius LT-10257, Lithuania
| | - Douglas E Feldman
- Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA 90033, USA.
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Shashi V, Schoch K, Spillmann R, Cope H, Tan QKG, Walley N, Pena L, McConkie-Rosell A, Jiang YH, Stong N, Need AC, Goldstein DB. A comprehensive iterative approach is highly effective in diagnosing individuals who are exome negative. Genet Med 2019; 21:161-172. [PMID: 29907797 PMCID: PMC6295275 DOI: 10.1038/s41436-018-0044-2] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 04/09/2018] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Sixty to seventy-five percent of individuals with rare and undiagnosed phenotypes remain undiagnosed after exome sequencing (ES). With standard ES reanalysis resolving 10-15% of the ES negatives, further approaches are necessary to maximize diagnoses in these individuals. METHODS In 38 ES negative patients an individualized genomic-phenotypic approach was employed utilizing (1) phenotyping; (2) reanalyses of FASTQ files, with innovative bioinformatics; (3) targeted molecular testing; (4) genome sequencing (GS); and (5) conferring of clinical diagnoses when pathognomonic clinical findings occurred. RESULTS Certain and highly likely diagnoses were made in 18/38 (47%) individuals, including identifying two new developmental disorders. The majority of diagnoses (>70%) were due to our bioinformatics, phenotyping, and targeted testing identifying variants that were undetected or not prioritized on prior ES. GS diagnosed 3/18 individuals with structural variants not amenable to ES. Additionally, tentative diagnoses were made in 3 (8%), and in 5 individuals (13%) candidate genes were identified. Overall, diagnoses/potential leads were identified in 26/38 (68%). CONCLUSIONS Our comprehensive approach to ES negatives maximizes the ES and clinical data for both diagnoses and candidate gene identification, without GS in the majority. This iterative approach is cost-effective and is pertinent to the current conundrum of ES negatives.
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Affiliation(s)
- Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA.
| | - Kelly Schoch
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Rebecca Spillmann
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Heidi Cope
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Queenie K-G Tan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicole Walley
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Loren Pena
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Allyn McConkie-Rosell
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Yong-Hui Jiang
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, North Carolina, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University, New York, New York, USA
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Fu C, Luo S, Zhang Y, Fan X, D'Gama AM, Zhang X, Zheng H, Su J, Li C, Luo J, Agrawal PB, Li Q, Chen S. Chromosomal microarray and whole exome sequencing identify genetic causes of congenital hypothyroidism with extra-thyroidal congenital malformations. Clin Chim Acta 2018; 489:103-108. [PMID: 30508507 DOI: 10.1016/j.cca.2018.11.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/24/2018] [Accepted: 11/29/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Congenital hypothyroidism (CH) is the most common neonatal endocrine disorder. Although most patients present with isolated CH, some patients present with CH and extra-thyroidal congenital malformations (ECMs), for which less is known about the underlying genetics. The aim of this study was to investigate the genetic mechanisms in patients with CH and ECMs using chromosomal microarray (CMA) and whole exome sequencing (WES). METHODS Peripheral venous blood samples were collected from 16 patients with CH and ECMs. Genomic DNA was extracted from peripheral blood leukocytes. CMA and WES were performed to detect copy number and single nucleotide variants. RESULTS CMA identified clinically significant copy number variants in 7 patients consistent with their phenotypes. For 6 of them, the genotype and phenotype suggested a syndromic diagnosis, and the remaining patient carried a pathogenic microdeletion and microduplication including GLIS3. WES analysis identified 9 different variants in 7 additional patients. The variants included 2 known mutations (c.1096C>T (p.Arg366Trp) in KCNQ1 and c.848C>A (p.Pro283Gln) in NKX2-5) and 7 novel variants: one nonsense mutation (c.4330C>T (p.Arg1444*) in ASXL3), one frameshift mutation (c.1253_1259delACTCTGG (p.Asp418fs) in TG), three missense variants (c.1472C>T (p.Thr491Ile) in TG, c.4604A>G (p.Asp1535Gly) in TG, and c.2139G>T (p.Glu713Asp) in DUOX2, and two splice site variants (c.944-1G>C and c.3693 + 1G>T) in DUOX2. CONCLUSIONS We report the first genetic study of CH patients with ECMs using CMA and WES. Overall, our detection rate for pathogenic and possibly pathogenic variants was 87.5% (14/16). We report 7 novel variants, expanding the mutational spectrum of TG, DUOX2, and ASXL3.
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Affiliation(s)
- Chunyun Fu
- Medical Science Laboratory, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China; Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Shiyu Luo
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Yue Zhang
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Xin Fan
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Alissa M D'Gama
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Xiaofei Zhang
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Haiyang Zheng
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Jiasun Su
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Chuan Li
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Jingsi Luo
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Qifei Li
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA 02115, USA.
| | - Shaoke Chen
- Department of Genetic Metabolism, Children's Hospital, Maternal and Child Health Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, People's Republic of China.
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Turnpenny PD, Wright MJ, Sloman M, Caswell R, van Essen AJ, Gerkes E, Pfundt R, White SM, Shaul-Lotan N, Carpenter L, Schaefer GB, Fryer A, Innes AM, Forbes KP, Chung WK, McLaughlin H, Henderson LB, Roberts AE, Heath KE, Paumard-Hernández B, Gener B, Fawcett KA, Gjergja-Juraški R, Pilz DT, Fry AE, Fry AE. Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features. Am J Hum Genet 2018; 103:786-793. [PMID: 30343942 DOI: 10.1016/j.ajhg.2018.09.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/22/2018] [Indexed: 12/15/2022] Open
Abstract
PCGF2 encodes the polycomb group ring finger 2 protein, a transcriptional repressor involved in cell proliferation, differentiation, and embryogenesis. PCGF2 is a component of the polycomb repressive complex 1 (PRC1), a multiprotein complex which controls gene silencing through histone modification and chromatin remodelling. We report the phenotypic characterization of 13 patients (11 unrelated individuals and a pair of monozygotic twins) with missense mutations in PCGF2. All the mutations affected the same highly conserved proline in PCGF2 and were de novo, excepting maternal mosaicism in one. The patients demonstrated a recognizable facial gestalt, intellectual disability, feeding problems, impaired growth, and a range of brain, cardiovascular, and skeletal abnormalities. Computer structural modeling suggests the substitutions alter an N-terminal loop of PCGF2 critical for histone biding. Mutant PCGF2 may have dominant-negative effects, sequestering PRC1 components into complexes that lack the ability to interact efficiently with histones. These findings demonstrate the important role of PCGF2 in human development and confirm that heterozygous substitutions of the Pro65 residue of PCGF2 cause a recognizable syndrome characterized by distinctive craniofacial, neurological, cardiovascular, and skeletal features.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Andrew E Fry
- Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4XW, UK; Division of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
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Marcogliese PC, Shashi V, Spillmann RC, Stong N, Rosenfeld JA, Koenig MK, Martínez-Agosto JA, Herzog M, Chen AH, Dickson PI, Lin HJ, Vera MU, Salamon N, Graham JM, Ortiz D, Infante E, Steyaert W, Dermaut B, Poppe B, Chung HL, Zuo Z, Lee PT, Kanca O, Xia F, Yang Y, Smith EC, Jasien J, Kansagra S, Spiridigliozzi G, El-Dairi M, Lark R, Riley K, Koeberl DD, Golden-Grant K, Yamamoto S, Wangler MF, Mirzaa G, Hemelsoet D, Lee B, Nelson SF, Goldstein DB, Bellen HJ, Pena LDM. IRF2BPL Is Associated with Neurological Phenotypes. Am J Hum Genet 2018; 103:245-260. [PMID: 30057031 PMCID: PMC6081494 DOI: 10.1016/j.ajhg.2018.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 07/02/2018] [Indexed: 12/23/2022] Open
Abstract
Interferon regulatory factor 2 binding protein-like (IRF2BPL) encodes a member of the IRF2BP family of transcriptional regulators. Currently the biological function of this gene is obscure, and the gene has not been associated with a Mendelian disease. Here we describe seven individuals who carry damaging heterozygous variants in IRF2BPL and are affected with neurological symptoms. Five individuals who carry IRF2BPL nonsense variants resulting in a premature stop codon display severe neurodevelopmental regression, hypotonia, progressive ataxia, seizures, and a lack of coordination. Two additional individuals, both with missense variants, display global developmental delay and seizures and a relatively milder phenotype than those with nonsense alleles. The IRF2BPL bioinformatics signature based on population genomics is consistent with a gene that is intolerant to variation. We show that the fruit-fly IRF2BPL ortholog, called pits (protein interacting with Ttk69 and Sin3A), is broadly detected, including in the nervous system. Complete loss of pits is lethal early in development, whereas partial knockdown with RNA interference in neurons leads to neurodegeneration, revealing a requirement for this gene in proper neuronal function and maintenance. The identified IRF2BPL nonsense variants behave as severe loss-of-function alleles in this model organism, and ectopic expression of the missense variants leads to a range of phenotypes. Taken together, our results show that IRF2BPL and pits are required in the nervous system in humans and flies, and their loss leads to a range of neurological phenotypes in both species.
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Affiliation(s)
- Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Rebecca C Spillmann
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mary Kay Koenig
- Division of Child & Adolescent Neurology, Department of Pediatrics, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Julián A Martínez-Agosto
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Child and Adolescent Psychiatry, Resnick Neuropsychiatric Hospital, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Matthew Herzog
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Agnes H Chen
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Patricia I Dickson
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Henry J Lin
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Moin U Vera
- Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Noriko Salamon
- Department of Radiology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - John M Graham
- Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Damara Ortiz
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Elena Infante
- Children's Hospital of Pittsburgh, University of Pittsburgh Medical Center, University of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Wouter Steyaert
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bart Dermaut
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Bruce Poppe
- Department of Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Hyung-Lok Chung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei-Tseng Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yaping Yang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward C Smith
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Joan Jasien
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sujay Kansagra
- Division of Neurology, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gail Spiridigliozzi
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mays El-Dairi
- Department of Ophthalmology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Lark
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kacie Riley
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dwight D Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katie Golden-Grant
- Division of Genetic Medicine, Seattle Children's Hospital, Seattle, WA 98105, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA
| | - Ghayda Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98105, USA; Department of Pediatrics, University of Washington, Seattle, WA 98105, USA
| | - Dimitri Hemelsoet
- Department of Neurology, Ghent University Hospital, 9000 Ghent, Belgium
| | - Brendan Lee
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Stanley F Nelson
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Program in Developmental Biology, Baylor College of Medicine, Houston, TX 77030, USA; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX 77030, USA; Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Howard Hughes Medical Institute, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke University School of Medicine, Durham, NC 27710, USA.
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Liu N, Schoch K, Luo X, Pena LDM, Bhavana VH, Kukolich MK, Stringer S, Powis Z, Radtke K, Mroske C, Deak KL, McDonald MT, McConkie-Rosell A, Markert ML, Kranz PG, Stong N, Need AC, Bick D, Amaral MD, Worthey EA, Levy S, Wangler MF, Bellen HJ, Shashi V, Yamamoto S. Functional variants in TBX2 are associated with a syndromic cardiovascular and skeletal developmental disorder. Hum Mol Genet 2018; 27:2454-2465. [PMID: 29726930 PMCID: PMC6030957 DOI: 10.1093/hmg/ddy146] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/07/2018] [Accepted: 04/16/2018] [Indexed: 12/15/2022] Open
Abstract
The 17 genes of the T-box family are transcriptional regulators that are involved in all stages of embryonic development, including craniofacial, brain, heart, skeleton and immune system. Malformation syndromes have been linked to many of the T-box genes. For example, haploinsufficiency of TBX1 is responsible for many structural malformations in DiGeorge syndrome caused by a chromosome 22q11.2 deletion. We report four individuals with an overlapping spectrum of craniofacial dysmorphisms, cardiac anomalies, skeletal malformations, immune deficiency, endocrine abnormalities and developmental impairments, reminiscent of DiGeorge syndrome, who are heterozygotes for TBX2 variants. The p.R20Q variant is shared by three affected family members in an autosomal dominant manner; the fourth unrelated individual has a de novo p.R305H mutation. Bioinformatics analyses indicate that these variants are rare and predict them to be damaging. In vitro transcriptional assays in cultured cells show that both variants result in reduced transcriptional repressor activity of TBX2. We also show that the variants result in reduced protein levels of TBX2. Heterologous over-expression studies in Drosophila demonstrate that both p.R20Q and p.R305H function as partial loss-of-function alleles. Hence, these and other data suggest that TBX2 is a novel candidate gene for a new multisystem malformation disorder.
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Affiliation(s)
- Ning Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Kelly Schoch
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Xi Luo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Loren D M Pena
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | | | - Mary K Kukolich
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Sarah Stringer
- Department of Genetics, Cook Children’s Hospital, Fort Worth, TX, USA
| | - Zöe Powis
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | - Kelly Radtke
- Clinical Genomics, Ambry Genetics, Aliso Viejo, CA, USA
| | | | - Kristen L Deak
- Department of Pathology, Duke University, Durham, NC, USA
| | - Marie T McDonald
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Allyn McConkie-Rosell
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - M Louise Markert
- Division of Allergy and Immunology, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Peter G Kranz
- Division of Neuroradiology, Department of Radiology, Duke Health, Durham, NC, USA
| | - Nicholas Stong
- Institute for Genomic Medicine, Columbia University, New York, NY, USA
| | - Anna C Need
- Division of Brain Sciences, Department of Medicine, Imperial College London, London, UK
| | - David Bick
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Michael F Wangler
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
- Howard Hughes Medical Institute, Houston, TX, USA
| | - Vandana Shashi
- Division of Medical Genetics, Department of Pediatrics, Duke Health, Durham, NC, USA
| | - Shinya Yamamoto
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children’s Hospital, Houston, TX, USA
- Program in Developmental Biology, Baylor College of Medicine, Houston, TX, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, USA
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48
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Reuter CM, Brimble E, DeFilippo C, Dries AM, Enns GM, Ashley EA, Bernstein JA, Fisher PG, Wheeler MT. A New Approach to Rare Diseases of Children: The Undiagnosed Diseases Network. J Pediatr 2018; 196:291-297.e2. [PMID: 29331327 PMCID: PMC5924635 DOI: 10.1016/j.jpeds.2017.12.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/09/2017] [Accepted: 12/14/2017] [Indexed: 10/18/2022]
Affiliation(s)
- Chloe M. Reuter
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elise Brimble
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Colette DeFilippo
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA,Stanford Children’s Health, Palo Alto, CA, 94304, USA
| | - Annika M. Dries
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | | | - Gregory M. Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Euan A. Ashley
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonathan A. Bernstein
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA,Stanford Children’s Health, Palo Alto, CA, 94304, USA
| | - Paul Graham Fisher
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew T. Wheeler
- Stanford Center for Undiagnosed Diseases, Stanford University School of Medicine, Stanford, CA, 94305, USA,Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
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49
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Jiménez-Romero S, Carrasco-Salas P, Benítez-Burraco A. Language and Cognitive Impairment Associated with a Novel p.Cys63Arg Change in the MED13L Transcriptional Regulator. Mol Syndromol 2018; 9:83-91. [PMID: 29593475 DOI: 10.1159/000485638] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/17/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in the MED13L gene, which encodes a subunit of a transcriptional regulatory complex, result in a complex phenotype entailing physical and cognitive anomalies. Deep language impairment has been reported in affected individuals, mostly in patients with copy number variations. We report on a child with a nonsynonymous p.Cys63Arg change in MED13L (chr12:116675396A>G, GRCh37) who exhibits profound language impairment in the expressive domain, cognitive delay, behavioral disturbances, and an autism-like phenotype. Because of the brain areas in which MED13L is expressed and because of the functional links between MED13L and the products of selected candidate genes for cognitive disorders involving language deficits, the proband's linguistic phenotype may result from changes in a functional network important for language development and evolution.
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Affiliation(s)
- Salud Jiménez-Romero
- Maimónides Institute of Biomedical Research, Córdoba, Spain.,Department of Psychology, University of Córdoba, Córdoba, Spain
| | | | - Antonio Benítez-Burraco
- Department of Spanish, Linguistics, and Theory of Literature, University of Seville, Seville, Spain
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50
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Chinen Y, Nakamura S, Ganaha A, Hayashi S, Inazawa J, Yanagi K, Nakanishi K, Kaname T, Naritomi K. Mild prominence of the Sylvian fissure in a Bainbridge-Ropers syndrome patient with a novel frameshift variant in ASXL3. Clin Case Rep 2017; 6:330-336. [PMID: 29445472 PMCID: PMC5799615 DOI: 10.1002/ccr3.1361] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 11/27/2017] [Accepted: 12/10/2017] [Indexed: 12/28/2022] Open
Abstract
A Japanese boy aged 7 years with Bainbridge‐Ropers syndrome (BRPS) had a prominent domed forehead without metric ridge, mild prominence of the Sylvian fissure with bitemporal hollowing, and a heterozygous de novo novel variant “p.P1010Lfs*14” in ASXL3 gene in addition to typical findings of BRPS.
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Affiliation(s)
- Yasutsugu Chinen
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Sadao Nakamura
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Akira Ganaha
- Department of Otorhinolaryngology, Head and Neck Surgery Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Shin Hayashi
- Department of Molecular Cytogenetics Medical Research Institute Tokyo Medical and Dental University Tokyo Japan.,Hard Tissue Genome Research Center Tokyo Medical and Dental University Tokyo Japan
| | - Johji Inazawa
- Department of Molecular Cytogenetics Medical Research Institute Tokyo Medical and Dental University Tokyo Japan.,Hard Tissue Genome Research Center Tokyo Medical and Dental University Tokyo Japan
| | - Kumiko Yanagi
- Department of Genome Medicine National Center for Child Health and Development Tokyo Japan
| | - Koichi Nakanishi
- Department of Pediatrics Faculty of Medicine University of the Ryukyus Nishihara Japan
| | - Tadashi Kaname
- Department of Genome Medicine National Center for Child Health and Development Tokyo Japan
| | - Kenji Naritomi
- Okinawa Nanbu Habilitation and Medical Center Naha Japan
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