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Diaz Escarcega R, Murambadoro K, Valencia R, Moruno-Manchon JF, Furr Stimming EE, Jung SY, Tsvetkov AS. Sphingosine kinase 2 regulates protein ubiquitination networks in neurons. Mol Cell Neurosci 2024; 130:103948. [PMID: 38909878 DOI: 10.1016/j.mcn.2024.103948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/31/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024] Open
Abstract
Two sphingosine kinase isoforms, sphingosine kinase 1 (SPHK1) and sphingosine kinase 2 (SPHK2), synthesize the lipid sphingosine-1-phosphate (S1P) by phosphorylating sphingosine. SPHK1 is a cytoplasmic kinase, and SPHK2 is localized to the nucleus and other organelles. In the cytoplasm, the SPHK1/S1P pathway modulates autophagy and protein ubiquitination, among other processes. In the nucleus, the SPHK2/S1P pathway regulates transcription. Here, we hypothesized that the SPHK2/S1P pathway governs protein ubiquitination in neurons. We found that ectopic expression of SPHK2 increases ubiquitinated substrate levels in cultured neurons and pharmacologically inhibiting SPHK2 decreases protein ubiquitination. With mass spectrometry, we discovered that inhibiting SPHK2 affects lipid and synaptic protein networks as well as a ubiquitin-dependent protein network. Several ubiquitin-conjugating and hydrolyzing proteins, such as the E3 ubiquitin-protein ligases HUWE1 and TRIP12, the E2 ubiquitin-conjugating enzyme UBE2Z, and the ubiquitin-specific proteases USP15 and USP30, were downregulated by SPHK2 inhibition. Using RNA sequencing, we found that inhibiting SPHK2 altered lipid and neuron-specific gene networks, among others. Genes that encode the corresponding proteins from the ubiquitin-dependent protein network that we discovered with mass spectrometry were not affected by inhibiting SPHK2, indicating that the SPHK2/S1P pathway regulates ubiquitination at the protein level. We also show that both SPHK2 and HUWE1 were upregulated in the striatum of a mouse model of Huntington's disease, the BACHD mice, indicating that our findings are relevant to neurodegenerative diseases. Our results identify SPHK2/S1P as a novel regulator of protein ubiquitination networks in neurons and provide a new target for developing therapies for neurodegenerative diseases.
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Affiliation(s)
- Rocio Diaz Escarcega
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America
| | - Karen Murambadoro
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America
| | - Ricardo Valencia
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America
| | - Jose Felix Moruno-Manchon
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America
| | - Erin E Furr Stimming
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America
| | - Sung Yun Jung
- Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX 77030, United States of America.
| | - Andrey S Tsvetkov
- Department of Neurology, University of Texas McGovern Medical School, Houston, TX 77030, United States of America; The University of Texas Graduate School of Biomedical Sciences, Houston, TX 77030, United States of America; UTHealth Consortium on Aging, the University of Texas McGovern Medical School, Houston, TX 77030, United States of America.
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2
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Sahajpal N, Ziats C, Chaubey A, DuPont BR, Abidi F, Schwartz CE, Stevenson RE. Clinical findings in individuals with duplication of genes associated with X-linked intellectual disability. Clin Genet 2024; 105:173-184. [PMID: 37899624 DOI: 10.1111/cge.14445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/25/2023] [Accepted: 10/13/2023] [Indexed: 10/31/2023]
Abstract
Duplication of all genes associated with X-linked intellectual disability (XLID) have been reported but the majority of the duplications include more than one XLID gene. It is exceptional for whole XLID gene duplications to cause the same phenotype as sequence variants or deletions of the same gene. Duplication of PLP1, the gene associated with Pelizaeus-Merzbacher syndrome, is the most notable duplication of this type. More commonly, duplication of XLID genes results in very different phenotypes than sequence alterations or deletions. Duplication of MECP2 is widely recognized as a duplication of this type, but a number of others exist. The phenotypes associated with gene duplications are often milder than those caused by deletions and sequence variants. Among some duplications that are clinically significant, marked skewing of X-inactivation in female carriers has been observed. This report describes the phenotypic consequences of duplication of 22 individual XLID genes, of which 10 are described for the first time.
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Affiliation(s)
- Nikhil Sahajpal
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Catherine Ziats
- Genetics Department, Shodair Children's Hospital, Helena, Montana, USA
| | - Alka Chaubey
- Clinical and Scientific Affairs, Bionano Genomics, San Diego, California, USA
| | - Barbara R DuPont
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Fatima Abidi
- Diagnostic Laboratories, Greenwood Genetic Center, Greenwood, South Carolina, USA
| | - Charles E Schwartz
- Department of Pediatrics and Human Development, Michigan State University, Grand Rapids, Michigan, USA
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3
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Poot M. Methods of Detection and Mechanisms of Origin of Complex Structural Genome Variations. Methods Mol Biol 2024; 2825:39-65. [PMID: 38913302 DOI: 10.1007/978-1-0716-3946-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Based on classical karyotyping, structural genome variations (SVs) have generally been considered to be either "simple" (with one or two breakpoints) or "complex" (with more than two breakpoints). Studying the breakpoints of SVs at nucleotide resolution revealed additional, subtle structural variations, such that even "simple" SVs turned out to be "complex." Genome-wide sequencing methods, such as fosmid and paired-end mapping, short-read and long-read whole genome sequencing, and single-molecule optical mapping, also indicated that the number of SVs per individual was considerably larger than expected from karyotyping and high-resolution chromosomal array-based studies. Interestingly, SVs were detected in studies of cohorts of individuals without clinical phenotypes. The common denominator of all SVs appears to be a failure to accurately repair DNA double-strand breaks (DSBs) or to halt cell cycle progression if DSBs persist. This review discusses the various DSB response mechanisms during the mitotic cell cycle and during meiosis and their regulation. Emphasis is given to the molecular mechanisms involved in the formation of translocations, deletions, duplications, and inversions during or shortly after meiosis I. Recently, CRISPR-Cas9 studies have provided unexpected insights into the formation of translocations and chromothripsis by both breakage-fusion-bridge and micronucleus-dependent mechanisms.
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Affiliation(s)
- Martin Poot
- Department of Human Genetics, University of Wuerzburg, Wuerzburg, Germany
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4
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Deshmukh SP, Couser NL. Facial and ocular manifestations of male patients affected by the HUWE1-related intellectual developmental disorder. INTERNATIONAL JOURNAL OF MOLECULAR EPIDEMIOLOGY AND GENETICS 2023; 14:34-41. [PMID: 38021253 PMCID: PMC10658174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
Turner-type X-linked syndromic intellectual developmental disorder (MRXST) is a rare neurodevelopmental disorder. MRXST is caused by pathogenic variants in the HUWE1 gene on chromosome Xp11.22. The HUWE1 gene encodes a ubiquitin ligase, which has downstream effects on the n-MYC protein and DLL3 Notch ligand, ultimately affecting neuronal differentiation. In addition to intellectual disability and developmental delay, other clinical features such as absent or delayed speech, skeletal abnormalities, abnormalities in hands or feet, seizures, and hypotonia have been described in case reports. Facial dysmorphic features and eye manifestations have been reported in patients with MRXST, but have not been identified as distinctive to this condition. We report two cases of individuals affected by HUWE1-Related Intellectual Developmental Disorder and present a review of literature of male patients affected by this disorder. Based on the literature review and findings in our two patients, it is our observation that patients with MRXST present with distinctive features, which include broad nasal tip, root, or prominent nose (39%), blepharophimosis (27%), epicanthic folds (25%), ear abnormalities (25%), thin upper lip (23%), and deep set eyes (23%). Furthermore, we note that oculofacial abnormalities are seen more frequently in patients with missense variants than patients with duplications in the HUWE1 gene. The findings noted in this paper may help clinicians suspect a diagnosis of MRXST when presented with these distinctive ocular and facial features.
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Affiliation(s)
| | - Natario L Couser
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of MedicineRichmond, VA, USA
- Department of Ophthalmology, Virginia Commonwealth University School of MedicineRichmond, VA, USA
- Department of Pediatrics, Virginia Commonwealth University School of Medicine, Children’s Hospital of Richmond at VCURichmond, VA, USA
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5
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Monda JK, Ge X, Hunkeler M, Donovan KA, Ma MW, Jin CY, Leonard M, Fischer ES, Bennett EJ. HAPSTR1 localizes HUWE1 to the nucleus to limit stress signaling pathways. Cell Rep 2023; 42:112496. [PMID: 37167062 DOI: 10.1016/j.celrep.2023.112496] [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: 11/21/2022] [Revised: 03/21/2023] [Accepted: 04/25/2023] [Indexed: 05/13/2023] Open
Abstract
HUWE1 is a large, enigmatic HECT-domain ubiquitin ligase implicated in the regulation of diverse pathways, including DNA repair, apoptosis, and differentiation. How HUWE1 engages its structurally diverse substrates and how HUWE1 activity is regulated are unknown. Using unbiased quantitative proteomics, we find that HUWE1 targets substrates in a largely cell-type-specific manner. However, we identify C16orf72/HAPSTR1 as a robust HUWE1 substrate in multiple cell lines. Previously established physical and genetic interactions between HUWE1 and HAPSTR1 suggest that HAPSTR1 positively regulates HUWE1 function. Here, we show that HAPSTR1 is required for HUWE1 nuclear localization and nuclear substrate targeting. Nuclear HUWE1 is required for both cell proliferation and modulation of stress signaling pathways, including p53 and nuclear factor κB (NF-κB)-mediated signaling. Combined, our results define a role for HAPSTR1 in gating critical nuclear HUWE1 functions.
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Affiliation(s)
- Julie K Monda
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Xuezhen Ge
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Moritz Hunkeler
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Michelle W Ma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Cyrus Y Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Marilyn Leonard
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Eric J Bennett
- School of Biological Sciences, Department of Cell and Developmental Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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6
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Santos-Rebouças CB, Boy R, Fernandes GNS, Gonçalves AP, Abdala BB, Gonzalez LGC, Dos Santos JM, Pimentel MMG. A novel Xp11.22 duplication involving HUWE1 in a male with syndromic intellectual disability and additional neurological findings. Eur J Med Genet 2023; 66:104716. [PMID: 36731745 DOI: 10.1016/j.ejmg.2023.104716] [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: 04/08/2022] [Revised: 01/23/2023] [Accepted: 01/25/2023] [Indexed: 01/31/2023]
Abstract
Sequence variants and duplications in the HECT, UBA and WWE domain -containing 1 (HUWE1) E3 ubiquitin ligase gene have been associated with X-linked mild to severe intellectual disability (ID), but a solid phenotype pattern among the affected males is still remaining to be established. Here, we report a male patient with sporadic, severe and syndromic ID, carrying a novel and unique 842 kb duplication at Xp11.22, including the dosage-sensitive HUWE1 gene and other fifteen curated RefSeq genes. Expression analysis in the patient and his female relatives confirmed increased HUWE1 mRNA levels, with different X-chromosome inactivation patterns among the female carriers. Our patient differs from those previously described by us and others as he presents encephalomalacia at brain Magnetic Resonance Imaging and diffuse bilaterally and synchronous intercritical irritating paroxysms at electroencephalogram. Overall, our clinical, molecular, and neurological findings sum up the previous data, expanding the phenotype spectrum in Xp11.22 copy gains involving the whole HUWE1 gene in both males and female carriers in light of X-chromosome inactivation patterns.
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Affiliation(s)
- Cíntia B Santos-Rebouças
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil.
| | - Raquel Boy
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriela N S Fernandes
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andressa P Gonçalves
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bianca B Abdala
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lucas G C Gonzalez
- Pedro Ernesto University Hospital, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jussara M Dos Santos
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Márcia M G Pimentel
- Department of Genetics, Institute of Biology Roberto Alcantara Gomes, State University of Rio de Janeiro, Rio de Janeiro, Brazil
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7
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Pitfalls of whole exome sequencing in undefined clinical conditions with a suspected genetic etiology. Genes Genomics 2022; 45:637-655. [PMID: 36454368 DOI: 10.1007/s13258-022-01341-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/26/2022] [Indexed: 12/03/2022]
Abstract
BACKGROUND Whole-Exome Sequencing (WES) is a valuable tool for the molecular diagnosis of patients with a suspected genetic condition. In complex and heterogeneous diseases, the interpretation of WES variants is more challenging given the absence of diagnostic handles and other reported cases with overlapping clinical presentations. OBJECTIVE To describe candidate variants emerging from trio-WES and possibly associated with the clinical phenotype in clinically heterogeneous conditions. METHODS We performed WES in ten patients from eight families, selected because of the lack of a clear clinical diagnosis or suspicion, the presence of multiple clinical signs, and the negative results of traditional genetic tests. RESULTS Although we identified ten candidate variants, reaching the diagnosis of these cases is challenging, given the complexity and the rarity of these syndromes and because affected genes are already associated with known genetic diseases only partially recapitulating patients' phenotypes. However, the identification of these variants could shed light into the definition of new genotype-phenotype correlations. Here, we describe the clinical and molecular data of these cases with the aim of favoring the match with other similar cases and, hopefully, confirm our diagnostic hypotheses. CONCLUSION This study emphasizes the major limitations associated with WES data interpretation, but also highlights its clinical utility in unraveling novel genotype-phenotype correlations in complex and heterogeneous undefined clinical conditions with a suspected genetic etiology.
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8
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Pouyo R, Chung K, Delacroix L, Malgrange B. The ubiquitin-proteasome system in normal hearing and deafness. Hear Res 2022; 426:108366. [PMID: 34645583 DOI: 10.1016/j.heares.2021.108366] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/03/2021] [Accepted: 09/23/2021] [Indexed: 12/16/2022]
Abstract
Post-translational modifications of proteins are essential for the proper development and function of many tissues and organs, including the inner ear. Ubiquitination is a highly selective post-translational modification that involves the covalent conjugation of ubiquitin to a substrate protein. The most common outcome of protein ubiquitination is degradation by the ubiquitin-proteasome system (UPS), preventing the accumulation of misfolded, damaged, and excess proteins. In addition to proteasomal degradation, ubiquitination regulates other cellular processes, such as transcription, translation, endocytosis, receptor activity, and subcellular localization. All of these processes are essential for cochlear development and maintenance, as several studies link impairment of UPS with altered cochlear development and hearing loss. In this review, we provide insight into the well-oiled machinery of UPS with a focus on its confirmed role in normal hearing and deafness and potential therapeutic strategies to prevent and treat UPS-associated hearing loss.
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Affiliation(s)
- Ronald Pouyo
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Keshi Chung
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Laurence Delacroix
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium
| | - Brigitte Malgrange
- GIGA-Stem Cells, Developmental Neurobiology Unit, University of Liege, Avenue hippocrate 15, B36 1st Floor B, Liege 4000, Belgium.
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9
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Qi L, Xu X, Qi X. The giant E3 ligase HUWE1 is linked to tumorigenesis, spermatogenesis, intellectual disability, and inflammatory diseases. Front Cell Infect Microbiol 2022; 12:905906. [PMID: 35937685 PMCID: PMC9355080 DOI: 10.3389/fcimb.2022.905906] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
E3 ubiquitin ligases determine the substrate specificity and catalyze the ubiquitination of lysine residues. HUWE1 is a catalytic HECT domain-containing giant E3 ligase that contains a substrate-binding ring structure, and mediates the ubiquitination of more than 40 diverse substrates. HUWE1 serves as a central node in cellular stress responses, cell growth and death, signal transduction, etc. The expanding atlas of HUWE1 substrates presents a major challenge for the potential therapeutic application of HUWE1 in a particular disease. In addition, HUWE1 has been demonstrated to play contradictory roles in certain aspects of tumor progression in either an oncogenic or a tumor-suppressive manner. We recently defined novel roles of HUWE1 in promoting the activation of multiple inflammasomes. Inflammasome activation-mediated immune responses might lead to multifunctional effects on tumor therapy, inflammation, and autoimmune diseases. In this review, we summarize the known substrates and pleiotropic functions of HUWE1 in different types of cells and models, including its involvement in development, cancer, neuronal disorder and infectious disease. We also discuss the advances in cryo-EM-structural analysis for a functional-mechanistic understanding of HUWE1 in modulating the multitudinous diverse substrates, and introduce the possibility of revisiting the comprehensive roles of HUWE1 in multiple aspects within one microenvironment, which will shed light on the potential therapeutic application of targeting giant E3 ligases like HUWE1.
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Affiliation(s)
- Lu Qi
- Department of Orthopedics, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaoqing Xu
- Department of Oncology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Xiaopeng Qi
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Clinical Laboratory/Qilu Hospital, Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Xiaopeng Qi,
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10
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Yahia A, Ayed IB, Hamed AA, Mohammed IN, Elseed MA, Bakhiet AM, Guillot-Noel L, Abozar F, Adil R, Emad S, Abubaker R, Musallam MA, Eltazi IZM, Omer Z, Maaroof OM, Soussi A, Bouzid A, Kmiha S, Kamoun H, Salih MA, Ahmed AE, Elsayed L, Masmoudi S, Stevanin G. Genetic diagnosis in Sudanese and Tunisian families with syndromic intellectual disability through exome sequencing. Ann Hum Genet 2022; 86:181-194. [PMID: 35118659 DOI: 10.1111/ahg.12460] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/24/2021] [Accepted: 01/17/2022] [Indexed: 12/20/2022]
Abstract
BACKGROUND Intellectual disability is a form of neurodevelopmental disorders that begin in childhood and is characterized by substantial intellectual difficulties as well as difficulties in conceptual, social, and practical areas of living. Several genetic and nongenetic factors contribute to its development; however, its most severe forms are generally attributed to single-gene defects. High-throughput technologies and data sharing contributed to the diagnosis of hundreds of single-gene intellectual disability subtypes. METHOD We applied exome sequencing to identify potential variants causing syndromic intellectual disability in six Sudanese patients from four unrelated families. Data sharing through the Varsome portal corroborated the diagnosis of one of these patients and a Tunisian patient investigated through exome sequencing. Sanger sequencing validated the identified variants and their segregation with the phenotypes in the five studied families. RESULT We identified three pathogenic/likely pathogenic variants in CCDC82, ADAT3, and HUWE1 and variants of uncertain significance in HERC2 and ATP2B3. The patients with the CCDC82 variants had microcephaly and spasticity, two signs absent in the two previously reported families with CCDC82-related intellectual disability. CONCLUSION In conclusion, we report new patients with pathogenic mutations in the genes CCDC82, ADAT3, and HUWE1. We also highlight the possibility of extending the CCDC82-linked phenotype to include spastic paraplegia and microcephaly.
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Affiliation(s)
- Ashraf Yahia
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Biochemistry, Faculty of Medicine, National University, Khartoum, Sudan.,Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Ikhlas Ben Ayed
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia.,Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia
| | - Ahlam A Hamed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Inaam N Mohammed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Maha A Elseed
- Department of Pediatrics, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Aisha M Bakhiet
- Department of Psychiatry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Lena Guillot-Noel
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
| | - Fatima Abozar
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rawaa Adil
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Sara Emad
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Rayan Abubaker
- Institute of Endemic Diseases, University of Khartoum, Khartoum, Sudan.,National University Biomedical Research Institute (NUBRI), National University, Khartoum, Sudan
| | | | - Isra Z M Eltazi
- Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Zulfa Omer
- Department of Hematology and Medical Oncology, University of Cincinnati Medical Center, Cincinnati, Ohio, USA
| | - Omer M Maaroof
- Council of Diagnostic Radiology, Sudan Medical Specialization Board, Khartoum, Sudan
| | - Amal Soussi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Amal Bouzid
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Sana Kmiha
- Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia.,Department of pediatrics, Hedi Chaker Hospital, Sfax, Tunisia
| | - Hassen Kamoun
- Medical Genetic Department, Hedi Chaker Hospital, Sfax, Tunisia.,Laboratory of Human Molecular Genetics, LR33ES99, Faculty of Medicine of Sfax, University of Sfax, Sfax, Tunisia
| | - Mustafa A Salih
- Division of Pediatric Neurology, Department of Pediatrics, College of Medicine, King Saud University, Riyadh, Saudi Arabia.,Department of Pediatrics, College of Medicine, AlMughtaribeen University, Khartoum, Sudan
| | - Ammar E Ahmed
- Department of Physiology, Faculty of Medicine, University of Khartoum, Khartoum, Sudan
| | - Liena Elsayed
- Department of Biochemistry, Faculty of Medicine, University of Khartoum, Khartoum, Sudan.,Department of Basic Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes (LPCMC), LR15CBS07, Center of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Giovanni Stevanin
- Institut du Cerveau - Paris Brain Institute, ICM, Sorbonne Université, INSERM, CNRS, APHP, Paris, France.,Ecole Pratique des Hautes Etudes, EPHE, PSL Research University, Paris, France
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11
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Suthakaran N, Wiggins J, Giles A, Opperman KJ, Grill B, Dawson-Scully K. O-GlcNAc transferase OGT-1 and the ubiquitin ligase EEL-1 modulate seizure susceptibility in C. elegans. PLoS One 2021; 16:e0260072. [PMID: 34797853 PMCID: PMC8604358 DOI: 10.1371/journal.pone.0260072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Neurodevelopmental disorders such as epilepsy and autism have been linked to an imbalance of excitation and inhibition (E/I) in the central nervous system. The simplicity and tractability of C. elegans allows our electroconvulsive seizure (ES) assay to be used as a behavioral readout of the locomotor circuit and neuronal function. C. elegans possess conserved nervous system features such as gamma-aminobutyric acid (GABA) and GABA receptors in inhibitory neurotransmission, and acetylcholine (Ach) and acetylcholine receptors in excitatory neurotransmission. Our previously published data has shown that decreasing inhibition in the motor circuit, via GABAergic manipulation, will extend the time of locomotor recovery following electroshock. Similarly, mutations in a HECT E3 ubiquitin ligase called EEL-1 leads to impaired GABAergic transmission, E/I imbalance and altered sensitivity to electroshock. Mutations in the human ortholog of EEL-1, called HUWE1, are associated with both syndromic and non-syndromic intellectual disability. Both EEL-1 and its previously established binding protein, OGT-1, are expressed in GABAergic motor neurons, localize to GABAergic presynaptic terminals, and function in parallel to regulate GABA neuron function. In this study, we tested behavioral responses to electroshock in wildtype, ogt-1, eel-1 and ogt-1; eel-1 double mutants. Both ogt-1 and eel-1 null mutants have decreased inhibitory GABAergic neuron function and increased electroshock sensitivity. Consistent with EEL-1 and OGT-1 functioning in parallel pathways, ogt-1; eel-1 double mutants showed enhanced electroshock susceptibility. Expression of OGT-1 in the C. elegans nervous system rescued enhanced electroshock defects in ogt-1; eel-1 double mutants. Application of a GABA agonist, Baclofen, decreased electroshock susceptibility in all animals. Our C. elegans electroconvulsive seizure assay was the first to model a human X-linked Intellectual Disability (XLID) associated with epilepsy and suggests a potential novel role for the OGT-1/EEL-1 complex in seizure susceptibility.
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Affiliation(s)
- Nirthieca Suthakaran
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Jonathan Wiggins
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
| | - Andrew Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Karla J. Opperman
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
| | - Brock Grill
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, Washington, United States of America
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
- Department of Pharmacology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Ken Dawson-Scully
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, Florida, United States of America
- * E-mail:
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Loss-of-function and missense variants in NSD2 cause decreased methylation activity and are associated with a distinct developmental phenotype. Genet Med 2021; 23:1474-1483. [PMID: 33941880 PMCID: PMC8354849 DOI: 10.1038/s41436-021-01158-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 11/16/2022] Open
Abstract
Purpose Despite a few recent reports of patients harboring truncating variants in NSD2, a gene considered critical for the Wolf–Hirschhorn syndrome (WHS) phenotype, the clinical spectrum associated with NSD2 pathogenic variants remains poorly understood. Methods We collected a comprehensive series of 18 unpublished patients carrying heterozygous missense, elongating, or truncating NSD2 variants; compared their clinical data to the typical WHS phenotype after pooling them with ten previously described patients; and assessed the underlying molecular mechanism by structural modeling and measuring methylation activity in vitro. Results The core NSD2-associated phenotype includes mostly mild developmental delay, prenatal-onset growth retardation, low body mass index, and characteristic facial features distinct from WHS. Patients carrying missense variants were significantly taller and had more frequent behavioral/psychological issues compared with those harboring truncating variants. Structural in silico modeling suggested interference with NSD2’s folding and function for all missense variants in known structures. In vitro testing showed reduced methylation activity and failure to reconstitute H3K36me2 in NSD2 knockout cells for most missense variants. Conclusion NSD2 loss-of-function variants lead to a distinct, rather mild phenotype partially overlapping with WHS. To avoid confusion for patients, NSD2 deficiency may be named Rauch–Steindl syndrome after the delineators of this phenotype.
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Stern S, Hacohen N, Meiner V, Yagel S, Zenvirt S, Shkedi-Rafid S, Macarov M, Valsky DV, Porat S, Yanai N, Frumkin A, Daum H. Universal chromosomal microarray analysis reveals high proportion of copy-number variants in low-risk pregnancies. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 57:813-820. [PMID: 32202684 DOI: 10.1002/uog.22026] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/12/2020] [Accepted: 03/16/2020] [Indexed: 06/10/2023]
Abstract
OBJECTIVES To evaluate the yield and utility of the routine use of chromosomal microarray analysis (CMA) for prenatal genetic diagnosis in a large cohort of pregnancies with normal ultrasound (US) at the time of genetic testing, compared with pregnancies with abnormal US findings. METHODS We reviewed all prenatal CMA results in our center between November 2013 and December 2018. The prevalence of different CMA results in pregnancies with normal US at the time of genetic testing ('low-risk pregnancies'), was compared with that in pregnancies with abnormal US findings ('high-risk pregnancies'). Medical records were searched in order to evaluate subsequent US follow-up and the outcome of pregnancies with a clinically relevant copy-number variant (CNV), i.e. a pathogenic or likely pathogenic CNV or a susceptibility locus for disease with > 10% penetrance, related to early-onset disease in the low-risk group. RESULTS In a cohort of 6431 low-risk pregnancies that underwent CMA, the prevalence of a clinically significant CNV related to early-onset disease was 1.1% (72/6431), which was significantly lower than the prevalence in high-risk pregnancies (4.9% (65/1326)). Of the low-risk pregnancies, 0.4% (27/6431) had a pathogenic or likely pathogenic CNV, and another 0.7% (45/6431) had a susceptibility locus with more than 10% penetrance. Follow-up of the low-risk pregnancies with a clinically significant early-onset CNV revealed that 31.9% (23/72) were terminated, while outcome data were missing in 26.4% (19/72). In 16.7% (12/72) of low-risk pregnancies, an US abnormality was discovered later on in gestation, after genetic testing had been performed. CONCLUSION Although the background risk of identifying a clinically significant early-onset abnormal CMA result in pregnancies with a low a-priori risk is lower than that observed in high-risk pregnancies, the risk is substantial and should be conveyed to all pregnant women. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- S Stern
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - N Hacohen
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - V Meiner
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Yagel
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Zenvirt
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Shkedi-Rafid
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - M Macarov
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - D V Valsky
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - S Porat
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - N Yanai
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - A Frumkin
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - H Daum
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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Czakó M, Till Á, Zima J, Zsigmond A, Szabó A, Maász A, Melegh B, Hadzsiev K. Xp11.2 Duplication in Females: Unique Features of a Rare Copy Number Variation. Front Genet 2021; 12:635458. [PMID: 33936165 PMCID: PMC8080037 DOI: 10.3389/fgene.2021.635458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/22/2021] [Indexed: 11/13/2022] Open
Abstract
Among the diseases with X-linked inheritance and intellectual disability, duplication of the Xp11.23p11.22 region is indeed a rare phenomenon, with less than 90 cases known in the literature. Most of them have been recognized with the routine application of array techniques, as these copy number variations (CNVs) are highly variable in size, occurring in recurrent and non-recurrent forms. Its pathogenic role is not debated anymore, but the information available about the pathomechanism, especially in affected females, is still very limited. It has been observed that the phenotype in females varies from normal to severe, which does not correlate with the size of the duplication or the genes involved, and which makes it very difficult to give an individual prognosis. Among the patients studied by the authors because of intellectual disability, epilepsy, and minor anomalies, overlapping duplications affecting the Xp11.23p11.22 region were detected in three females. Based on our detailed phenotype analysis, we concluded that Xp11.23p11.22 duplication is a neurodevelopmental disorder.
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Affiliation(s)
- Márta Czakó
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Ágnes Till
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - Judith Zima
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - Anna Zsigmond
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary
| | - András Szabó
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Anita Maász
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, Pécs, Hungary
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Aprigliano R, Aksu ME, Bradamante S, Mihaljevic B, Wang W, Rian K, Montaldo NP, Grooms KM, Fordyce Martin SL, Bordin DL, Bosshard M, Peng Y, Alexov E, Skinner C, Liabakk NB, Sullivan GJ, Bjørås M, Schwartz CE, van Loon B. Increased p53 signaling impairs neural differentiation in HUWE1-promoted intellectual disabilities. Cell Rep Med 2021; 2:100240. [PMID: 33948573 PMCID: PMC8080178 DOI: 10.1016/j.xcrm.2021.100240] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 01/18/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023]
Abstract
Essential E3 ubiquitin ligase HUWE1 (HECT, UBA, and WWE domain containing 1) regulates key factors, such as p53. Although mutations in HUWE1 cause heterogenous neurodevelopmental X-linked intellectual disabilities (XLIDs), the disease mechanisms common to these syndromes remain unknown. In this work, we identify p53 signaling as the central process altered in HUWE1-promoted XLID syndromes. By focusing on Juberg-Marsidi syndrome (JMS), one of the severest XLIDs, we show that increased p53 signaling results from p53 accumulation caused by HUWE1 p.G4310R destabilization. This further alters cell-cycle progression and proliferation in JMS cells. Modeling of JMS neurodevelopment reveals majorly impaired neural differentiation accompanied by increased p53 signaling. The neural differentiation defects can be successfully rescued by reducing p53 levels and restoring the expression of p53 target genes, in particular CDKN1A/p21. In summary, our findings suggest that increased p53 signaling underlies HUWE1-promoted syndromes and impairs XLID JMS neural differentiation.
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Affiliation(s)
- Rossana Aprigliano
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zürich, Switzerland
| | - Merdane Ezgi Aksu
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Stefano Bradamante
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, 7049 Trondheim, Norway
| | - Boris Mihaljevic
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Wei Wang
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Kristin Rian
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Nicola P. Montaldo
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Kayla Mae Grooms
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Sarah L. Fordyce Martin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Diana L. Bordin
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Matthias Bosshard
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zürich, Switzerland
| | - Yunhui Peng
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29631, USA
| | - Emil Alexov
- Computational Biophysics and Bioinformatics, Department of Physics and Astronomy, Clemson University, Clemson, SC 29631, USA
| | | | - Nina-Beate Liabakk
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
| | - Gareth J. Sullivan
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, 0315 Oslo, Norway
- Hybrid Technology Hub, Centre of Excellence, Institute of Basic Medical Sciences, University of Oslo, 0315 Oslo, Norway
| | - Magnar Bjørås
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, 7049 Trondheim, Norway
- Department of Microbiology, Oslo University Hospital, Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, 0372 Oslo, Norway
| | | | - Barbara van Loon
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), 7049 Trondheim, Norway
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zürich, Switzerland
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, 7049 Trondheim, Norway
- Corresponding author
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16
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Kawabe H, Stegmüller J. The role of E3 ubiquitin ligases in synapse function in the healthy and diseased brain. Mol Cell Neurosci 2021; 112:103602. [DOI: 10.1016/j.mcn.2021.103602] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/06/2021] [Accepted: 02/02/2021] [Indexed: 02/08/2023] Open
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17
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Palmer EE, Carroll R, Shaw M, Kumar R, Minoche AE, Leffler M, Murray L, Macintosh R, Wright D, Troedson C, McKenzie F, Townshend S, Ward M, Nawaz U, Ravine A, Runke CK, Thorland EC, Hummel M, Foulds N, Pichon O, Isidor B, Le Caignec C, Demeer B, Andrieux J, Albarazi SH, Bye A, Sachdev R, Kirk EP, Cowley MJ, Field M, Gecz J. RLIM Is a Candidate Dosage-Sensitive Gene for Individuals with Varying Duplications of Xq13, Intellectual Disability, and Distinct Facial Features. Am J Hum Genet 2020; 107:1157-1169. [PMID: 33159883 PMCID: PMC7820564 DOI: 10.1016/j.ajhg.2020.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022] Open
Abstract
Interpretation of the significance of maternally inherited X chromosome variants in males with neurocognitive phenotypes continues to present a challenge to clinical geneticists and diagnostic laboratories. Here we report 14 males from 9 families with duplications at the Xq13.2-q13.3 locus with a common facial phenotype, intellectual disability (ID), distinctive behavioral features, and a seizure disorder in two cases. All tested carrier mothers had normal intelligence. The duplication arose de novo in three mothers where grandparental testing was possible. In one family the duplication segregated with ID across three generations. RLIM is the only gene common to our duplications. However, flanking genes duplicated in some but not all the affected individuals included the brain-expressed genes NEXMIF, SLC16A2, and the long non-coding RNA gene FTX. The contribution of the RLIM-flanking genes to the phenotypes of individuals with different size duplications has not been fully resolved. Missense variants in RLIM have recently been identified to cause X-linked ID in males, with heterozygous females typically having normal intelligence and highly skewed X chromosome inactivation. We detected consistent and significant increase of RLIM mRNA and protein levels in cells derived from seven affected males from five families with the duplication. Subsequent analysis of MDM2, one of the targets of the RLIM E3 ligase activity, showed consistent downregulation in cells from the affected males. All the carrier mothers displayed normal RLIM mRNA levels and had highly skewed X chromosome inactivation. We propose that duplications at Xq13.2-13.3 including RLIM cause a recognizable but mild neurocognitive phenotype in hemizygous males.
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Affiliation(s)
- Elizabeth E Palmer
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia; School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia; Kinghorn Centre for Clinical Genomics, Garvan Institute, Darlinghurst, Sydney, NSW 2010, Australia.
| | - Renee Carroll
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Marie Shaw
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Raman Kumar
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Andre E Minoche
- St Vincent's Clinical School, University of New South Wales, Sydney, NSW 2010, Australia
| | - Melanie Leffler
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Lucinda Murray
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | | | - Dale Wright
- Discipline of Genomic Medicine and Discipline of Child & Adolescent Health, University of Sydney, Sydney, NSW 2010, Australia; Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Chris Troedson
- Children's Hospital at Westmead, Sydney, NSW 2145, Australia
| | - Fiona McKenzie
- School of Paediatrics and Child Health, University of Western Australia, Perth, WA 6009, Australia; Genetic Services of Western Australia, Perth, WA 6008, Australia
| | | | - Michelle Ward
- Genetic Services of Western Australia, Perth, WA 6008, Australia
| | - Urwah Nawaz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia
| | - Anja Ravine
- Department of Cytogenetics, The Children's Hospital at Westmead, Westmead, NSW 2145, Australia; Pathwest Laboratory Medicine WA, Perth, WA 6008, Australia
| | - Cassandra K Runke
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Erik C Thorland
- Genomics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, Scottsdale, AZ 85259, USA
| | - Marybeth Hummel
- West Virginia University School of Medicine, Department of Pediatrics, Section of Medical Genetics Morgantown, WV 26506-9600, USA
| | - Nicola Foulds
- Wessex Clinical Genetics Services, Southampton SO16 5YA, UK
| | - Olivier Pichon
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Bertrand Isidor
- Service de génétique médicale - Unité de Génétique Clinique, CHU de Nantes - Hôtel Dieu, Nantes 44093, France
| | - Cédric Le Caignec
- Service de génétique médicale, Institut fédératif de Biologie, CHU Hopital Purpan, Toulouse 31059, France
| | - Bénédicte Demeer
- Center for Human Genetics, CLAD Nord de France, CHU Amiens-Picardie, Amiens 80080, France; CHIMERE EA 7516, University Picardie Jules Verne, Amiens 80025, France
| | - Joris Andrieux
- Institut de Biochimie et Génétique Moléculaire, CHU Lille, Lille 59000, France
| | | | - Ann Bye
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Rani Sachdev
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Edwin P Kirk
- School of Women's and Children's Health, UNSW Medicine, University of New South Wales, Randwick, NSW 2031, Australia; Sydney Children's Hospital, Randwick, NSW 2031, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Research Centre, University of New South Wales, Randwick, NSW 2033, Australia
| | - Mike Field
- Genetics of Learning Disability Service, Waratah, NSW 2298, Australia
| | - Jozef Gecz
- Adelaide Medical School and the Robinson Research Institute, University of Adelaide, Adelaide, SA 5000, Australia; Healthy Mothers, Babies and Children, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia.
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Di Palo A, Siniscalchi C, Salerno M, Russo A, Gravholt CH, Potenza N. What microRNAs could tell us about the human X chromosome. Cell Mol Life Sci 2020; 77:4069-4080. [PMID: 32356180 PMCID: PMC7854456 DOI: 10.1007/s00018-020-03526-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/18/2020] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNA) are small-non coding RNAs endowed with great regulatory power, thus playing key roles not only in almost all physiological pathways, but also in the pathogenesis of several diseases. Surprisingly, genomic distribution analysis revealed the highest density of miRNA sequences on the X chromosome; this evolutionary conserved mammalian feature equips females with a larger miRNA machinery than males. However, miRNAs contribution to some X-related conditions, properties or functions is still poorly explored. With the aim to support and focus research in the field, this review analyzes the literature and databases about X-linked miRNAs, trying to understand how miRNAs could contribute to emerging gender-biased functions and pathological mechanisms, such as immunity and cancer. A fine map of miRNA sequences on the X chromosome is reported, and their known functions are discussed; in addition, bioinformatics functional analyses of the whole X-linked miRNA targetome (predicted and validated) were performed. The emerging scenario points to different gaps in the knowledge that should be filled with future experimental investigations, also in terms of possible implications and pathological perspectives for X chromosome aneuploidy syndromes, such as Turner and Klinefelter syndromes.
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Affiliation(s)
- Armando Di Palo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Chiara Siniscalchi
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Mariacarolina Salerno
- Pediatric Endocrine Unit, Department of Translational Medical Sciences, University of Naples Federico II, Naples, Italy
| | - Aniello Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy
| | - Claus Højbjerg Gravholt
- Department of Endocrinology and Internal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Nicoletta Potenza
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Caserta, Italy.
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Wang Q, Chen P, Liu J, Lou J, Liu Y, Yuan H. Xp11.22 duplications in four unrelated Chinese families: delineating the genotype-phenotype relationship for HSD17B10 and FGD1. BMC Med Genomics 2020; 13:66. [PMID: 32381089 PMCID: PMC7206777 DOI: 10.1186/s12920-020-0728-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Xp11.22 duplications have been reported to contribute to nonsyndromic intellectual disability (ID). The HUWE1 gene has been identified in all male Xp11.22 duplication patients and is associated with nonsyndromic ID. Currently, few Xp11.22 duplication cases have been reported in the Chinese population, with limited knowledge regarding the role of other genes in this interval. CASE PRESENTATION We investigated four unrelated Chinese male Xp11.22 duplication patients, performed a comprehensive clinical evaluation for the patients and discussed the role of other genes in this interval. All patients presented with similar clinical features, including ID, speech impairments and motor delay, which were mostly consistent with those of the Xp11.22 duplication described previously. We searched and compared all cases and noted that one of the probands (Family 1) and DECIPHER case 263,219, who carried small overlapping duplications at Xp11.22 that only covered the entire HSD17B10 gene, also suffered from ID, suggesting the important role of HSD17B10 in this interval. Furthermore, three patients (two probands in Families 3 and 4 and DECIPHER case 249,490) had strikingly similar hypogonadism phenotypes, including micropenis, small testes and cryptorchidism, which have not been previously described in Xp11.22 duplication patients. Interestingly, the FGD1 gene was duplicated only in these three patients. Sufficient evidence has suggested that haploinsufficiency of the FGD1 gene causes Aarskog-Scott syndrome, which is characterized by hypogonadism and other abnormalities. Given that, we are the first group to propose that FGD1 may be a potential dosage-sensitive gene responsible for the hypogonadism observed in our patients. CONCLUSION We reported novel genotypes and phenotypes in Chinese male Xp11.22 duplication patients, and the HSD17B10 and FGD1 genes may be involved.
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Affiliation(s)
- Qingming Wang
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China
| | - Pengliang Chen
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Jianxin Liu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
| | - Jiwu Lou
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China
| | - Yanhui Liu
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China.
| | - Haiming Yuan
- Dongguan Maternal and Child Health Care Hospital, Dongguan, 523120, China.
- Dongguan Institute of Reproductive and Genetic Research, Dongguan, 523120, China.
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20
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Giles AC, Grill B. Roles of the HUWE1 ubiquitin ligase in nervous system development, function and disease. Neural Dev 2020; 15:6. [PMID: 32336296 PMCID: PMC7184716 DOI: 10.1186/s13064-020-00143-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 04/07/2020] [Indexed: 02/07/2023] Open
Abstract
Huwe1 is a highly conserved member of the HECT E3 ubiquitin ligase family. Here, we explore the growing importance of Huwe1 in nervous system development, function and disease. We discuss extensive progress made in deciphering how Huwe1 regulates neural progenitor proliferation and differentiation, cell migration, and axon development. We highlight recent evidence indicating that Huwe1 regulates inhibitory neurotransmission. In covering these topics, we focus on findings made using both vertebrate and invertebrate in vivo model systems. Finally, we discuss extensive human genetic studies that strongly implicate HUWE1 in intellectual disability, and heighten the importance of continuing to unravel how Huwe1 affects the nervous system.
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Affiliation(s)
- Andrew C Giles
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Jupiter, Florida, 33458, USA.
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21
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Tejada MI, Ibarluzea N. Non-syndromic X linked intellectual disability: Current knowledge in light of the recent advances in molecular and functional studies. Clin Genet 2020; 97:677-687. [PMID: 31898314 DOI: 10.1111/cge.13698] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 12/09/2019] [Accepted: 12/24/2019] [Indexed: 12/23/2022]
Abstract
Since the discovery of the FMR1 gene and the clinical and molecular characterization of Fragile X Syndrome in 1991, more than 141 genes have been identified in the X-chromosome in these 28 years thanks to applying continuously evolving molecular techniques to X-linked intellectual disability (XLID) families. In the past decade, array comparative genomic hybridization and next generation sequencing technologies have accelerated gene discovery exponentially. Classically, XLID has been subdivided in syndromic intellectual disability (S-XLID)-where intellectual disability (ID) is always associated with other recognizable physical and/or neurological features-and non-specific or non-syndromic intellectual disability (NS-XLID) where the only common feature is ID. Nevertheless, new advances on the study of these entities have showed that this classification is not always clear-cut because distinct variants in several of these XLID genes can result in S-XLID as well as in NS-XLID. This review focuses on the current knowledge on the XLID genes involved in non-syndromic forms, with the emphasis on their pathogenic mechanism, thus allowing the possibility to elucidate why some of them can give both syndromic and non-syndromic phenotypes.
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Affiliation(s)
- María Isabel Tejada
- Genetics Service, Cruces University Hospital, Osakidetza Basque Health Service, Barakaldo, Spain.,Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
| | - Nekane Ibarluzea
- Biocruces-Bizkaia Health Research Institute, Barakaldo, Spain.,Clinical Group, Centre for Biomedical Research on Rare Diseases (CIBERER), Valencia, Spain
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22
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Frints SGM, Ozanturk A, Rodríguez Criado G, Grasshoff U, de Hoon B, Field M, Manouvrier-Hanu S, E Hickey S, Kammoun M, Gripp KW, Bauer C, Schroeder C, Toutain A, Mihalic Mosher T, Kelly BJ, White P, Dufke A, Rentmeester E, Moon S, Koboldt DC, van Roozendaal KEP, Hu H, Haas SA, Ropers HH, Murray L, Haan E, Shaw M, Carroll R, Friend K, Liebelt J, Hobson L, De Rademaeker M, Geraedts J, Fryns JP, Vermeesch J, Raynaud M, Riess O, Gribnau J, Katsanis N, Devriendt K, Bauer P, Gecz J, Golzio C, Gontan C, Kalscheuer VM. Pathogenic variants in E3 ubiquitin ligase RLIM/RNF12 lead to a syndromic X-linked intellectual disability and behavior disorder. Mol Psychiatry 2019; 24:1748-1768. [PMID: 29728705 DOI: 10.1038/s41380-018-0065-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 02/28/2018] [Indexed: 12/25/2022]
Abstract
RLIM, also known as RNF12, is an X-linked E3 ubiquitin ligase acting as a negative regulator of LIM-domain containing transcription factors and participates in X-chromosome inactivation (XCI) in mice. We report the genetic and clinical findings of 84 individuals from nine unrelated families, eight of whom who have pathogenic variants in RLIM (RING finger LIM domain-interacting protein). A total of 40 affected males have X-linked intellectual disability (XLID) and variable behavioral anomalies with or without congenital malformations. In contrast, 44 heterozygous female carriers have normal cognition and behavior, but eight showed mild physical features. All RLIM variants identified are missense changes co-segregating with the phenotype and predicted to affect protein function. Eight of the nine altered amino acids are conserved and lie either within a domain essential for binding interacting proteins or in the C-terminal RING finger catalytic domain. In vitro experiments revealed that these amino acid changes in the RLIM RING finger impaired RLIM ubiquitin ligase activity. In vivo experiments in rlim mutant zebrafish showed that wild type RLIM rescued the zebrafish rlim phenotype, whereas the patient-specific missense RLIM variants failed to rescue the phenotype and thus represent likely severe loss-of-function mutations. In summary, we identified a spectrum of RLIM missense variants causing syndromic XLID and affecting the ubiquitin ligase activity of RLIM, suggesting that enzymatic activity of RLIM is required for normal development, cognition and behavior.
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Affiliation(s)
- Suzanna G M Frints
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands. .,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands.
| | - Aysegul Ozanturk
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | | | - Ute Grasshoff
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Bas de Hoon
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands.,Department of Gynaecology and Obstetrics, Erasmus University Medical Center, Rotterdam, 3015 CN, The Netherlands
| | - Michael Field
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Sylvie Manouvrier-Hanu
- Clinique de Génétique médicale Guy Fontaine, Centre de référence maladies rares Anomalies du développement Hôpital Jeanne de Flandre, Lille, 59000, France.,EA 7364 RADEME Maladies Rares du Développement et du Métabolisme, Faculté de Médecine, Université de Lille, Lille, 59000, France
| | - Scott E Hickey
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA
| | - Molka Kammoun
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Karen W Gripp
- Alfred I. duPont Hospital for Children Nemours, Wilmington, DE, 19803, USA
| | - Claudia Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Christopher Schroeder
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Annick Toutain
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Theresa Mihalic Mosher
- Division of Molecular & Human Genetics, Nationwide Children's Hospital, Columbus, OH, 43205, USA.,Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Peter White
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Andreas Dufke
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Eveline Rentmeester
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Sungjin Moon
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Daniel C Koboldt
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, 43205, USA.,The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Kees E P van Roozendaal
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Hao Hu
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Stefan A Haas
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Hans-Hilger Ropers
- Department of Human Molecular Genetics, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany
| | - Lucinda Murray
- GOLD (Genetics of Learning and Disability) Service, Hunter Genetics, Waratah, NSW, 2298, Australia
| | - Eric Haan
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Marie Shaw
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Renee Carroll
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia
| | - Kathryn Friend
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Jan Liebelt
- South Australian Clinical Genetics Service, SA Pathology (at Women's and Children's Hospital), North Adelaide, SA, 5006, Australia
| | - Lynne Hobson
- Genetics and Molecular Pathology, SA Pathology, Adelaide, SA, 5006, Australia
| | - Marjan De Rademaeker
- Centre for Medical Genetics, Reproduction and Genetics, Reproduction Genetics and Regenerative Medicine, Vrije Universiteit Brussel (VUB), UZ Brussel, 1090, Brussels, Belgium
| | - Joep Geraedts
- Department of Clinical Genetics, Maastricht University Medical Center+, azM, Maastricht, 6202 AZ, The Netherlands.,Department of Genetics and Cell Biology, School for Oncology and Developmental Biology, GROW, FHML, Maastricht University, Maastricht, 6200 MD, The Netherlands
| | - Jean-Pierre Fryns
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Joris Vermeesch
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Martine Raynaud
- Service de Génétique, Hôpital Bretonneau, CHU de Tours, Tours, 37044, France.,UMR 1253, iBrain, Université de Tours, Inserm, Tours, 37032, France
| | - Olaf Riess
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Joost Gribnau
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Nicholas Katsanis
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA
| | - Koen Devriendt
- Center for Human Genetics, University Hospitals Leuven, Leuven, 3000, Belgium
| | - Peter Bauer
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, 72076, Germany
| | - Jozef Gecz
- Adelaide Medical School and Robinson Research Institute, The University of Adelaide, Adelaide, SA, 5000, Australia.,South Australian Health and Medical Research Institute, Adelaide, SA, 5000, Australia
| | - Christelle Golzio
- Center for Human Disease Modeling and Departments of Pediatrics and Psychiatry, Duke University, Durham, NC, 27710, USA.,Institut de Génétique et de Biologie Moléculaire et Cellulaire, Department of Translational Medicine and Neurogenetics; Centre National de la Recherche Scientifique, UMR7104; Institut National de la Santé et de la Recherche Médicale, U964, Université de Strasbourg, 67400, Illkirch, France
| | - Cristina Gontan
- Department of Developmental Biology, Erasmus University Medical Center, Rotterdam, 3015 CN, Rotterdam, The Netherlands
| | - Vera M Kalscheuer
- Research Group Development and Disease, Max Planck Institute for Molecular Genetics, Berlin, 14195, Germany.
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23
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Hui KK, Chen YK, Endo R, Tanaka M. Translation from the Ribosome to the Clinic: Implication in Neurological Disorders and New Perspectives from Recent Advances. Biomolecules 2019; 9:E680. [PMID: 31683805 PMCID: PMC6920867 DOI: 10.3390/biom9110680] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/27/2019] [Accepted: 10/29/2019] [Indexed: 12/12/2022] Open
Abstract
De novo protein synthesis by the ribosome and its multitude of co-factors must occur in a tightly regulated manner to ensure that the correct proteins are produced accurately at the right time and, in some cases, also in the proper location. With novel techniques such as ribosome profiling and cryogenic electron microscopy, our understanding of this basic biological process is better than ever and continues to grow. Concurrently, increasing attention is focused on how translational regulation in the brain may be disrupted during the progression of various neurological disorders. In fact, translational dysregulation is now recognized as the de facto pathogenic cause for some disorders. Novel mechanisms including ribosome stalling, ribosome-associated quality control, and liquid-liquid phase separation are closely linked to translational regulation, and may thus be involved in the pathogenic process. The relationships between translational dysregulation and neurological disorders, as well as the ways through which we may be able to reverse those detrimental effects, will be examined in this review.
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Affiliation(s)
- Kelvin K Hui
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Yi-Kai Chen
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Ryo Endo
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
| | - Motomasa Tanaka
- Laboratory for Protein Conformation Diseases, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan.
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24
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Takata A, Nakashima M, Saitsu H, Mizuguchi T, Mitsuhashi S, Takahashi Y, Okamoto N, Osaka H, Nakamura K, Tohyama J, Haginoya K, Takeshita S, Kuki I, Okanishi T, Goto T, Sasaki M, Sakai Y, Miyake N, Miyatake S, Tsuchida N, Iwama K, Minase G, Sekiguchi F, Fujita A, Imagawa E, Koshimizu E, Uchiyama Y, Hamanaka K, Ohba C, Itai T, Aoi H, Saida K, Sakaguchi T, Den K, Takahashi R, Ikeda H, Yamaguchi T, Tsukamoto K, Yoshitomi S, Oboshi T, Imai K, Kimizu T, Kobayashi Y, Kubota M, Kashii H, Baba S, Iai M, Kira R, Hara M, Ohta M, Miyata Y, Miyata R, Takanashi JI, Matsui J, Yokochi K, Shimono M, Amamoto M, Takayama R, Hirabayashi S, Aiba K, Matsumoto H, Nabatame S, Shiihara T, Kato M, Matsumoto N. Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy. Nat Commun 2019; 10:2506. [PMID: 31175295 PMCID: PMC6555845 DOI: 10.1038/s41467-019-10482-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/13/2019] [Indexed: 12/30/2022] Open
Abstract
Although there are many known Mendelian genes linked to epileptic or developmental and epileptic encephalopathy (EE/DEE), its genetic architecture is not fully explained. Here, we address this incompleteness by analyzing exomes of 743 EE/DEE cases and 2366 controls. We observe that damaging ultra-rare variants (dURVs) unique to an individual are significantly overrepresented in EE/DEE, both in known EE/DEE genes and the other non-EE/DEE genes. Importantly, enrichment of dURVs in non-EE/DEE genes is significant, even in the subset of cases with diagnostic dURVs (P = 0.000215), suggesting oligogenic contribution of non-EE/DEE gene dURVs. Gene-based analysis identifies exome-wide significant (P = 2.04 × 10−6) enrichment of damaging de novo mutations in NF1, a gene primarily linked to neurofibromatosis, in infantile spasm. Together with accumulating evidence for roles of oligogenic or modifier variants in severe neurodevelopmental disorders, our results highlight genetic complexity in EE/DEE, and indicate that EE/DEE is not an aggregate of simple Mendelian disorders. Many causative genes are known for epileptic or developmental and epileptic encephalopathies (EE/DEE) yet a genetic diagnosis cannot be made for many patients. Here, the authors analyse whole exome sequencing data from a Japanese case−control cohort to identify common, rare and ultra-rare coding variants associated with EE/DEE.
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Affiliation(s)
- Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
| | - Mitsuko Nakashima
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.,Department of Biochemistry, Hamamatsu University School of Medicine, 1-20-1 Handayama, Higashi-ku, Hamamatsu, 431-3192, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Yukitoshi Takahashi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Hitoshi Osaka
- Department of Pediatrics, Jichi Medical University, 3311-1 Yakushiji, Shimotsuke, 329-0498, Japan
| | - Kazuyuki Nakamura
- Department of Pediatrics, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan
| | - Jun Tohyama
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, 1-14-1 Masago, Nishi-ku, Niigata, 950-2085, Japan
| | - Kazuhiro Haginoya
- Department of Pediatric Neurology, Miyagi Children's Hospital, 4-3-17 Ochiai, Aoba-ku, Sendai, 989-3126, Japan
| | - Saoko Takeshita
- Department of Pediatrics, Yokohama City University Medical Center, 4-57 Urafunecho, Minami-ku, Yokohama, 232-0024, Japan
| | - Ichiro Kuki
- Department of Pediatric Neurology, Osaka City General Hospital, 2-13-22 Miyakojimahondori, Miyakojima-ku, Osaka, 534-0021, Japan
| | - Tohru Okanishi
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Tomohide Goto
- Division of Neurology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa, Minami-ku, Yokohama, 232-8555, Japan
| | - Masayuki Sasaki
- Department of Child Neurology, National Center of Neurology and Psychiatry, 4-1-1 Ogawahigashi, Kodaira, 187-8551, Japan
| | - Yasunari Sakai
- Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kazuhiro Iwama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Gaku Minase
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Eri Imagawa
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Chihiro Ohba
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hiromi Aoi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Tomohiro Sakaguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Kouhei Den
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Rina Takahashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan
| | - Hiroko Ikeda
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Tokito Yamaguchi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Kazuki Tsukamoto
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Shinsaku Yoshitomi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Taikan Oboshi
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Katsumi Imai
- National Epilepsy Center, NHO Shizuoka Institute of Epilepsy and Neurological Disorders, 886 Urushiyama, Aoi-ku, Shizuoka, 420-8688, Japan
| | - Tomokazu Kimizu
- Department of Pediatric Neurology, Osaka Women's and Children's Hospital, 840 Murodo-cho, Izumi, Osaka, 594-1101, Japan
| | - Yu Kobayashi
- Department of Child Neurology, NHO Nishiniigata Chuo Hospital, 1-14-1 Masago, Nishi-ku, Niigata, 950-2085, Japan
| | - Masaya Kubota
- Division of Neurology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Hirofumi Kashii
- Division of Neurology, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Shimpei Baba
- Department of Child Neurology, Comprehensive Epilepsy Center, Seirei Hamamatsu General Hospital, 2-12-12 Sumiyoshi, Naka-ku, Hamamatsu, 430-8558, Japan
| | - Mizue Iai
- Division of Neurology, Kanagawa Children's Medical Center, 2-138-4 Mutsukawa, Minami-ku, Yokohama, 232-8555, Japan
| | - Ryutaro Kira
- Department of Pediatric Neurology, Fukuoka Children's Hospital, 5-1-1 Kashiiteriha, Higashi-ku, Fukuoka, 813-0017, Japan
| | - Munetsugu Hara
- Department of Pediatrics and Child Health, Kurume University School of Medicine, 67 Asahi-machi, Kurume, Fukuoka, 830-0011, Japan
| | - Masayasu Ohta
- Department of Neuropediatrics, Aiseikai Memorial Ibaraki Welfare Medical Center, 1872-1 Motoyoshida-cho, Mito, 310-0836, Japan
| | - Yohane Miyata
- Department of Neuropediatrics, Tokyo Metropolitan Neurological Hospital, 2-6-1 Musashidai, Fuchu, 183-0042, Japan
| | - Rie Miyata
- Department of Pediatrics, Tokyo-kita Medical Center, 4-17-56 Akabanedai, Kita-ku, Tokyo, 115-0053, Japan
| | - Jun-Ichi Takanashi
- Department of Pediatrics, Tokyo Women's Medical University Yachiyo Medical Center, 477-96 Owadashinden, Yachiyo, 276-8524, Japan
| | - Jun Matsui
- Department of Pediatrics, Shiga University of Medical Science, Setatsukinowacho, Otsu, 520-2192, Japan
| | - Kenji Yokochi
- Department of Pediatric Neurology, Seirei-Mikatahara General Hospital, 3453 Mikatahara-cho, Kita-ku, Hamamatsu, 431-1304, Japan
| | - Masayuki Shimono
- Department of Pediatrics, School of Medicine, University of Occupational and Environmental Health, 1-1 Iseigaoka, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Masano Amamoto
- Kutakyushu Municipal Yahata Hospital Pediatric Emergency Center, 4-18-1 Nishihonmachi, Yahatahigashi-ku, Kutakyushu, 805-8534, Japan
| | - Rumiko Takayama
- Hokkaido Medical Center for Child Health and Rehabilitation, 1-240-6 Kanayama 1-jo, Teine-ku, Sapporo, 006-0041, Japan
| | - Shinichi Hirabayashi
- Division of Neurology, Nagano Children's Hospital, 3100 Toyoshina, Azumino, 399-8288, Japan
| | - Kaori Aiba
- Department of Pediatrics, Toyohashi Municipal Hospital, 50 Aza Hachiken Nishi, Aotake-Cho, Toyohashi, 441-8570, Japan
| | - Hiroshi Matsumoto
- Department of Pediatrics, National Defense Medical College, 3-2 Namiki, Tokorozawa, 359-8513, Japan
| | - Shin Nabatame
- Department of Pediatrics, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan
| | - Takashi Shiihara
- Department of Neurology, Gunma Children's Medical Center, 779 Shimohakoda, Hokkitsu-machi, Shibukawa, 377-8577, Japan
| | - Mitsuhiro Kato
- Department of Pediatrics, Yamagata University Faculty of Medicine, 2-2-2 Iida-nishi, Yamagata, 990-9585, Japan.,Department of Pediatrics, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8666, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, 236-0004, Japan.
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25
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Muthusamy B, Nguyen TT, Bandari AK, Basheer S, Selvan LDN, Chandel D, Manoj J, Gayen S, Seshagiri S, Chandra Girimaji S, Pandey A. Exome sequencing reveals a novel splice site variant in HUWE1 gene in patients with suspected Say-Meyer syndrome. Eur J Med Genet 2019; 63:103635. [PMID: 30797980 DOI: 10.1016/j.ejmg.2019.02.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Revised: 02/11/2019] [Accepted: 02/17/2019] [Indexed: 12/30/2022]
Abstract
Say-Meyer syndrome is a rare and clinically heterogeneous syndrome characterized by trigonocephaly, short stature, developmental delay and hypotelorism. Nine patients with this syndrome have been reported thus far although no causative gene has yet been identified. Here, we report two siblings with clinical phenotypes of Say-Meyer syndrome with moderate to severe intellectual disability and autism spectrum disorder. Cytogenetics and array-based comparative genomic hybridization did not reveal any chromosome abnormalities or copy number alterations. Exome sequencing of the patients revealed a novel X-linked recessive splice acceptor site variant c.145-2A > G in intron 5 of HUWE1 gene in both affected siblings. RT-PCR and sequencing revealed the use of an alternate cryptic splice acceptor site downstream, which led to deletion of six nucleotides resulting loss of two amino acids p.(Cys49-Glu50del) in HUWE1 protein. Deletion of these two amino acids, which are located in a highly conserved region, is predicted to be deleterious and quite likely to affect the function of HUWE1 protein. This is the first report of a potential candidate gene mutation for Say-Meyer syndrome, which was initially described four decades ago.
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Affiliation(s)
- Babylakshmi Muthusamy
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India; Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Thong T Nguyen
- Department of Molecular Biology and Metabolic Disease, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Aravind K Bandari
- Institute of Bioinformatics, International Technology Park, Bangalore, 560066, India; Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India; Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Salah Basheer
- Department of Child and Adolescent Psychiatry, NIMHANS, Hosur Road, Bangalore, 560029, India
| | | | - Deepshikha Chandel
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Jesna Manoj
- Department of Child and Adolescent Psychiatry, NIMHANS, Hosur Road, Bangalore, 560029, India
| | - Srimonta Gayen
- Department of Molecular Reproduction, Development and Genetics, Division of Biological Sciences, Indian Institute of Science, Bangalore, India
| | - Somasekar Seshagiri
- Department of Molecular Biology and Metabolic Disease, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Satish Chandra Girimaji
- Department of Child and Adolescent Psychiatry, NIMHANS, Hosur Road, Bangalore, 560029, India.
| | - Akhilesh Pandey
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India; Department of Laboratory Medicine and Pathology, Rochester, MN, 55905, USA; Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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26
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Extensive cellular heterogeneity of X inactivation revealed by single-cell allele-specific expression in human fibroblasts. Proc Natl Acad Sci U S A 2018; 115:13015-13020. [PMID: 30510006 DOI: 10.1073/pnas.1806811115] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-chromosome inactivation (XCI) provides a dosage compensation mechanism where, in each female cell, one of the two X chromosomes is randomly silenced. However, some genes on the inactive X chromosome and outside the pseudoautosomal regions escape from XCI and are expressed from both alleles (escapees). We investigated XCI at single-cell resolution combining deep single-cell RNA sequencing with whole-genome sequencing to examine allelic-specific expression in 935 primary fibroblast and 48 lymphoblastoid single cells from five female individuals. In this framework we integrated an original method to identify and exclude doublets of cells. In fibroblast cells, we have identified 55 genes as escapees including five undescribed escapee genes. Moreover, we observed that all genes exhibit a variable propensity to escape XCI in each cell and cell type and that each cell displays a distinct expression profile of the escapee genes. A metric, the Inactivation Score-defined as the mean of the allelic expression profiles of the escapees per cell-enables us to discover a heterogeneous and continuous degree of cellular XCI with extremes represented by "inactive" cells, i.e., cells exclusively expressing the escaping genes from the active X chromosome and "escaping" cells expressing the escapees from both alleles. We found that this effect is associated with cell-cycle phases and, independently, with the XIST expression level, which is higher in the quiescent phase (G0). Single-cell allele-specific expression is a powerful tool to identify novel escapees in different tissues and provide evidence of an unexpected cellular heterogeneity of XCI.
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27
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Chen D, Gehringer M, Lorenz S. Developing Small-Molecule Inhibitors of HECT-Type Ubiquitin Ligases for Therapeutic Applications: Challenges and Opportunities. Chembiochem 2018; 19:2123-2135. [PMID: 30088849 PMCID: PMC6471174 DOI: 10.1002/cbic.201800321] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Indexed: 12/11/2022]
Abstract
The ubiquitin system regulates countless physiological and disease-associated processes and has emerged as an attractive entryway for therapeutic efforts. With over 600 members in the human proteome, ubiquitin ligases are the most diverse class of ubiquitylation enzymes and pivotal in encoding specificity in ubiquitin signaling. Although considerable progress has been made in the identification of small molecules targeting RING ligases, relatively little is known about the "druggability" of HECT (homologous to E6AP C terminus) ligases, many of which are critically implicated in human pathologies. A major obstacle to optimizing the few available ligands is our incomplete understanding of their inhibitory mechanisms and the structural basis of catalysis in HECT ligases. Here, we survey recent approaches to manipulate the activities of HECT ligases with small molecules to showcase the particular challenges and opportunities these enzymes hold as therapeutic targets.
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Affiliation(s)
- Dan Chen
- Rudolf Virchow Center for Experimental BiomedicineUniversity of WürzburgJosef-Schneider-Strasse 2, Haus D1597080WürzburgGermany
| | - Matthias Gehringer
- Institute of Pharmaceutical SciencesDepartment of Pharmaceutical/Medicinal ChemistryUniversity of TübingenAuf der Morgenstelle 872076TübingenGermany
| | - Sonja Lorenz
- Rudolf Virchow Center for Experimental BiomedicineUniversity of WürzburgJosef-Schneider-Strasse 2, Haus D1597080WürzburgGermany
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28
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Malhotra A, Sharma U, Puhan S, Chandra Bandari N, Kharb A, Arifa PP, Thakur L, Prakash H, Vasquez KM, Jain A. Stabilization of miRNAs in esophageal cancer contributes to radioresistance and limits efficacy of therapy. Biochimie 2018; 156:148-157. [PMID: 30326253 DOI: 10.1016/j.biochi.2018.10.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 10/11/2018] [Indexed: 12/15/2022]
Abstract
The five-year survival rate of esophageal cancer patients is less than 20%. This may be due to increased resistance (acquired or intrinsic) of tumor cells to chemo/radiotherapies, often caused by aberrant cell cycle, deregulated apoptosis, increases in growth factor signaling pathways, and/or changes in the proteome network. In addition, deregulation in non-coding RNA-mediated signaling pathways may contribute to resistance to therapies. At the molecular level, these resistance factors have now been linked to various microRNA (miRNAs), which have recently been shown to control cell development, differentiation and neoplasia. The increased stability and dysregulated expression of miRNAs have been associated with increased resistance to various therapies in several cancers, including esophageal cancer. Therefore, miRNAs represent the next generation of molecules with tremendous potential as biomarkers and therapeutic targets. However, detailed studies on miRNA-based therapeutic interventions are still in their infancy. Hence, in this review, we have summarized the current status of microRNAs in dictating the resistance/sensitivity of tumor cells to chemotherapy and radiotherapy. In addition, we have discussed various strategies to increase radiosensitivity, including targeted therapy, and the use of miRNAs as radiosensitive/radioresistance biomarkers for esophageal cancer in the clinical setting.
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Affiliation(s)
- Akshay Malhotra
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Uttam Sharma
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Shyamly Puhan
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Naga Chandra Bandari
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Anjali Kharb
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - P P Arifa
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Lovlesh Thakur
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India
| | - Hridayesh Prakash
- Laboratory Oncology Unit, Institute Rotary Cancer Hospital, All India Institute of Medical Sciences, Ansari Nagar, New Delhi, 110029, India; Institute of Virology and Immunology, Amity University, NOIDA, India.
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd, Austin, TX, 78723, USA
| | - Aklank Jain
- Department of Animal Sciences, Central University of Punjab, Bathinda, Punjab, India.
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29
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Kao SH, Wu HT, Wu KJ. Ubiquitination by HUWE1 in tumorigenesis and beyond. J Biomed Sci 2018; 25:67. [PMID: 30176860 PMCID: PMC6122628 DOI: 10.1186/s12929-018-0470-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Accepted: 08/28/2018] [Indexed: 01/19/2023] Open
Abstract
Ubiquitination modulates a large repertoire of cellular functions and thus, dysregulation of the ubiquitin system results in multiple human diseases, including cancer. Ubiquitination requires an E3 ligase, which is responsible for substrate recognition and conferring specificity to ubiquitination. HUWE1 is a multifaceted HECT domain-containing ubiquitin E3 ligase, which catalyzes both mono-ubiquitination and K6-, K48- and K63-linked poly-ubiquitination of its substrates. Many of the substrates of HUWE1 play a crucial role in maintaining the homeostasis of cellular development. Not surprisingly, dysregulation of HUWE1 is associated with tumorigenesis and metastasis. HUWE1 is frequently overexpressed in solid tumors, but can be downregulated in brain tumors, suggesting that HUWE1 may possess differing cell-specific functions depending on the downstream targets of HUWE1. This review introduces some important discoveries of the HUWE1 substrates, including those controlling proliferation and differentiation, apoptosis, DNA repair, and responses to stress. In addition, we review the signaling pathways HUWE1 participates in and obstacles to the identification of HUWE1 substrates. We also discuss up-to-date potential therapeutic designs using small molecules or ubiquitin variants (UbV) against the HUWE1 activity. These molecular advances provide a translational platform for future bench-to-bed studies. HUWE1 is a critical ubiquitination modulator during the tumor progression and may serve as a possible therapeutic target for cancer treatment.
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Affiliation(s)
- Shih-Han Kao
- Research Center for Tumor Medical Science, China Medical University, No. 91, Hseuh-Shih Rd, Taichung, 40402, Taiwan. .,Drug Development Center, China Medical University, Taichung, 40402, Taiwan.
| | - Han-Tsang Wu
- Department of Cell and Tissue Engineering, Changhua Christian Hospital, Changhua City, 500, Taiwan
| | - Kou-Juey Wu
- Research Center for Tumor Medical Science, China Medical University, No. 91, Hseuh-Shih Rd, Taichung, 40402, Taiwan. .,Drug Development Center, China Medical University, Taichung, 40402, Taiwan. .,Institute of New Drug Development, Taichung, 40402, Taiwan. .,Graduate Institutes of Biomedical Sciences, China Medical University, Taichung, 40402, Taiwan. .,Departmet of Medical Research, China Medical University Hospital, Taichung, 40402, Taiwan.
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30
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Fritzen D, Kuechler A, Grimmel M, Becker J, Peters S, Sturm M, Hundertmark H, Schmidt A, Kreiß M, Strom TM, Wieczorek D, Haack TB, Beck-Wödl S, Cremer K, Engels H. De novo FBXO11 mutations are associated with intellectual disability and behavioural anomalies. Hum Genet 2018; 137:401-411. [PMID: 29796876 DOI: 10.1007/s00439-018-1892-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/17/2018] [Indexed: 12/26/2022]
Abstract
Intellectual disability (ID) has an estimated prevalence of 1.5-2%. In most affected individuals, its genetic basis remains unclear. Whole exome sequencing (WES) studies have identified a multitude of novel causative gene defects and have shown that a large proportion of sporadic ID cases results from de novo mutations. Here, we present two unrelated individuals with similar clinical features and deleterious de novo variants in FBXO11 detected by WES. Individual 1, a 14-year-old boy, has mild ID as well as mild microcephaly, corrected cleft lip and alveolus, hyperkinetic disorder, mild brain atrophy and minor facial dysmorphism. WES detected a heterozygous de novo 1 bp insertion in the splice donor site of exon 3. Individual 2, a 3-year-old boy, showed ID and pre- and postnatal growth retardation, postnatal mild microcephaly, hyperkinetic and restless behaviour, as well as mild dysmorphism. WES detected a heterozygous de novo frameshift mutation. While ten individuals with ID and de novo variants in FBXO11 have been reported as part of larger studies, only one of the reports has some additional clinical data. Interestingly, the latter individual carries the identical mutation as our individual 2 and also displays ID, intrauterine growth retardation, microcephaly, behavioural anomalies, and dysmorphisms. Thus, we confirm deleterious de novo mutations in FBXO11 as a cause of ID and start the delineation of the associated clinical picture which may also comprise postnatal microcephaly or borderline small head size and behavioural anomalies.
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Affiliation(s)
- Daniel Fritzen
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Alma Kuechler
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
| | - Mona Grimmel
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
| | - Jessica Becker
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Sophia Peters
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Marc Sturm
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
| | - Hela Hundertmark
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Axel Schmidt
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Martina Kreiß
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Tim M Strom
- Institute of Human Genetics, Helmholtz Zentrum München, Ingolstaedter Landstr. 1, 85764, Neuherberg, Germany
- Institute of Human Genetics, Technische Universität München, Trogerstraße 32, 81675, München, Germany
| | - Dagmar Wieczorek
- Institut für Humangenetik, Universitätsklinikum Essen, Universität Duisburg-Essen, Hufelandstraße 55, 45147, Essen, Germany
- Heinrich-Heine-University, Medical Faculty, Institute of Human Genetics, Universitätsstr. 1, 40225, Düsseldorf, Germany
| | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
- Institute of Human Genetics, Technische Universität München, Trogerstraße 32, 81675, München, Germany
| | - Stefanie Beck-Wödl
- Institute of Medical Genetics and Applied Genomics, University of Tübingen, Calwerstrasse 7, 72076, Tübingen, Germany
| | - Kirsten Cremer
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany
| | - Hartmut Engels
- Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital Bonn, Sigmund-Freud-Str. 25, 53127, Bonn, Germany.
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31
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Montagne L, Derhourhi M, Piton A, Toussaint B, Durand E, Vaillant E, Thuillier D, Gaget S, De Graeve F, Rabearivelo I, Lansiaux A, Lenne B, Sukno S, Desailloud R, Cnop M, Nicolescu R, Cohen L, Zagury JF, Amouyal M, Weill J, Muller J, Sand O, Delobel B, Froguel P, Bonnefond A. CoDE-seq, an augmented whole-exome sequencing, enables the accurate detection of CNVs and mutations in Mendelian obesity and intellectual disability. Mol Metab 2018; 13:1-9. [PMID: 29784605 PMCID: PMC6026315 DOI: 10.1016/j.molmet.2018.05.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 01/15/2023] Open
Abstract
Objective The molecular diagnosis of extreme forms of obesity, in which accurate detection of both copy number variations (CNVs) and point mutations, is crucial for an optimal care of the patients and genetic counseling for their families. Whole-exome sequencing (WES) has benefited considerably this molecular diagnosis, but its poor ability to detect CNVs remains a major limitation. We aimed to develop a method (CoDE-seq) enabling the accurate detection of both CNVs and point mutations in one step. Methods CoDE-seq is based on an augmented WES method, using probes distributed uniformly throughout the genome. CoDE-seq was validated in 40 patients for whom chromosomal DNA microarray was available. CNVs and mutations were assessed in 82 children/young adults with suspected Mendelian obesity and/or intellectual disability and in their parents when available (ntotal = 145). Results CoDE-seq not only detected all of the 97 CNVs identified by chromosomal DNA microarrays but also found 84 additional CNVs, due to a better resolution. When compared to CoDE-seq and chromosomal DNA microarrays, WES failed to detect 37% and 14% of CNVs, respectively. In the 82 patients, a likely molecular diagnosis was achieved in >30% of the patients. Half of the genetic diagnoses were explained by CNVs while the other half by mutations. Conclusions CoDE-seq has proven cost-efficient and highly effective as it avoids the sequential genetic screening approaches currently used in clinical practice for the accurate detection of CNVs and point mutations. Whole-exome sequencing (WES) poorly detects CNVs. Whole-genome sequencing remains expensive and hard to handle in clinical practice. CoDE-seq (based on an augmented WES protocol) accurately detect CNVs. CoDE-seq is highly effective for the diagnosis of obesity & intellectual disability.
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Affiliation(s)
- Louise Montagne
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France; Department of Pediatrics, Saint Antoine Pediatric Hospital, Saint Vincent de Paul Hospital, Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Catholic University of Lille, Lille, France.
| | - Mehdi Derhourhi
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Amélie Piton
- Molecular diagnostic laboratory, Strasbourg University Hospitals, Strasbourg, France
| | - Bénédicte Toussaint
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Emmanuelle Durand
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Emmanuel Vaillant
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Dorothée Thuillier
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Stefan Gaget
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Franck De Graeve
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Iandry Rabearivelo
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Amélie Lansiaux
- Department of Medical Research, Saint Philibert Hospital, Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Lomme, France
| | - Bruno Lenne
- Department of Cytogenetics-Medical Genetics, Saint Vincent de Paul Hospital, Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Catholic University of Lille, Lille, France
| | - Sylvie Sukno
- Department of Paediatric Neurology, Saint Antoine Paediatric Hospital, Saint Vincent de Paul Hospital, Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Catholic University of Lille, Lille, France
| | - Rachel Desailloud
- Department of Endocrinology-Nutrition, University of Picardie Jules Verne, Amiens, France
| | - Miriam Cnop
- ULB Center for Diabetes Research, Université Libre de Bruxelles, Brussels, Belgium; Division of Endocrinology, Erasmus Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Ramona Nicolescu
- Department of Pediatrics, General Hospital Citadelle, Liège, Belgium
| | - Lior Cohen
- Genetic Institute, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Jean-François Zagury
- Laboratoire Génomique, Bioinformatique et Applications, EA4627, Conservatoire National des Arts et Métiers, Paris, France
| | - Mélanie Amouyal
- Inserm U1141, Robert Debré Hospital, Paris Diderot-Paris 7 University, Paris, France
| | - Jacques Weill
- Pediatric Endocrine Department, Lille hospital, Lille, France
| | - Jean Muller
- Molecular diagnostic laboratory, Strasbourg University Hospitals, Strasbourg, France; Inserm U1112, Fédération de Médecine Translationnelle de Strasbourg (FMTS), University of Strasbourg, Strasbourg, France
| | - Olivier Sand
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France
| | - Bruno Delobel
- Department of Cytogenetics-Medical Genetics, Saint Vincent de Paul Hospital, Groupement des Hôpitaux de l'Institut Catholique de Lille (GHICL), Catholic University of Lille, Lille, France
| | - Philippe Froguel
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France; Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, United Kingdom.
| | - Amélie Bonnefond
- CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, University of Lille, Lille, France; Department of Medicine, Section of Genomics of Common Disease, Imperial College London, London, United Kingdom.
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32
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Opperman KJ, Mulcahy B, Giles AC, Risley MG, Birnbaum RL, Tulgren ED, Dawson-Scully K, Zhen M, Grill B. The HECT Family Ubiquitin Ligase EEL-1 Regulates Neuronal Function and Development. Cell Rep 2018; 19:822-835. [PMID: 28445732 DOI: 10.1016/j.celrep.2017.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 03/01/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022] Open
Abstract
Genetic changes in the HECT ubiquitin ligase HUWE1 are associated with intellectual disability, but it remains unknown whether HUWE1 functions in post-mitotic neurons to affect circuit function. Using genetics, pharmacology, and electrophysiology, we show that EEL-1, the HUWE1 ortholog in C. elegans, preferentially regulates GABAergic presynaptic transmission. Decreasing or increasing EEL-1 function alters GABAergic transmission and the excitatory/inhibitory (E/I) balance in the worm motor circuit, which leads to impaired locomotion and increased sensitivity to electroshock. Furthermore, multiple mutations associated with intellectual disability impair EEL-1 function. Although synaptic transmission defects did not result from abnormal synapse formation, sensitizing genetic backgrounds revealed that EEL-1 functions in the same pathway as the RING family ubiquitin ligase RPM-1 to regulate synapse formation and axon termination. These findings from a simple model circuit provide insight into the molecular mechanisms required to obtain E/I balance and could have implications for the link between HUWE1 and intellectual disability.
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Affiliation(s)
- Karla J Opperman
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada
| | - Andrew C Giles
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Monica G Risley
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Rayna L Birnbaum
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA; Harriet L. Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Erik D Tulgren
- Department of Pharmacology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ken Dawson-Scully
- Department of Biological Sciences, Florida Atlantic University, Boca Raton, FL 33431, USA
| | - Mei Zhen
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics and Physiology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brock Grill
- Department of Neuroscience, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA.
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HUWE1 variants cause dominant X-linked intellectual disability: a clinical study of 21 patients. Eur J Hum Genet 2017; 26:64-74. [PMID: 29180823 DOI: 10.1038/s41431-017-0038-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 09/05/2017] [Accepted: 09/09/2017] [Indexed: 01/03/2023] Open
Abstract
Whole-gene duplications and missense variants in the HUWE1 gene (NM_031407.6) have been reported in association with intellectual disability (ID). Increased gene dosage has been observed in males with non-syndromic mild to moderate ID with speech delay. Missense variants reported previously appear to be associated with severe ID in males and mild or no ID in obligate carrier females. Here, we report the largest cohort of patients with HUWE1 variants, consisting of 14 females and 7 males, with 15 different missense variants and one splice site variant. Clinical assessment identified common clinical features consisting of moderate to profound ID, delayed or absent speech, short stature with small hands and feet and facial dysmorphism consisting of a broad nasal tip, deep set eyes, epicanthic folds, short palpebral fissures, and a short philtrum. We describe for the first time that females can be severely affected, despite preferential inactivation of the affected X chromosome. Three females with the c.329 G > A p.Arg110Gln variant, present with a phenotype of mild ID, specific facial features, scoliosis and craniosynostosis, as reported previously in a single patient. In these females, the X inactivation pattern appeared skewed in favour of the affected transcript. In summary, HUWE1 missense variants may cause syndromic ID in both males and females.
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Impaired oxidative stress response characterizes HUWE1-promoted X-linked intellectual disability. Sci Rep 2017; 7:15050. [PMID: 29118367 PMCID: PMC5678168 DOI: 10.1038/s41598-017-15380-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/25/2017] [Indexed: 12/21/2022] Open
Abstract
Mutations in the HECT, UBA and WWE domain-containing 1 (HUWE1) E3 ubiquitin ligase cause neurodevelopmental disorder X-linked intellectual disability (XLID). HUWE1 regulates essential processes such as genome integrity maintenance. Alterations in the genome integrity and accumulation of mutations have been tightly associated with the onset of neurodevelopmental disorders. Though HUWE1 mutations are clearly implicated in XLID and HUWE1 regulatory functions well explored, currently much is unknown about the molecular basis of HUWE1-promoted XLID. Here we showed that the HUWE1 expression is altered and mutation frequency increased in three different XLID individual (HUWE1 p.R2981H, p.R4187C and HUWE1 duplication) cell lines. The effect was most prominent in HUWE1 p.R4187C XLID cells and was accompanied with decreased DNA repair capacity and hypersensitivity to oxidative stress. Analysis of HUWE1 substrates revealed XLID-specific down-regulation of oxidative stress response DNA polymerase (Pol) λ caused by hyperactive HUWE1 p.R4187C. The subsequent restoration of Polλ levels counteracted the oxidative hypersensitivity. The observed alterations in the genome integrity maintenance may be particularly relevant in the cortical progenitor zones of human brain, as suggested by HUWE1 immunofluorescence analysis of cerebral organoids. These results provide evidence that impairments of the fundamental cellular processes, like genome integrity maintenance, characterize HUWE1-promoted XLID.
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Lv F, Ma M, Liu W, Xu X, Song Y, Li L, Jiang Y, Wang O, Xia W, Xing X, Qiu Z, Li M. A novel large fragment deletion in PLS3 causes rare X-linked early-onset osteoporosis and response to zoledronic acid. Osteoporos Int 2017. [PMID: 28620780 DOI: 10.1007/s00198-017-4094-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
UNLABELLED We identified a novel large fragment deletion from intron 9 to 3'UTR in PLS3 (E10-E16del) in one Chinese boy with X-linked early-onset osteoporosis and vertebral fractures, which expanded the pathogenic spectrum of X-linked early-onset osteoporosis. Treatment with zoledronic acid was beneficial for increasing BMD and reshaping the vertebral bodies of this patient. INTRODUCTION X-linked early-onset osteoporosis is a rare disease, which is characterized by low bone mineral density (BMD), vertebral compression fractures (VCFs), and/or long bone fractures. We aimed to detect the phenotype and the underlying pathogenic mutation of X-linked early-onset osteoporosis in a boy from a nonconsanguineous Chinese family. METHODS We investigated the pathogenic mutation of the patient with X-linked early-onset osteoporosis by targeted next-generation sequencing and confirmed it by Sanger sequencing. We also observed the effects of zoledronic acid on fracture frequency and BMD of the patient. RESULTS Low BMD and multiple VCFs were the main phenotypes of X-linked early-onset osteoporosis. We identified a total of 12,229 bp deletion in PLS3, involving intron 9 to the 3'UTR (E10-E16 del). This large fragment deletion might be mediated by Alu repeats and microhomology of 26 bp at each breakpoint junction. Zoledronic acid treatment could significantly increase the Z-score of BMD and reshape the compressed vertebral bodies. CONCLUSION We identified a large fragment deletion mutation in PLS3 for the first time and elucidated the possible mechanism of the deletion, which led to X-linked early-onset osteoporosis and multiple vertebral fractures. Our findings would enrich the etiology spectrum of this rare disease.
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Affiliation(s)
- F Lv
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - M Ma
- Department of Pediatrics, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China
| | - W Liu
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - X Xu
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - Y Song
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - L Li
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - Y Jiang
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - O Wang
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - W Xia
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - X Xing
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China
| | - Z Qiu
- Department of Pediatrics, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, 100730, People's Republic of China.
| | - M Li
- Department of Endocrinology, Key Laboratory of Endocrinology of Ministry of Health, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Science, Beijing, 100730, People's Republic of China.
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Grau C, Starkovich M, Azamian MS, Xia F, Cheung SW, Evans P, Henderson A, Lalani SR, Scott DA. Xp11.22 deletions encompassing CENPVL1, CENPVL2, MAGED1 and GSPT2 as a cause of syndromic X-linked intellectual disability. PLoS One 2017; 12:e0175962. [PMID: 28414775 PMCID: PMC5393878 DOI: 10.1371/journal.pone.0175962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/03/2017] [Indexed: 12/27/2022] Open
Abstract
By searching a clinical database of over 60,000 individuals referred for array-based CNV analyses and online resources, we identified four males from three families with intellectual disability, developmental delay, hypotonia, joint hypermobility and relative macrocephaly who carried small, overlapping deletions of Xp11.22. The maximum region of overlap between their deletions spanned ~430 kb and included two pseudogenes, CENPVL1 and CENPVL2, whose functions are not known, and two protein coding genes-the G1 to S phase transition 2 gene (GSPT2) and the MAGE family member D1 gene (MAGED1). Deletions of this ~430 kb region have not been previously implicated in human disease. Duplications of GSPT2 have been documented in individuals with intellectual disability, but the phenotypic consequences of a loss of GSPT2 function have not been elucidated in humans or mouse models. Changes in MAGED1 have not been associated with intellectual disability in humans, but loss of MAGED1 function is associated with neurocognitive and neurobehavioral phenotypes in mice. In all cases, the Xp11.22 deletion was inherited from an unaffected mother. Studies performed on DNA from one of these mothers did not show evidence of skewed X-inactivation. These results suggest that deletions of an ~430 kb region on chromosome Xp11.22 that encompass CENPVL1, CENPVL2, GSPT2 and MAGED1 cause a distinct X-linked syndrome characterized by intellectual disability, developmental delay, hypotonia, joint hypermobility and relative macrocephaly. Loss of GSPT2 and/or MAGED1 function may contribute to the intellectual disability and developmental delay seen in males with these deletions.
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Affiliation(s)
- Christina Grau
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Molly Starkovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, Unite States of America
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, Unite States of America
| | - Patricia Evans
- Departments of Pediatrics and Neurology, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Alex Henderson
- The Newcastle upon Tyne Hospitals, Newcastle upon Tyne, England
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
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Krist DT, Foote PK, Statsyuk AV. UbFluor: A Fluorescent Thioester to Monitor HECT E3 Ligase Catalysis. ACTA ACUST UNITED AC 2017; 9:11-37. [PMID: 28253433 DOI: 10.1002/cpch.17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
HECT E3 ubiquitin ligases (∼28 are known) are associated with many phenotypes in eukaryotes and are important drug targets. However, assays used to screen for small molecule inhibitors of HECT E3s are complex and require ATP, Ub, E1, E2, and HECT E3 enzymes, producing three covalent thioester enzyme intermediates E1∼Ub, E2∼Ub, and HECT E3∼Ub (where ∼ indicates a thioester bond), and mixtures of polyubiquitin chains. To reduce the complexity of the assay, we developed a novel class of fluorescent probes, UbFluor, that act as mechanistically relevant pseudosubstrates of HECT E3s. These probes undergo a direct transthiolation reaction with the catalytic cysteine of HECT E3s, producing the catalytically active HECT E3∼Ub thioester accompanied by fluorophore release. Thus, a fluorescence polarization assay can continuously monitor UbFluor consumption by HECT E3s, and changes in UbFluor consumption rendered by biochemical point mutations or small molecule modulation of HECT E3 activity. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- David T Krist
- Northwestern University, Department of Chemistry, Chemistry of Life Processes Institute, Evanston, Illinois
| | - Peter K Foote
- Northwestern University, Department of Chemistry, Chemistry of Life Processes Institute, Evanston, Illinois
| | - Alexander V Statsyuk
- Northwestern University, Department of Chemistry, Chemistry of Life Processes Institute, Evanston, Illinois
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Gauthier-Vasserot A, Thauvin-Robinet C, Bruel AL, Duffourd Y, St-Onge J, Jouan T, Rivière JB, Heron D, Donadieu J, Bellanné-Chantelot C, Briandet C, Huet F, Kuentz P, Lehalle D, Duplomb-Jego L, Gautier E, Maystadt I, Pinson L, Amram D, El Chehadeh S, Melki J, Julia S, Faivre L, Thevenon J. Application of whole-exome sequencing to unravel the molecular basis of undiagnosed syndromic congenital neutropenia with intellectual disability. Am J Med Genet A 2016; 173:62-71. [DOI: 10.1002/ajmg.a.37969] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 08/02/2016] [Indexed: 12/19/2022]
Affiliation(s)
| | - Christel Thauvin-Robinet
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD); Centre Hospitalier Universitaire Dijon; Dijon France
| | - Ange-Line Bruel
- GAD EA4271; Université de Bourgogne Franche-Comté; Dijon France
| | - Yannis Duffourd
- GAD EA4271; Université de Bourgogne Franche-Comté; Dijon France
| | - Judith St-Onge
- GAD EA4271; Université de Bourgogne Franche-Comté; Dijon France
| | - Thibaud Jouan
- GAD EA4271; Université de Bourgogne Franche-Comté; Dijon France
| | | | - Delphine Heron
- Département de Génétique et Centre de Référence « Déficiences intellectuelles de causes rares »; AP-HP; Groupe Hospitalier Pitié-Salpêtrière; Paris France
| | - Jean Donadieu
- Service d'Hémato-Oncologie Pédiatrique; Registre des neutropénies congénitales; AP-HP Hôpital Trousseau; Paris France
| | | | | | - Frédéric Huet
- Service de Pédiatrie 1; Hôpital d'Enfants; CHU Dijon France
| | - Paul Kuentz
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
| | - Daphné Lehalle
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
| | - Laurence Duplomb-Jego
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
| | - Elodie Gautier
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
| | - Isabelle Maystadt
- Centre de Génétique Humaine; Institut de Pathologie et Génétique (I.P.G); Gosselies (Charleroi) Belgium
| | - Lucile Pinson
- Département de Génétique Médicale; CHRU Montpellier; Faculté de Médecine de Montpellier-Nimes; Université Montpellier 1; Inserm; Montpellier France
| | - Daniel Amram
- Unité de Génétique Clinique; CH Intercommunal de Créteil; Créteil France
| | - Salima El Chehadeh
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
| | - Judith Melki
- Unité Mixte de Recherche-1169; INSERM; France; University Paris-Sud, le Kremlin-Bicêtre; France
| | - Sophia Julia
- Service de Génétique Médicale; CHU Toulouse; Toulouse France
| | - Laurence Faivre
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD); Centre Hospitalier Universitaire Dijon; Dijon France
| | - Julien Thevenon
- Centre de Génétique et Centre de Référence Maladies Rares « Anomalies du Développement et Syndromes Malformatifs de l'Interrégion Est »; Hôpital d'Enfants; CHU Dijon France
- Fédération Hospitalo-Universitaire Médecine Translationnelle et Anomalies du Développement (TRANSLAD); Centre Hospitalier Universitaire Dijon; Dijon France
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Cheng YF, Tong M, Edge ASB. Destabilization of Atoh1 by E3 Ubiquitin Ligase Huwe1 and Casein Kinase 1 Is Essential for Normal Sensory Hair Cell Development. J Biol Chem 2016; 291:21096-21109. [PMID: 27542412 DOI: 10.1074/jbc.m116.722124] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 12/22/2022] Open
Abstract
Proneural basic helix-loop-helix transcription factor, Atoh1, plays a key role in the development of sensory hair cells. We show here that the level of Atoh1 must be accurately controlled by degradation of the protein in addition to the regulation of Atoh1 gene expression to achieve normal cellular patterning during development of the cochlear sensory epithelium. The stability of Atoh1 was regulated by the ubiquitin proteasome system through the action of Huwe1, a HECT-domain, E3 ubiquitin ligase. An interaction between Huwe1 and Atoh1 could be visualized by a proximity ligation assay and was confirmed by co-immunoprecipitation and mass spectrometry. Transfer of a lysine 48-linked polyubiquitin chain to Atoh1 by Huwe1 could be demonstrated both in intact cells and in a cell-free system, and proteasome inhibition or Huwe1 silencing increased Atoh1 levels. The interaction with Huwe1 and polyubiquitylation were blocked by disruption of casein kinase 1 (CK1) activity, and mass spectrometry and mutational analysis identified serine 334 as an important phosphorylation site for Atoh1 ubiquitylation and subsequent degradation. Phosphorylation by CK1 thus targeted the protein for degradation. Development of an extra row of inner hair cells in the cochlea and an approximate doubling in the number of afferent synapses was observed after embryonic or early postnatal deletion of Huwe1 in cochlear-supporting cells, and hair cells died in the early postnatal period when Huwe1 was knocked out in the developing cochlea. These data indicate that the regulation of Atoh1 by the ubiquitin proteasome pathway is necessary for hair cell fate determination and survival.
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Affiliation(s)
- Yen-Fu Cheng
- From the Program in Speech and Hearing Bioscience and Technology, Harvard University/Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, the Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, and the Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02115
| | - Mingjie Tong
- the Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, and the Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02115
| | - Albert S B Edge
- From the Program in Speech and Hearing Bioscience and Technology, Harvard University/Massachusetts Institute of Technology, Cambridge, Massachusetts 02138, the Eaton-Peabody Laboratory, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts 02114, and the Department of Otology and Laryngology, Harvard Medical School, Boston, Massachusetts 02115
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Louros SR, Osterweil EK. Perturbed proteostasis in autism spectrum disorders. J Neurochem 2016; 139:1081-1092. [PMID: 27365114 PMCID: PMC5215415 DOI: 10.1111/jnc.13723] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 06/10/2016] [Accepted: 06/24/2016] [Indexed: 12/30/2022]
Abstract
Dynamic changes in synaptic strength rely on de novo protein synthesis and protein degradation by the ubiquitin proteasome system (UPS). Disruption of either of these cellular processes will result in significant impairments in synaptic plasticity and memory formation. Mutations in several genes encoding regulators of mRNA translation and members of the UPS have been associated with an increased risk for the development of autism spectrum disorders. It is possible that these mutations result in a similar imbalance in protein homeostasis (proteostasis) at the synapse. This review will summarize recent work investigating the role of the UPS in synaptic plasticity at glutamatergic synapses, and propose that dysfunctional proteostasis is a common consequence of several genetic mutations linked to autism spectrum disorders.
Dynamic changes in synaptic strength rely on de novo protein synthesis and protein degradation by the ubiquitin proteasome system (UPS). Disruption of either of these cellular processes will result in significant impairments in synaptic plasticity and memory formation. Mutations in several genes encoding regulators of mRNA translation (i.e. FMR1) and protein degradation (i.e. UBE3A) have been associated with an increased risk for autism spectrum disorders and intellectual disability (ASD/ID). These mutations similarly disrupt protein homeostasis (proteostasis). Compensatory changes that reset the rate of proteostasis may contribute to the neurological symptoms of ASD/ID. This review summarizes recent work investigating the role of the UPS in synaptic plasticity at glutamatergic synapses, and proposes that dysfunctional proteostasis is a common consequence of several genetic mutations linked to ASD.
This article is part of a mini review series: “Synaptic Function and Dysfunction in Brain Diseases”.
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Affiliation(s)
- Susana R Louros
- Centre for Integrative Physiology/Patrick Wild Centre, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
| | - Emily K Osterweil
- Centre for Integrative Physiology/Patrick Wild Centre, University of Edinburgh, Hugh Robson Building, George Square, Edinburgh, EH8 9XD, UK
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Fieremans N, Van Esch H, Holvoet M, Van Goethem G, Devriendt K, Rosello M, Mayo S, Martinez F, Jhangiani S, Muzny DM, Gibbs RA, Lupski JR, Vermeesch JR, Marynen P, Froyen G. Identification of Intellectual Disability Genes in Female Patients with a Skewed X-Inactivation Pattern. Hum Mutat 2016; 37:804-11. [PMID: 27159028 DOI: 10.1002/humu.23012] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Revised: 04/22/2016] [Accepted: 04/26/2016] [Indexed: 12/30/2022]
Abstract
Intellectual disability (ID) is a heterogeneous disorder with an unknown molecular etiology in many cases. Previously, X-linked ID (XLID) studies focused on males because of the hemizygous state of their X chromosome. Carrier females are generally unaffected because of the presence of a second normal allele, or inactivation of the mutant X chromosome in most of their cells (skewing). However, in female ID patients, we hypothesized that the presence of skewing of X-inactivation would be an indicator for an X chromosomal ID cause. We analyzed the X-inactivation patterns of 288 females with ID, and found that 22 (7.6%) had extreme skewing (>90%), which is significantly higher than observed in the general population (3.6%; P = 0.029). Whole-exome sequencing of 19 females with extreme skewing revealed causal variants in six females in the XLID genes DDX3X, NHS, WDR45, MECP2, and SMC1A. Interestingly, variants in genes escaping X-inactivation presumably cause both XLID and skewing of X-inactivation in three of these patients. Moreover, variants likely accounting for skewing only were detected in MED12, HDAC8, and TAF9B. All tested candidate causative variants were de novo events. Hence, extreme skewing is a good indicator for the presence of X-linked variants in female patients.
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Affiliation(s)
- Nathalie Fieremans
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium.,Human Genome Laboratory, VIB Center for the Biology of Disease, Leuven, Belgium
| | - Hilde Van Esch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Maureen Holvoet
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Gert Van Goethem
- Het GielsBos, Gierle, Belgium and Department of Neurology, University Hospital of Antwerp (UZA), Antwerp, Belgium
| | - Koenraad Devriendt
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Monica Rosello
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Sonia Mayo
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Francisco Martinez
- Genetics Unit, Hospital Universitario y Politecnico La Fe, Valencia, Spain
| | - Shalini Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - James R Lupski
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Department of Pediatrics, Baylor College of Medicine, Houston, Texas.,Texas Children's Hospital, Houston, Texas
| | - Joris R Vermeesch
- Center for Human Genetics, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Peter Marynen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
| | - Guy Froyen
- Human Genome Laboratory, Department of Human Genetics, KU Leuven, Belgium
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Moey C, Hinze SJ, Brueton L, Morton J, McMullan DJ, Kamien B, Barnett CP, Brunetti-Pierri N, Nicholl J, Gecz J, Shoubridge C. Xp11.2 microduplications including IQSEC2, TSPYL2 and KDM5C genes in patients with neurodevelopmental disorders. Eur J Hum Genet 2016; 24:373-80. [PMID: 26059843 PMCID: PMC4757771 DOI: 10.1038/ejhg.2015.123] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 03/26/2015] [Accepted: 05/06/2015] [Indexed: 01/06/2023] Open
Abstract
Copy number variations are a common cause of intellectual disability (ID). Determining the contribution of copy number variants (CNVs), particularly gains, to disease remains challenging. Here, we report four males with ID with sub-microscopic duplications at Xp11.2 and review the few cases with overlapping duplications reported to date. We established the extent of the duplicated regions in each case encompassing a minimum of three known disease genes TSPYL2, KDM5C and IQSEC2 with one case also duplicating the known disease gene HUWE1. Patients with a duplication encompassing TSPYL2, KDM5C and IQSEC2 without gains of nearby SMC1A and HUWE1 genes have not been reported thus far. All cases presented with ID and significant deficits of speech development. Some patients also manifested behavioral disturbances such as hyperactivity and attention-deficit/hyperactivity disorder. Lymphoblastic cell lines from patients show markedly elevated levels of TSPYL2, KDM5C and SMC1A, transcripts consistent with the extent of their CNVs. The duplicated region in our patients contains several genes known to escape X-inactivation, including KDM5C, IQSEC2 and SMC1A. In silico analysis of expression data in selected gene expression omnibus series indicates that dosage of these genes, especially IQSEC2, is similar in males and females despite the fact they escape from X-inactivation in females. Taken together, the data suggest that gains in Xp11.22 including IQSEC2 cause ID and are associated with hyperactivity and attention-deficit/hyperactivity disorder, and are likely to be dosage-sensitive in males.
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Affiliation(s)
- Ching Moey
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Susan J Hinze
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Louise Brueton
- Clinical Genetics unit, Birmingham Women's Hospital, Birmingham, UK
| | - Jenny Morton
- Clinical Genetics unit, Birmingham Women's Hospital, Birmingham, UK
| | | | | | | | - Nicola Brunetti-Pierri
- Department of Translational Medicine, Federico II University, Napoli, Italy
- Telethon Institute of Genetics and Medicine, Napoli, Italy
| | | | - Jozef Gecz
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Cheryl Shoubridge
- Department of Paediatrics, School of Paediatrics and Reproductive Health, University of Adelaide, Adelaide, South Australia, Australia
- Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
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A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability. Eur J Hum Genet 2016; 24:1117-23. [PMID: 26733290 DOI: 10.1038/ejhg.2015.267] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Revised: 11/03/2015] [Accepted: 11/26/2015] [Indexed: 12/15/2022] Open
Abstract
The IQSEC2 gene is located on chromosome Xp11.22 and encodes a guanine nucleotide exchange factor for the ADP-ribosylation factor family of small GTPases. This gene is known to have a significant role in cytoskeletal organization, dendritic spine morphology and synaptic organization. Variants in IQSEC2 cause moderate to severe intellectual disability in males and a variable phenotype in females because this gene escapes from X-chromosome inactivation. Here we report on the first splicing variant in IQSEC2 (g.88032_88033del; NG_021296.1) that co-segregates in a family diagnosed with an X-linked form of ID. In a percentage of the cells, the variant activates an intraexonic splice acceptor site that abolishes 26 amino acids from the highly conserved PH domain of IQSEC2 and creates a premature stop codon 36 amino acids later in exon 13. Interestingly, the percentage of aberrant splicing seems to correlate with the severity of the disease in each patient. The impact of this variant in the target tissue is unknown, but we can hypothesize that these differences may be related to the amount of abnormal IQSEC2 transcript. To our knowledge, we are reporting a novel mechanism of IQSEC2 involvement in ID. Variants that affect splicing are related to many genetic diseases and the understanding of their role in disease expands potential opportunities for gene therapy. Modulation of aberrant splicing transcripts can become a potent therapeutic approach for many of these diseases.
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Grams SE, Argiropoulos B, Lines M, Chakraborty P, Mcgowan-Jordan J, Geraghty MT, Tsang M, Eswara M, Tezcan K, Adams KL, Linck L, Himes P, Kostiner D, Zand DJ, Stalker H, Driscoll DJ, Huang T, Rosenfeld JA, Li X, Chen E. Genotype-phenotype characterization in 13 individuals with chromosome Xp11.22 duplications. Am J Med Genet A 2015; 170A:967-77. [PMID: 26692240 DOI: 10.1002/ajmg.a.37519] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/25/2015] [Indexed: 11/10/2022]
Abstract
We report 13 new individuals with duplications in Xp11.22-p11.23. The index family has one male and two female members in three generations with mild-severe intellectual disability (ID), speech delay, dysmorphic features, early puberty, constipation, and/or hand and foot abnormalities. Affected individuals were found to have two small duplications in Xp11.22 at nucleotide position (hg19) 50,112,063-50,456,458 bp (distal) and 53,160,114-53,713,154 bp (proximal). Collectively, these two regions include 14 RefSeq genes, prompting collection of a larger cohort of patients, in an attempt to delineate critical genes associated with the observed phenotype. In total, we have collected data on nine individuals with duplications overlapping the distal duplication region containing SHROOM4 and DGKK and eight individuals overlapping the proximal region including HUWE1. Duplications of HUWE1 have been previously associated with non-syndromic ID. Our data, with previously published reports, suggest that duplications involving SHROOM4 and DGKK may represent a new syndromic X-linked ID critical region associated with mild to severe ID, speech delay +/- dysarthria, attention deficit disorder, precocious puberty, constipation, and motor delay. We frequently observed foot abnormalities, 5th finger clinodactyly, tapering fingers, constipation, and exercise intolerance in patients with duplications of these two genes. Regarding duplications including the proximal region, our observations agree with previous studies, which have found associations with intellectual disability. In addition, expressive language delay, failure to thrive, motor delay, and 5th finger clinodactyly were also frequently observed in patients with the proximal duplication.
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Affiliation(s)
- Sarah E Grams
- Department of Medical Genetics, Kaiser Permanente, San Francisco, California
| | - Bob Argiropoulos
- Alberta Children's Hospital Research Institute for Child and Maternal Health, Alberta, Canada
| | - Matthew Lines
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Pranesh Chakraborty
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Jean Mcgowan-Jordan
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Michael T Geraghty
- Department of Genetics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada.,Department of Pediatrics, University of Ottawa, Ottawa, Ontario, Canada
| | - Marilyn Tsang
- Department of Genetics, Sutter Memorial Hospital, Sacramento, California
| | - Marthand Eswara
- Department of Genetics, Sutter Memorial Hospital, Sacramento, California
| | - Kamer Tezcan
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Kelly L Adams
- Department of Genetics, Kaiser Permanente, Sacramento, California
| | - Leesa Linck
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Patricia Himes
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Dana Kostiner
- Department of Medical Genetics, Kaiser Permanente, Portland, Oregon
| | - Dina J Zand
- Department of Medical Genetics, Children's National Medical Center, Washington DC
| | - Heather Stalker
- Department of Genetics, University of Florida, Gainesville, Florida
| | | | - Taosheng Huang
- Department of Human Genetics, Children's Hospital of Orange County, Orange, California
| | - Jill A Rosenfeld
- Signature Genomic Laboratories, Perkin Elmer, Inc., Spokane, Washington
| | - Xu Li
- Department of Genetics, Kaiser Permanente, San Jose, California
| | - Emily Chen
- Department of Medical Genetics, Kaiser Permanente, San Francisco, California.,Department of Genetics, Kaiser Permanente, San Jose, California
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Federici F, Mulugeta E, Schoenmakers S, Wassenaar E, Hoogerbrugge JW, van der Heijden GW, van Cappellen WA, Slotman JA, van IJcken WFJ, Laven JSE, Grootegoed JA, Baarends WM. Incomplete meiotic sex chromosome inactivation in the domestic dog. BMC Genomics 2015; 16:291. [PMID: 25884295 PMCID: PMC4399420 DOI: 10.1186/s12864-015-1501-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 03/30/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In mammalian meiotic prophase, homologous chromosome recognition is aided by formation and repair of programmed DNA double-strand breaks (DSBs). Subsequently, stable associations form through homologous chromosome synapsis. In male mouse meiosis, the largely heterologous X and Y chromosomes synapse only in their short pseudoautosomal regions (PARs), and DSBs persist along the unsynapsed non-homologous arms of these sex chromosomes. Asynapsis of these arms and the persistent DSBs then trigger transcriptional silencing through meiotic sex chromosome inactivation (MSCI), resulting in formation of the XY body. This inactive state is partially maintained in post-meiotic haploid spermatids (postmeiotic sex chromatin repression, PSCR). For the human, establishment of MSCI and PSCR have also been reported, but X-linked gene silencing appears to be more variable compared to mouse. To gain more insight into the regulation and significance of MSCI and PSCR among different eutherian species, we have performed a global analysis of XY pairing dynamics, DSB repair, MSCI and PSCR in the domestic dog (Canis lupus familiaris), for which the complete genome sequence has recently become available, allowing a thorough comparative analyses. RESULTS In addition to PAR synapsis between X and Y, we observed extensive self-synapsis of part of the dog X chromosome, and rapid loss of known markers of DSB repair from that part of the X. Sequencing of RNA from purified spermatocytes and spermatids revealed establishment of MSCI. However, the self-synapsing region of the X displayed higher X-linked gene expression compared to the unsynapsed area in spermatocytes, and was post-meiotically reactivated in spermatids. In contrast, genes in the PAR, which are expected to escape MSCI, were expressed at very low levels in both spermatocytes and spermatids. Our comparative analysis was then used to identify two X-linked genes that may escape MSCI in spermatocytes, and 21 that are specifically re-activated in spermatids of human, mouse and dog. CONCLUSIONS Our data indicate that MSCI is incomplete in the dog. This may be partially explained by extensive, but transient, self-synapsis of the X chromosome, in association with rapid completion of meiotic DSB repair. In addition, our comparative analysis identifies novel candidate male fertility genes.
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Affiliation(s)
- Federica Federici
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Eskeatnaf Mulugeta
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Present address: Institut Curie, Genetics and Developmental Biology, Unit 11 et 13 rue Pierre et Marie Curie, 75248, Paris, Cedex 05, France.
| | - Sam Schoenmakers
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Evelyne Wassenaar
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Jos W Hoogerbrugge
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Godfried W van der Heijden
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands. .,Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wiggert A van Cappellen
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Johan A Slotman
- Department of Pathology, Erasmus Optical Imaging Centre, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Wilfred F J van IJcken
- Erasmus Center for Biomics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands.
| | - Joop S E Laven
- Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - J Anton Grootegoed
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
| | - Willy M Baarends
- Department of Developmental Biology, Erasmus MC, University Medical Center, PO BOX 2040, 3000 CA, Rotterdam, The Netherlands.
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46
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Papuc SM, Hackmann K, Andrieux J, Vincent-Delorme C, Budişteanu M, Arghir A, Schrock E, Ţuţulan-Cuniţă AC, Di Donato N. Microduplications of 3p26.3p26.2 containing CRBN gene in patients with intellectual disability and behavior abnormalities. Eur J Med Genet 2015; 58:319-23. [PMID: 25858704 DOI: 10.1016/j.ejmg.2015.03.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Accepted: 03/24/2015] [Indexed: 10/23/2022]
Abstract
We report on the clinical data and molecular cytogenetic findings in three unrelated patients presenting with intellectual disability and behavior abnormalities. An overlapping microduplication involving 3p26.2-26.3 was identified in these patients. All three aberrations were confirmed and proven to be parentally inherited. The sizes of the duplications were different, with a common minimal region of 423,754 bp containing two genes - TRNT1 and CRBN. Here, we hypothesize that the copy number gain of CRBN gene might be responsible for developmental delay/intellectual disability.
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Affiliation(s)
- Sorina M Papuc
- Victor Babeş National Institute of Pathology, Medical Genetics Laboratory, Bucharest, Romania
| | - Karl Hackmann
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, TU Dresden, Dresden, Germany
| | - Joris Andrieux
- Laboratoire de Génétique Médicale, Hôpital Jeanne de Flandre, CHRU de Lille, France
| | | | - Magdalena Budişteanu
- Victor Babeş National Institute of Pathology, Medical Genetics Laboratory, Bucharest, Romania; Prof. Dr. Alex. Obregia Clinical Hospital of Psychiatry, Bucharest, Romania
| | - Aurora Arghir
- Victor Babeş National Institute of Pathology, Medical Genetics Laboratory, Bucharest, Romania
| | - Evelin Schrock
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, TU Dresden, Dresden, Germany
| | | | - Nataliya Di Donato
- Institut fuer Klinische Genetik, Medizinische Fakultaet Carl Gustav Carus, TU Dresden, Dresden, Germany
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47
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Katsumi M, Ishikawa H, Tanaka Y, Saito K, Kobori Y, Okada H, Saito H, Nakabayashi K, Matsubara Y, Ogata T, Fukami M, Miyado M. Microhomology-mediated microduplication in the y chromosomal azoospermia factor a region in a male with mild asthenozoospermia. Cytogenet Genome Res 2015; 144:285-9. [PMID: 25765000 DOI: 10.1159/000377649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/26/2015] [Indexed: 11/19/2022] Open
Abstract
Y chromosomal azoospermia factor (AZF) regions AZFa, AZFb and AZFc represent hotspots for copy number variations (CNVs) in the human genome; yet the number of reports of AZFa-linked duplications remains limited. Nonallelic homologous recombination has been proposed as the underlying mechanism of CNVs in AZF regions. In this study, we identified a hitherto unreported microduplication in the AZFa region in a Japanese male individual. The 629,812-bp duplication contained 22 of 46 exons of USP9Y, encoding the putative fine tuner of spermatogenesis, together with all exons of 3 other genes/pseudogenes. The breakpoints of the duplication resided in the DNA/TcMar-Tigger repeat and nonrepeat sequences, respectively, and were associated with a 2-bp microhomology, but not with short nucleotide stretches. The breakpoint-flanking regions were not enriched with GC content, palindromes, or noncanonical DNA structures. Semen analysis of the individual revealed a normal sperm concentration and mildly reduced sperm motility. The paternal DNA sample of the individual was not available for genetic analysis. The results indicate that CNVs in AZF regions can be generated by microhomology-mediated break-induced replication in the absence of known rearrangement-inducing DNA features. AZFa-linked microduplications likely permit production of a normal amount of sperm, although the precise clinical consequences of these CNVs await further investigation.
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Affiliation(s)
- Momori Katsumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
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48
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Leroy C, Jacquemont ML, Doray B, Lamblin D, Cormier-Daire V, Philippe A, Nusbaum S, Patrat C, Steffann J, Colleaux L, Vekemans M, Romana S, Turleau C, Malan V. Xq25 duplication: the crucial role of the STAG2
gene in this novel human cohesinopathy. Clin Genet 2015; 89:68-73. [DOI: 10.1111/cge.12567] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/02/2015] [Accepted: 02/05/2015] [Indexed: 01/24/2023]
Affiliation(s)
- C. Leroy
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
| | - M.-L. Jacquemont
- Service de Néonatologie; Centre Hospitalier Universitaire de la Réunion; Saint-Pierre France
| | - B. Doray
- Service de Génétique; Centre Hospitalier Universitaire de La Réunion, Hôpital Félix Guyon; Saint-Denis France
| | - D. Lamblin
- Fondation Père Favron; CAMSP; Saint-Louis France
| | - V. Cormier-Daire
- Service de Génétique; Hôpital Necker-Enfants Malades; Paris France
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
| | - A. Philippe
- Service de Génétique; Hôpital Necker-Enfants Malades; Paris France
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
- Institut IMAGINE; INSERM UMR_S1163, Hôpital Necker-Enfants Malades; Paris France
| | - S. Nusbaum
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
| | - C. Patrat
- Laboratoire de Biologie De la Reproduction; Groupe Hospitalier Bichat-Claude Bernard; Paris France
| | - J. Steffann
- Service de Génétique; Hôpital Necker-Enfants Malades; Paris France
| | - L. Colleaux
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
- Institut IMAGINE; INSERM UMR_S1163, Hôpital Necker-Enfants Malades; Paris France
| | - M. Vekemans
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
| | - S. Romana
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
| | - C. Turleau
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
| | - V. Malan
- Service de Cytogénétique; Hôpital Necker-Enfants Malades; Paris France
- Sorbonne Paris Cité; Université Paris Descartes; Paris France
- Institut IMAGINE; INSERM UMR_S1163, Hôpital Necker-Enfants Malades; Paris France
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49
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Brečević L, Rinčić M, Krsnik Ž, Sedmak G, Hamid AB, Kosyakova N, Galić I, Liehr T, Borovečki F. Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci 2015; 6:59-86. [PMID: 28123791 PMCID: PMC4936614 DOI: 10.1515/tnsci-2015-0007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/29/2014] [Indexed: 12/14/2022] Open
Abstract
We describe an as yet unreported neocentric small supernumerary marker chromosome (sSMC) derived from chromosome 1p21.3p21.2. It was present in 80% of the lymphocytes in a male patient with intellectual disability, severe speech deficit, mild dysmorphic features, and hyperactivity with elements of autism spectrum disorder (ASD). Several important neurodevelopmental genes are affected by the 3.56 Mb copy number gain of 1p21.3p21.2, which may be considered reciprocal in gene content to the recently recognized 1p21.3 microdeletion syndrome. Both 1p21.3 deletions and the presented duplication display overlapping symptoms, fitting the same disorder category. Contribution of coding and non-coding genes to the phenotype is discussed in the light of cellular and intercellular homeostasis disequilibrium. In line with this the presented 1p21.3p21.2 copy number gain correlated to 1p21.3 microdeletion syndrome verifies the hypothesis of a cumulative effect of the number of deregulated genes - homeostasis disequilibrium leading to overlapping phenotypes between microdeletion and microduplication syndromes. Although miR-137 appears to be the major player in the 1p21.3p21.2 region, deregulation of the DPYD (dihydropyrimidine dehydrogenase) gene may potentially affect neighboring genes underlying the overlapping symptoms present in both the copy number loss and copy number gain of 1p21. Namely, the all-in approach revealed that DPYD is a complex gene whose expression is epigenetically regulated by long non-coding RNAs (lncRNAs) within the locus. Furthermore, the long interspersed nuclear element-1 (LINE-1) L1MC1 transposon inserted in DPYD intronic transcript 1 (DPYD-IT1) lncRNA with its parasites, TcMAR-Tigger5b and pair of Alu repeats appears to be the “weakest link” within the DPYD gene liable to break. Identification of the precise mechanism through which DPYD is epigenetically regulated, and underlying reasons why exactly the break (FRA1E) happens, will consequently pave the way toward preventing severe toxicity to the antineoplastic drug 5-fluorouracil (5-FU) and development of the causative therapy for the dihydropyrimidine dehydrogenase deficiency.
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Affiliation(s)
- Lukrecija Brečević
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- E-mail: ;
| | - Martina Rinčić
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Goran Sedmak
- Croatian Institute for Brain Research, University of Zagreb Medical School, Šalata 12, 10000 Zagreb, Croatia
| | - Ahmed B. Hamid
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Nadezda Kosyakova
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Ivan Galić
- Center for Rehabilitation Stančić, Stančić bb, 10370 Stančić, Croatia
| | - Thomas Liehr
- Jena University Hospital, Friedrich Schiller University, Institute of Human Genetics, Kollegiengasse 10, 07743 Jena, Germany
| | - Fran Borovečki
- Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb Medical School, University Hospital Center Zagreb, Šalata 2, 10000 Zagreb, Croatia
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50
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Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints. Am J Hum Genet 2015; 96:208-20. [PMID: 25640679 DOI: 10.1016/j.ajhg.2014.12.017] [Citation(s) in RCA: 112] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 12/15/2014] [Indexed: 11/23/2022] Open
Abstract
Interpreting the genomic and phenotypic consequences of copy-number variation (CNV) is essential to understanding the etiology of genetic disorders. Whereas deletion CNVs lead obviously to haploinsufficiency, duplications might cause disease through triplosensitivity, gene disruption, or gene fusion at breakpoints. The mutational spectrum of duplications has been studied at certain loci, and in some cases these copy-number gains are complex chromosome rearrangements involving triplications and/or inversions. However, the organization of clinically relevant duplications throughout the genome has yet to be investigated on a large scale. Here we fine-mapped 184 germline duplications (14.7 kb-25.3 Mb; median 532 kb) ascertained from individuals referred for diagnostic cytogenetics testing. We performed next-generation sequencing (NGS) and whole-genome sequencing (WGS) to sequence 130 breakpoints from 112 subjects with 119 CNVs and found that most (83%) were tandem duplications in direct orientation. The remainder were triplications embedded within duplications (8.4%), adjacent duplications (4.2%), insertional translocations (2.5%), or other complex rearrangements (1.7%). Moreover, we predicted six in-frame fusion genes at sequenced duplication breakpoints; four gene fusions were formed by tandem duplications, one by two interconnected duplications, and one by duplication inserted at another locus. These unique fusion genes could be related to clinical phenotypes and warrant further study. Although most duplications are positioned head-to-tail adjacent to the original locus, those that are inverted, triplicated, or inserted can disrupt or fuse genes in a manner that might not be predicted by conventional copy-number assays. Therefore, interpreting the genetic consequences of duplication CNVs requires breakpoint-level analysis.
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