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Aoki S, Higashimoto K, Hidaka H, Ohtsuka Y, Aoki S, Mishima H, Yoshiura KI, Nakabayashi K, Hata K, Yatsuki H, Hara S, Ohba T, Katabuchi H, Soejima H. Aberrant hypomethylation at imprinted differentially methylated regions is involved in biparental placental mesenchymal dysplasia. Clin Epigenetics 2022; 14:64. [PMID: 35581658 PMCID: PMC9115938 DOI: 10.1186/s13148-022-01280-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/18/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Placental mesenchymal dysplasia (PMD) is a morphological abnormality resembling partial hydatidiform moles. It is often associated with androgenetic/biparental mosaicism (ABM) and complicated by Beckwith-Wiedemann syndrome (BWS), an imprinting disorder. These phenomena suggest an association between PMD and aberrant genomic imprinting, particularly of CDKN1C and IGF2. The existence of another type of PMD containing the biparental genome has been reported. However, the frequency and etiology of biparental PMD are not yet fully understood. RESULTS We examined 44 placental specimens from 26 patients with PMD: 19 of these were macroscopically normal and 25 exhibited macroscopic PMD. Genotyping by DNA microarray or short tandem repeat analysis revealed that approximately 35% of the macroscopic PMD specimens could be classified as biparental, while the remainder were ABM. We performed a DNA methylation analysis using bisulfite pyrosequencing of 15 placenta-specific imprinted differentially methylated regions (DMRs) and 36 ubiquitous imprinted DMRs. As expected, most DMRs in the macroscopic PMD specimens with ABM exhibited the paternal epigenotype. Importantly, the biparental macroscopic PMD specimens exhibited frequent aberrant hypomethylation at seven of the placenta-specific DMRs. Allelic expression analysis using single-nucleotide polymorphisms revealed that five imprinted genes associated with these aberrantly hypomethylated DMRs were biallelically expressed. Frequent aberrant hypomethylation was observed at five ubiquitous DMRs, including GRB10 but not ICR2 or ICR1, which regulate the expression of CDKN1C and IGF2, respectively. Whole-exome sequencing performed on four biparental macroscopic PMD specimens did not reveal any pathological genetic abnormalities. Clinical and molecular analyses of babies born from pregnancies with PMD revealed four cases with BWS, each exhibiting different molecular characteristics, and those between BWS and PMD specimens were not always the same. CONCLUSION These data clarify the prevalence of biparental PMD and ABM-PMD and strongly implicate hypomethylation of DMRs in the pathogenesis of biparental PMD, particularly placenta-specific DMRs and the ubiquitous GRB10, but not ICR2 or ICR1. Aberrant hypomethylation of DMRs was partial, indicating that it occurs after fertilization. PMD is an imprinting disorder, and it may be a missing link between imprinting disorders and placental disorders incompatible with life, such as complete hydatidiform moles and partial hydatidiform moles.
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Affiliation(s)
- Saori Aoki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
| | - Hidenori Hidaka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Yasufumi Ohtsuka
- Department of Pediatrics, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Shigehisa Aoki
- Department of Pathology and Microbiology, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8523, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Hitomi Yatsuki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Satoshi Hara
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan
| | - Takashi Ohba
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Hidetaka Katabuchi
- Department of Obstetrics and Gynecology, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-8556, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, Saga, 849-8501, Japan.
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Heterozygous missense variant of the proteasome subunit β-type 9 causes neonatal-onset autoinflammation and immunodeficiency. Nat Commun 2021; 12:6819. [PMID: 34819510 PMCID: PMC8613290 DOI: 10.1038/s41467-021-27085-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 11/01/2021] [Indexed: 12/30/2022] Open
Abstract
Impaired proteasome activity due to genetic variants of certain subunits might lead to proteasome-associated autoinflammatory syndromes (PRAAS). Here we report a de novo heterozygous missense variant of the PSMB9 proteasome subunit gene in two unrelated Japanese infants resulting in amino acid substitution of the glycine (G) by aspartic acid (D) at position 156 of the encoded protein β1i. In addition to PRAAS-like manifestations, these individuals suffer from pulmonary hypertension and immunodeficiency, which are distinct from typical PRAAS symptoms. The missense variant results in impaired immunoproteasome maturation and activity, yet ubiquitin accumulation is hardly detectable in the patients. A mouse model of the heterozygous human genetic variant (Psmb9G156D/+) recapitulates the proteasome defects and the immunodeficiency phenotype of patients. Structurally, PSMB9 G156D interferes with the β-ring-βring interaction of the wild type protein that is necessary for 20S proteasome formation. We propose the term, proteasome-associated autoinflammatory syndrome with immunodeficiency (PRAAS-ID), to indicate a separate category of autoinflammatory diseases, similar to, but distinct from PRAAS, that describes the patients in this study. Genetic variants of proteasome subunit genes have been shown to associate with perturbed immune function. Here authors show that a heterozygous missense variant of the immunoproteasome subunit β-type 9 causes an autoinflammatory/immune deficiency syndrome in humans and in a mouse model.
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Nakano Y, Komiya C, Shimizu H, Mishima H, Shiba K, Tsujimoto K, Ikeda K, Kashimada K, Dateki S, Yoshiura KI, Ogawa Y, Yamada T. A case of ezetimibe-effective hypercholesterolemia with a novel heterozygous variant in ABCG5. Endocr J 2020; 67:1099-1105. [PMID: 32641618 DOI: 10.1507/endocrj.ej20-0044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Sitosterolemia is caused by homozygous or compound heterozygous gene mutations in either ATP-binding cassette subfamily G member 5 (ABCG5) or 8 (ABCG8). Since ABCG5 and ABCG8 play pivotal roles in the excretion of neutral sterols into feces and bile, patients with sitosterolemia present elevated levels of serum plant sterols and in some cases also hypercholesterolemia. A 48-year-old woman was referred to our hospital for hypercholesterolemia. She had been misdiagnosed with familial hypercholesterolemia at the age of 20 and her serum low-density lipoprotein cholesterol (LDL-C) levels had remained about 200-300 mg/dL at the former clinic. Although the treatment of hydroxymethylglutaryl-CoA (HMG-CoA) reductase inhibitors was ineffective, her serum LDL-C levels were normalized by ezetimibe, a cholesterol transporter inhibitor. We noticed that her serum sitosterol and campesterol levels were relatively high. Targeted analysis sequencing identified a novel heterozygous ABCG5 variant (c.203A>T; p.Ile68Asn) in the patient, whereas no mutations were found in low-density lipoprotein receptor (LDLR), proprotein convertase subtilisin/kexin type 9 (PCSK9), or Niemann-Pick C1-like intracellular cholesterol transporter 1 (NPC1L1). While sitosterolemia is a rare disease, a recent study has reported that the incidence of loss-of-function mutation in the ABCG5 or ABCG8 gene is higher than we thought at 1 in 220 individuals. The present case suggests that serum plant sterol levels should be examined and ezetimibe treatment should be considered in patients with hypercholesterolemia who are resistant to HMG-CoA reductase inhibitors.
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Affiliation(s)
- Yujiro Nakano
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Chikara Komiya
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Hitomi Shimizu
- Department of Pediatrics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaski 852-8501, Japan
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Kumiko Shiba
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Kazutaka Tsujimoto
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Kenji Ikeda
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Kenichi Kashimada
- Department of Pediatrics and Developmental Biology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
| | - Sumito Dateki
- Department of Pediatrics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaski 852-8501, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8501, Japan
| | - Yoshihiro Ogawa
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Tetsuya Yamada
- Department of Molecular Endocrinology and Metabolism, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo 113-8519, Japan
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Kim JD, Wang Y, Fujiwara T, Okuda S, Callahan TJ, Cohen KB. Open Agile text mining for bioinformatics: the PubAnnotation ecosystem. Bioinformatics 2020; 35:4372-4380. [PMID: 30937439 PMCID: PMC6821251 DOI: 10.1093/bioinformatics/btz227] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 03/16/2019] [Accepted: 03/29/2019] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Most currently available text mining tools share two characteristics that make them less than optimal for use by biomedical researchers: they require extensive specialist skills in natural language processing and they were built on the assumption that they should optimize global performance metrics on representative datasets. This is a problem because most end-users are not natural language processing specialists and because biomedical researchers often care less about global metrics like F-measure or representative datasets than they do about more granular metrics such as precision and recall on their own specialized datasets. Thus, there are fundamental mismatches between the assumptions of much text mining work and the preferences of potential end-users. RESULTS This article introduces the concept of Agile text mining, and presents the PubAnnotation ecosystem as an example implementation. The system approaches the problems from two perspectives: it allows the reformulation of text mining by biomedical researchers from the task of assembling a complete system to the task of retrieving warehoused annotations, and it makes it possible to do very targeted customization of the pre-existing system to address specific end-user requirements. Two use cases are presented: assisted curation of the GlycoEpitope database, and assessing coverage in the literature of pre-eclampsia-associated genes. AVAILABILITY AND IMPLEMENTATION The three tools that make up the ecosystem, PubAnnotation, PubDictionaries and TextAE are publicly available as web services, and also as open source projects. The dictionaries and the annotation datasets associated with the use cases are all publicly available through PubDictionaries and PubAnnotation, respectively.
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Affiliation(s)
- Jin-Dong Kim
- Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Chiba, Japan
| | - Yue Wang
- Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Chiba, Japan
| | - Toyofumi Fujiwara
- Database Center for Life Science, Research Organization of Information and Systems, Kashiwa, Chiba, Japan
| | - Shujiro Okuda
- Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tiffany J Callahan
- Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA
| | - K Bretonnel Cohen
- Computational Bioscience Program, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO, USA.,Université Paris-Saclay, LIMSI-ILES, France
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Morandi E, Cereda M, Incarnato D, Parlato C, Basile G, Anselmi F, Lauria A, Simon LM, Laurence Polignano I, Arruga F, Deaglio S, Tirtei E, Fagioli F, Oliviero S. HaTSPiL: A modular pipeline for high-throughput sequencing data analysis. PLoS One 2019; 14:e0222512. [PMID: 31613890 PMCID: PMC6793853 DOI: 10.1371/journal.pone.0222512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 08/30/2019] [Indexed: 11/25/2022] Open
Abstract
Background Next generation sequencing methods are widely adopted for a large amount of scientific purposes, from pure research to health-related studies. The decreasing costs per analysis led to big amounts of generated data and to the subsequent improvement of software for the respective analyses. As a consequence, many approaches have been developed to chain different software in order to obtain reliable and reproducible workflows. However, the large range of applications for NGS approaches entails the challenge to manage many different workflows without losing reliability. Methods We here present a high-throughput sequencing pipeline (HaTSPiL), a Python-powered CLI tool designed to handle different approaches for data analysis with a high level of reliability. The software relies on the barcoding of filenames using a human readable naming convention that contains any information regarding the sample needed by the software to automatically choose different workflows and parameters. HaTSPiL is highly modular and customisable, allowing the users to extend its features for any specific need. Conclusions HaTSPiL is licensed as Free Software under the MIT license and it is available at https://github.com/dodomorandi/hatspil.
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Affiliation(s)
- Edoardo Morandi
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Matteo Cereda
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Danny Incarnato
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | | | - Giulia Basile
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Francesca Anselmi
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Andrea Lauria
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | - Lisa Marie Simon
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
| | | | | | - Silvia Deaglio
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Elisa Tirtei
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children’s Hospital, Turin, Italy
| | - Franca Fagioli
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, City of Science and Health of Turin, Regina Margherita Children’s Hospital, Turin, Italy
| | - Salvatore Oliviero
- Department of Life Sciences and System Biology, University of Turin, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), Turin, Italy
- * E-mail: ,
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Morimoto Y, Yoshida S, Kinoshita A, Satoh C, Mishima H, Yamaguchi N, Matsuda K, Sakaguchi M, Tanaka T, Komohara Y, Imamura A, Ozawa H, Nakashima M, Kurotaki N, Kishino T, Yoshiura KI, Ono S. Nonsense mutation in CFAP43 causes normal-pressure hydrocephalus with ciliary abnormalities. Neurology 2019; 92:e2364-e2374. [PMID: 31004071 PMCID: PMC6598815 DOI: 10.1212/wnl.0000000000007505] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Objective To identify genes related to normal-pressure hydrocephalus (NPH) in one Japanese family with several members with NPH. Methods We performed whole-exome sequencing (WES) on a Japanese family with multiple individuals with NPH and identified a candidate gene. Then we generated knockout mouse using CRISPR/Cas9 to confirm the effect of the candidate gene on the pathogenesis of hydrocephalus. Results In WES, we identified a loss-of-function variant in CFAP43 that segregated with the disease. CFAP43 encoding cilia- and flagella-associated protein is preferentially expressed in the testis. Recent studies have revealed that mutations in this gene cause male infertility owing to morphologic abnormalities of sperm flagella. We knocked out mouse ortholog Cfap43 using CRISPR/Cas9 technology, resulting in Cfap43-deficient mice that exhibited a hydrocephalus phenotype with morphologic abnormality of motile cilia. Conclusion Our results strongly suggest that CFAP43 is responsible for morphologic or movement abnormalities of cilia in the brain that result in NPH.
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Affiliation(s)
- Yoshiro Morimoto
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Shintaro Yoshida
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Akira Kinoshita
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Chisei Satoh
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Hiroyuki Mishima
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Naohiro Yamaguchi
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Katsuya Matsuda
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Miako Sakaguchi
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Takeshi Tanaka
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Yoshihiro Komohara
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Akira Imamura
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Hiroki Ozawa
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Masahiro Nakashima
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Naohiro Kurotaki
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Tatsuya Kishino
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Koh-Ichiro Yoshiura
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan
| | - Shinji Ono
- From the Departments of Neuropsychiatry (Y.M., N.Y., H.O.) and Otolaryngology-Head and Neck Surgery (C.S.), Unit of Translation Medicine, and Department of Human Genetics (S.Y., A.K., H.M., K.-i.Y., S.O.), Nagasaki University Graduate School of Biomedical Sciences; Department of Tumor and Diagnostic Pathology, Atomic Bomb Disease Institute (K.M., M.N.), Central Laboratory, Institute of Tropical Medicine (NEKKEN) (M.S.), and Gene Research Center, Center for Frontier Life Sciences (T.K.), Nagasaki University; Department of Infectious Diseases (T.T.) and Child and Adolescent Psychiatry Community Partnership Unit (A.I.), Nagasaki University Hospital; Department of Cell Pathology (Y.K.), Graduate School of Medical Sciences, Kumamoto University; and Department of Clinical Psychology, Faculty of Medicine (N.K.), Kagawa University, Takamatsu, Japan.
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7
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Identification of a homozygous frameshift variant in RFLNA in a patient with a typical phenotype of spondylocarpotarsal synostosis syndrome. J Hum Genet 2019; 64:467-471. [PMID: 30796325 DOI: 10.1038/s10038-019-0581-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 01/24/2023]
Abstract
Spondylocarpotarsal synostosis syndrome, a rare syndromic skeletal disorder characterized by disrupted vertebral segmentation with vertebral fusion, scoliosis, short stature, and carpal/tarsal synostosis, has been associated with biallelic truncating mutations in the filamin B gene or monoallelic mutations in the myosin heavy chain 3 gene. We herein report the case of a patient with a typical phenotype of spondylocarpotarsal synostosis syndrome who had a homozygous frameshift mutation in the refilin A gene (RFLNA) [c.241delC, p.(Leu81Cysfs*111)], which encodes one of the filamin-binding proteins. Refilins, filamins, and myosins play critical roles in forming perinuclear actin caps, which change the nuclear morphology during cell migration and differentiation. The present study implies that RFLNA is an additional causative gene for spondylocarpotarsal synostosis syndrome in humans and a defect in forming actin bundles and perinuclear actin caps may be a critical mechanism for the development of spondylocarpotarsal synostosis syndrome.
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8
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Kikuiri T, Mishima H, Imura H, Suzuki S, Matsuzawa Y, Nakamura T, Fukumoto S, Yoshimura Y, Watanabe S, Kinoshita A, Yamada T, Shindoh M, Sugita Y, Maeda H, Yawaka Y, Mikoya T, Natsume N, Yoshiura KI. Patients with SATB2-associated syndrome exhibiting multiple odontomas. Am J Med Genet A 2018; 176:2614-2622. [PMID: 30575289 DOI: 10.1002/ajmg.a.40670] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 09/28/2018] [Accepted: 10/02/2018] [Indexed: 01/09/2023]
Abstract
Special AT-rich sequence-binding protein 2 (SATB2)-associated syndrome (SAS) is characterized by alterations of SATB2. Its clinical features include intellectual disability and craniofacial abnormalities, such as cleft palate, dysmorphic features, and dental abnormalities. Here, we describe three previously undiagnosed, unrelated patients with SAS who exhibited dental abnormalities, including multiple odontomas. Although isolated odontomas are common, multiple odontomas are rare. Individuals in families 1 and 3 underwent whole-exome sequencing. Patient 2 and parents underwent targeted amplicon sequencing. On the basis of the hg19/GRCh37 reference and the RefSeq mRNA NM_001172517, respective heterozygous mutations were found and validated in Patients 1, 2, and 3: a splice-site mutation (chr2:g.200137396C > T, c.1741-1G > A), a nonsense mutation (chr2:g.200213750G > A, c.847C > T, p.R283*), and a frame-shift mutations (chr2:g.200188589_200188590del, c.1478_1479del, p.Q493Rfs*19). All mutations occurred de novo. The mutations in Patients 1 and 3 were novel; the mutation in Patient 2 has been described previously. Tooth mesenchymal cells derived from Patient 2 showed diminished SATB2 expression. Multiple odontomas were evident in the patients in this report; however, this has not been recognized previously as a SAS-associated phenotype. We propose that multiple odontomas be considered as an occasional manifestation of SAS.
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Affiliation(s)
- Takashi Kikuiri
- Department of Dentistry for Children and Disabled Persons, Hokkaido University Graduate School of Dental Medicine, Sapporo, Hokkaido, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideto Imura
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Satoshi Suzuki
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yusuke Matsuzawa
- Department of Oral and Maxillofacial Surgery, Keiyukai Sapporo Hospital, Sapporo, Japan
| | - Takashi Nakamura
- Division of Molecular Pharmacology & Cell Biophysics, Department of Oral Biology, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Satoshi Fukumoto
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Yoshitaka Yoshimura
- Department of Molecular Cell Pharmacology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan
| | - Satoshi Watanabe
- Department of Pediatrics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takahiro Yamada
- Clinical Genetics Unit, Kyoto University Hospital, Kyoto, Japan
| | - Masanobu Shindoh
- Department of Oral Pathology and Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan.,Tenshi College School of Nursing and Nutrition, Sapporo, Japan
| | - Yoshihiko Sugita
- Department of Oral Pathology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Hatsuhiko Maeda
- Department of Oral Pathology, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Yasutaka Yawaka
- Department of Dentistry for Children and Disabled Persons, Hokkaido University Graduate School of Dental Medicine, Sapporo, Hokkaido, Japan
| | - Tadashi Mikoya
- Center for Advanced Oral Medicine, Hokkaido University Hospital, Sapporo, Japan
| | - Nagato Natsume
- Division of Research and Treatment for Oral and Maxillofacial Congenital Anomalies, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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9
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Morimoto Y, Shimada-Sugimoto M, Otowa T, Yoshida S, Kinoshita A, Mishima H, Yamaguchi N, Mori T, Imamura A, Ozawa H, Kurotaki N, Ziegler C, Domschke K, Deckert J, Umekage T, Tochigi M, Kaiya H, Okazaki Y, Tokunaga K, Sasaki T, Yoshiura KI, Ono S. Whole-exome sequencing and gene-based rare variant association tests suggest that PLA2G4E might be a risk gene for panic disorder. Transl Psychiatry 2018; 8:41. [PMID: 29391400 PMCID: PMC5804028 DOI: 10.1038/s41398-017-0088-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 11/09/2017] [Accepted: 11/30/2017] [Indexed: 12/31/2022] Open
Abstract
Panic disorder (PD) is characterized by recurrent and unexpected panic attacks, subsequent anticipatory anxiety, and phobic avoidance. Recent epidemiological and genetic studies have revealed that genetic factors contribute to the pathogenesis of PD. We performed whole-exome sequencing on one Japanese family, including multiple patients with panic disorder, which identified seven rare protein-altering variants. We then screened these genes in a Japanese PD case-control group (384 sporadic PD patients and 571 controls), resulting in the detection of three novel single nucleotide variants as potential candidates for PD (chr15: 42631993, T>C in GANC; chr15: 42342861, G>T in PLA2G4E; chr20: 3641457, G>C in GFRA4). Statistical analyses of these three genes showed that PLA2G4E yielded the lowest p value in gene-based rare variant association tests by Efficient and Parallelizable Association Container Toolbox algorithms; however, the p value did not reach the significance threshold in the Japanese. Likewise, in a German case-control study (96 sporadic PD patients and 96 controls), PLA2G4E showed the lowest p value but again did not reach the significance threshold. In conclusion, we failed to find any significant variants or genes responsible for the development of PD. Nonetheless, our results still leave open the possibility that rare protein-altering variants in PLA2G4E contribute to the risk of PD, considering the function of this gene.
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Affiliation(s)
- Yoshiro Morimoto
- 0000 0000 8902 2273grid.174567.6Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan ,0000 0000 8902 2273grid.174567.6Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Mihoko Shimada-Sugimoto
- 0000 0001 2151 536Xgrid.26999.3dDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takeshi Otowa
- grid.440938.2Graduate School of Clinical Psychology, Professional Degree Program in Clinical Psychology, Teikyo Heisei University, Tokyo, Japan
| | - Shintaro Yoshida
- 0000 0000 8902 2273grid.174567.6Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Kinoshita
- 0000 0000 8902 2273grid.174567.6Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroyuki Mishima
- 0000 0000 8902 2273grid.174567.6Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Yamaguchi
- 0000 0000 8902 2273grid.174567.6Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | | | - Akira Imamura
- 0000 0000 8902 2273grid.174567.6Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroki Ozawa
- 0000 0000 8902 2273grid.174567.6Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Kurotaki
- 0000 0000 8902 2273grid.174567.6Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Christiane Ziegler
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics, and Psychotherapy, Center of Mental Health, University of Würzburg, Würzburg, Germany ,grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Katharina Domschke
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics, and Psychotherapy, Center of Mental Health, University of Würzburg, Würzburg, Germany ,grid.5963.9Department of Psychiatry and Psychotherapy, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jürgen Deckert
- 0000 0001 1958 8658grid.8379.5Department of Psychiatry, Psychosomatics, and Psychotherapy, Center of Mental Health, University of Würzburg, Würzburg, Germany
| | - Tadashi Umekage
- 0000 0001 2151 536Xgrid.26999.3dDivision for Environment, Health and Safety, The University of Tokyo, Tokyo, Japan
| | - Mamoru Tochigi
- 0000 0000 9239 9995grid.264706.1Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Hisanobu Kaiya
- Panic Disorder Research Center, Warakukai Med. Corp, Tokyo, Japan
| | - Yuji Okazaki
- Department of Psychiatry, Koseikai Michino-o Hospital, Nagasaki, Japan
| | - Katsushi Tokunaga
- 0000 0001 2151 536Xgrid.26999.3dDepartment of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- 0000 0001 2151 536Xgrid.26999.3dDepartment of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Koh-ichiro Yoshiura
- 0000 0000 8902 2273grid.174567.6Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Ono
- Department of Neuropsychiatry, Unit of Translation Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan. .,Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan. .,Aino-Ariake Hospital, Unzen, Nagasaki, Japan.
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10
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Morimoto Y, Ono S, Imamura A, Okazaki Y, Kinoshita A, Mishima H, Nakane H, Ozawa H, Yoshiura KI, Kurotaki N. Deep sequencing reveals variations in somatic cell mosaic mutations between monozygotic twins with discordant psychiatric disease. Hum Genome Var 2017; 4:17032. [PMID: 28765789 PMCID: PMC5529667 DOI: 10.1038/hgv.2017.32] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 04/23/2017] [Accepted: 06/20/2017] [Indexed: 01/09/2023] Open
Abstract
Monozygotic (MZ) twins have been thought to be genetically identical. However, recent studies have shown discordant variants between them. We performed whole-exome sequencing (WES) in five MZ twin pairs with discordant neurodevelopmental disorders and one healthy control MZ twin to detect discordant variants. We identified three discordant variants confirmed by deep sequencing after analysis by personalized next-generation sequencing (NGS). Three mutations in FBXO38 (chr5:147774428;T>G), SMOC2 (chr6:169051385;A>G) and TDRP (chr8:442616;A>G), were detected with low allele frequency of mutant alleles on deep sequencing, suggesting that these loci are mosaic due to somatic mutations in a developmental stage. Our results suggest that deep sequencing analysis would be an adequate method to detect discordant mutations in candidate genes responsible for heritable diseases.
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Affiliation(s)
- Yoshiro Morimoto
- Department of Neuropsychiatry, Unit of Translation Medicine Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Shinji Ono
- Department of Neuropsychiatry, Unit of Translation Medicine Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.,Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Akira Imamura
- Department of Neuropsychiatry, Unit of Translation Medicine Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Yuji Okazaki
- Department of Psychiatry, Koseikai Michino-o Hospital, Nagasaki, Japan
| | - Akira Kinoshita
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hideyuki Nakane
- Unit of Rehabilitation Science, Department of Psychiatric Rehabilitation Science, University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Hiroki Ozawa
- Department of Neuropsychiatry, Unit of Translation Medicine Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Naohiro Kurotaki
- Department of Neuropsychiatry, Unit of Translation Medicine Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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11
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Konomoto T, Imamura H, Orita M, Tanaka E, Moritake H, Sato Y, Fujimoto S, Harita Y, Hisano S, Yoshiura KI, Nunoi H. Clinical and histological findings of autosomal dominant renal-limited disease with LMX1B mutation. Nephrology (Carlton) 2017; 21:765-73. [PMID: 26560070 DOI: 10.1111/nep.12666] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Revised: 10/29/2015] [Accepted: 11/03/2015] [Indexed: 12/18/2022]
Abstract
AIM Mutations of LMX1B cause nail-patella syndrome, a rare autosomal dominant disorder. Recently, LMX1B R246Q heterozygous mutations were recognised in nephropathy without extrarenal manifestation. The aim of this study was to clarify characteristics of nephropathy caused by R246Q mutation. METHODS Whole exome sequencing was performed on a large family with nonsyndromic autosomal dominant nephropathy without extrarenal manifestation. Clinical and histological findings of patients with LMX1B mutation were investigated. RESULTS LMX1B R246Q heterozygous mutation was identified in five patients over three generations. Proteinuria or haematoproteinuria was recognized by urinary screening from all patients in childhood. Proteinuria gradually increased to nephrotic levels and renal function decreased in adolescence. Two patients progressed to end-stage renal disease in adulthood. Renal histology demonstrated minimal change in childhood and focal segmental glomerulosclerosis in adulthood. Using electron microscopy, focal collagen deposition could be detected in glomeruli even when a "moth-eaten appearance" was not apparent in the glomerular basement membrane. In addition, podocin expression in glomerular podocytes was significantly decreased, even in the early stages of disease progression. CONCLUSION Comprehensive genetic analyses and collagen or tannic acid staining may be useful for diagnosis of LMX1B-associated nephropathy. While renal prognosis of R246Q may be worse than that of typical NPS nephropathy, signs of podocytopathy can be detected during the infantile period; thus, childhood urinary screening may facilitate early detection.
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Affiliation(s)
- Takao Konomoto
- Division of Pediatrics, Department of Developmental and Urological-Reproductive Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Hideaki Imamura
- Division of Pediatrics, Department of Developmental and Urological-Reproductive Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Mayuko Orita
- Division of Pediatrics, Department of Developmental and Urological-Reproductive Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Etsuko Tanaka
- Department of Pediatrics, Miyazaki Prefectural Miyazaki Hospital, Miyazaki, Japan
| | - Hiroshi Moritake
- Division of Pediatrics, Department of Developmental and Urological-Reproductive Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuji Sato
- Dialysis Division, University of Miyazaki Hospital, Miyazaki, Japan
| | - Shouichi Fujimoto
- Dialysis Division, University of Miyazaki Hospital, Miyazaki, Japan.,Department of Haemovascular Medicine and Artificial Organs, University of Miyazaki, Miyazaki, Japan
| | - Yutaka Harita
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Hisano
- Department of Pathology, Faculty of Medicine, Fukuoka University, Fukuoka, Japan
| | - Koh-Ichiro Yoshiura
- Department of Human Genetics, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
| | - Hiroyuki Nunoi
- Division of Pediatrics, Department of Developmental and Urological-Reproductive Medicine, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
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12
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De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development. Nat Genet 2017; 49:249-255. [PMID: 28067911 DOI: 10.1038/ng.3765] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 12/13/2016] [Indexed: 12/15/2022]
Abstract
Bosma arhinia microphthalmia syndrome (BAMS) is an extremely rare and striking condition characterized by complete absence of the nose with or without ocular defects. We report here that missense mutations in the epigenetic regulator SMCHD1 mapping to the extended ATPase domain of the encoded protein cause BAMS in all 14 cases studied. All mutations were de novo where parental DNA was available. Biochemical tests and in vivo assays in Xenopus laevis embryos suggest that these mutations may behave as gain-of-function alleles. This finding is in contrast to the loss-of-function mutations in SMCHD1 that have been associated with facioscapulohumeral muscular dystrophy (FSHD) type 2. Our results establish SMCHD1 as a key player in nasal development and provide biochemical insight into its enzymatic function that may be exploited for development of therapeutics for FSHD.
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13
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Tamura S, Higuchi K, Tamaki M, Inoue C, Awazawa R, Mitsuki N, Nakazawa Y, Mishima H, Takahashi K, Kondo O, Imai K, Morio T, Ohara O, Ogi T, Furukawa F, Inoue M, Yoshiura KI, Kanazawa N. Novel compound heterozygous DNA ligase IV mutations in an adolescent with a slowly-progressing radiosensitive-severe combined immunodeficiency. Clin Immunol 2015; 160:255-60. [PMID: 26172957 DOI: 10.1016/j.clim.2015.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/05/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022]
Abstract
We herein describe a case of a 17-year-old boy with intractable common warts, short stature, microcephaly and slowly-progressing pancytopenia. Simultaneous quantification of T-cell receptor recombination excision circles (TREC) and immunoglobulin κ-deleting recombination excision circles (KREC) suggested very poor generation of both T-cells and B-cells. By whole exome sequencing, novel compound heterozygous mutations were identified in the patient's DNA ligase IV (LIG4) gene. The diagnosis of LIG4 syndrome was confirmed by delayed DNA double-strand break repair kinetics in γ-irradiated fibroblasts from the patient and their restoration by an introduction of wild-type LIG4. Although the patient received allogeneic hematopoietic stem cell transplantation from his haploidentical mother, he unfortunately expired due to an insufficiently reconstructed immune system. An earlier definitive diagnosis using TREC/KREC quantification and whole exome sequencing would thereby allow earlier intervention, which would be essential for improving long-term survival in similar cases with slowly-progressing LIG4 syndrome masked in adolescents.
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Affiliation(s)
- Shinobu Tamura
- Department of Hematology and Oncology, Kinan Hospital, Wakayama, Japan
| | - Kohei Higuchi
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Masaharu Tamaki
- Department of Hematology and Oncology, Kinan Hospital, Wakayama, Japan
| | | | - Ryoko Awazawa
- Department of Dermatology, University of the Ryukyus, Okinawa, Japan
| | - Noriko Mitsuki
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuka Nakazawa
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis, Nagasaki University, Nagasaki, Japan; Department of Genome Repair, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Kenzo Takahashi
- Department of Dermatology, University of the Ryukyus, Okinawa, Japan
| | - Osamu Kondo
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Kohsuke Imai
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoo Ogi
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis, Nagasaki University, Nagasaki, Japan; Department of Genome Repair, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Fukumi Furukawa
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Masami Inoue
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Koh-ichiro Yoshiura
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Nobuo Kanazawa
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan.
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Lin CF, Valladares O, Childress DM, Klevak E, Geller ET, Hwang YC, Tsai EA, Schellenberg GD, Wang LS. DRAW+SneakPeek: analysis workflow and quality metric management for DNA-seq experiments. Bioinformatics 2013; 29:2498-500. [PMID: 23943636 PMCID: PMC3777113 DOI: 10.1093/bioinformatics/btt422] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Summary: We report our new DRAW+SneakPeek software for DNA-seq analysis. DNA resequencing analysis workflow (DRAW) automates the workflow of processing raw sequence reads including quality control, read alignment and variant calling on high-performance computing facilities such as Amazon elastic compute cloud. SneakPeek provides an effective interface for reviewing dozens of quality metrics reported by DRAW, so users can assess the quality of data and diagnose problems in their sequencing procedures. Both DRAW and SneakPeek are freely available under the MIT license, and are available as Amazon machine images to be used directly on Amazon cloud with minimal installation. Availability: DRAW+SneakPeek is released under the MIT license and is available for academic and nonprofit use for free. The information about source code, Amazon machine images and instructions on how to install and run DRAW+SneakPeek locally and on Amazon elastic compute cloud is available at the National Institute on Aging Genetics of Alzheimer’s Disease Data Storage Site (http://www.niagads.org/) and Wang lab Web site (http://wanglab.pcbi.upenn.edu/). Contact:gerardsc@mail.med.upenn.edu or lswang@mail.med.upenn.edu
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Affiliation(s)
- Chiao-Feng Lin
- Department of Pathology and Laboratory Medicine and Institute for Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA, Department of Physics, University of Washington, Seattle, WA 98105, USA, Genomics and Computational Biology Graduate Group, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA and Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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Mishima H, Aerts J, Katayama T, Bonnal RJP, Yoshiura KI. The Ruby UCSC API: accessing the UCSC genome database using Ruby. BMC Bioinformatics 2012; 13:240. [PMID: 22994508 PMCID: PMC3542311 DOI: 10.1186/1471-2105-13-240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2012] [Accepted: 09/17/2012] [Indexed: 12/26/2022] Open
Abstract
Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.
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Affiliation(s)
- Hiroyuki Mishima
- Department of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, 1-12-4 Sakamoto, Nagasaki, Nagasaki, 852-8523, Japan.
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