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Nakahara Y, Mitsui J, Date H, Porto KJ, Hayashi Y, Yamashita A, Kusakabe Y, Matsukawa T, Ishiura H, Yasuda T, Iwata A, Goto J, Ichikawa Y, Momose Y, Takahashi Y, Toda T, Ohta R, Yoshimura J, Morishita S, Gustavsson EK, Christy D, Maczis M, Farrer MJ, Kim HJ, Park SS, Jeon B, Zhang J, Gu W, Scholz SW, Singleton AB, Houlden H, Yabe I, Sasaki H, Matsushima M, Takashima H, Kikuchi A, Aoki M, Hara K, Kakita A, Yamada M, Takahashi H, Onodera O, Nishizawa M, Watanabe H, Ito M, Sobue G, Ishikawa K, Mizusawa H, Kanai K, Kuwabara S, Arai K, Koyano S, Kuroiwa Y, Hasegawa K, Yuasa T, Yasui K, Nakashima K, Ito H, Izumi Y, Kaji R, Kato T, Kusunoki S, Osaki Y, Horiuchi M, Yamamoto K, Shimada M, Miyagawa T, Kawai Y, Nishida N, Tokunaga K, Dürr A, Brice A, Filla A, Klockgether T, Wüllner U, Tanner CM, Kukull WA, Lee VMY, Masliah E, Low PA, Sandroni P, Ozelius L, Foroud T, Tsuji S. Genome-wide association study identifies a new susceptibility locus in PLA2G4C for Multiple System Atrophy. medRxiv 2023:2023.05.02.23289328. [PMID: 37425910 PMCID: PMC10327266 DOI: 10.1101/2023.05.02.23289328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
To elucidate the molecular basis of multiple system atrophy (MSA), a neurodegenerative disease, we conducted a genome-wide association study (GWAS) in a Japanese MSA case/control series followed by replication studies in Japanese, Korean, Chinese, European and North American samples. In the GWAS stage rs2303744 on chromosome 19 showed a suggestive association ( P = 6.5 × 10 -7 ) that was replicated in additional Japanese samples ( P = 2.9 × 10 -6 . OR = 1.58; 95% confidence interval, 1.30 to 1.91), and then confirmed as highly significant in a meta-analysis of East Asian population data ( P = 5.0 × 10 -15 . Odds ratio= 1.49; 95% CI 1.35 to 1.72). The association of rs2303744 with MSA remained significant in combined European/North American samples ( P =0.023. Odds ratio=1.14; 95% CI 1.02 to 1.28) despite allele frequencies being quite different between these populations. rs2303744 leads to an amino acid substitution in PLA2G4C that encodes the cPLA2γ lysophospholipase/transacylase. The cPLA2γ-Ile143 isoform encoded by the MSA risk allele has significantly decreased transacylase activity compared with the alternate cPLA2γ-Val143 isoform that may perturb membrane phospholipids and α-synuclein biology.
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Kimura M, Yoshimura J, Ozawa T, Shiraishi J, Hyogo M, Sawada T. Overcoming complete collapse of a VBX stent graft with endovascular treatment using a bare nitinol stent. AsiaIntervention 2023; 9:66-67. [PMID: 36936089 PMCID: PMC10015479 DOI: 10.4244/aij-d-22-00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 10/31/2022] [Indexed: 03/14/2023]
Affiliation(s)
- Masayoshi Kimura
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Jun Yoshimura
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Takaaki Ozawa
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Jun Shiraishi
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Masayuki Hyogo
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Takahisa Sawada
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
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3
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Hongo H, Miyawaki S, Teranishi Y, Mitsui J, Katoh H, Komura D, Tsubota K, Matsukawa T, Watanabe M, Kurita M, Yoshimura J, Dofuku S, Ohara K, Ishigami D, Okano A, Kato M, Hakuno F, Takahashi A, Kunita A, Ishiura H, Shin M, Nakatomi H, Nagao T, Goto H, Takahashi SI, Ushiku T, Ishikawa S, Okazaki M, Morishita S, Tsuji S, Saito N. Somatic GJA4 gain-of-function mutation in orbital cavernous venous malformations. Angiogenesis 2023; 26:37-52. [PMID: 35902510 PMCID: PMC9908695 DOI: 10.1007/s10456-022-09846-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/25/2022]
Abstract
Orbital cavernous venous malformation (OCVM) is a sporadic vascular anomaly of uncertain etiology characterized by abnormally dilated vascular channels. Here, we identify a somatic missense mutation, c.121G > T (p.Gly41Cys) in GJA4, which encodes a transmembrane protein that is a component of gap junctions and hemichannels in the vascular system, in OCVM tissues from 25/26 (96.2%) individuals with OCVM. GJA4 expression was detected in OCVM tissue including endothelial cells and the stroma, through immunohistochemistry. Within OCVM tissue, the mutation allele frequency was higher in endothelial cell-enriched fractions obtained using magnetic-activated cell sorting. Whole-cell voltage clamp analysis in Xenopus oocytes revealed that GJA4 c.121G > T (p.Gly41Cys) is a gain-of-function mutation that leads to the formation of a hyperactive hemichannel. Overexpression of the mutant protein in human umbilical vein endothelial cells led to a loss of cellular integrity, which was rescued by carbenoxolone, a non-specific gap junction/hemichannel inhibitor. Our data suggest that GJA4 c.121G > T (p.Gly41Cys) is a potential driver gene mutation for OCVM. We propose that hyperactive hemichannel plays a role in the development of this vascular phenotype.
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Affiliation(s)
- Hiroki Hongo
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Yu Teranishi
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroto Katoh
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daisuke Komura
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kinya Tsubota
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan
| | - Takashi Matsukawa
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masakatsu Watanabe
- Laboratory of Pattern Formation, Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
| | - Masakazu Kurita
- Department of Plastic, Reconstructive and Aesthetic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shogo Dofuku
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Kenta Ohara
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Daiichiro Ishigami
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Atsushi Okano
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Motoi Kato
- Department of Plastic, Reconstructive and Aesthetic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Fumihiko Hakuno
- Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Ayaka Takahashi
- Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiro Shin
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hirofumi Nakatomi
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Toshitaka Nagao
- Department of Anatomic Pathology, Tokyo Medical University, Tokyo, Japan
| | - Hiroshi Goto
- Department of Ophthalmology, Tokyo Medical University, Tokyo, Japan
| | - Shin-Ichiro Takahashi
- Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shumpei Ishikawa
- Department of Preventive Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mutsumi Okazaki
- Department of Plastic, Reconstructive and Aesthetic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Institute of Medical Genomics, International University of Health and Welfare, Narita, Chiba, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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Ikenaga C, Date H, Kanagawa M, Mitsui J, Ishiura H, Yoshimura J, Pinal‐Fernandez I, Mammen AL, Lloyd TE, Tsuji S, Shimizu J, Toda T, Goto J. Muscle transcriptomics shows overexpression of
cadherin 1
in inclusion body myositis. Ann Neurol 2022; 91:317-328. [PMID: 35064929 PMCID: PMC9092834 DOI: 10.1002/ana.26304] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/18/2022]
Abstract
Objective This study aimed to elucidate the molecular features of inclusion body myositis (IBM). Methods We performed RNA sequencing analysis of muscle biopsy samples from 67 participants, consisting of 58 myositis patients with the pathological finding of CD8‐positive T cells invading non‐necrotic muscle fibers expressing major histocompatibility complex class I (43 IBM, 6 polymyositis, and 9 unclassifiable myositis), and 9 controls. Results Cluster analysis, principal component analysis, and pathway analysis showed that differentially expressed genes and pathways identified in IBM and polymyositis were mostly comparable. However, pathways related to cell adhesion molecules were upregulated in IBM as compared with polymyositis and controls (p < 0.01). Notably, CDH1, which encodes the epidermal cell junction protein cadherin 1, was overexpressed in the muscles of IBM, which was validated by another RNA sequencing dataset from previous publications. Western blotting confirmed the presence of mature cadherin 1 protein in the muscles of IBM. Immunohistochemical staining confirmed the positivity for anti‐cadherin 1 antibody in the muscles of IBM, whereas there was no muscle fiber positive for anti‐cadherin 1 antibody in immune‐mediated necrotizing myopathy, antisynthetase syndrome, and controls. The fibers stained with anti‐cadherin 1 antibody did not have rimmed vacuoles or abnormal protein accumulation. Experimental skeletal muscle regeneration and differentiation systems showed that CDH1 is expressed during skeletal muscle regeneration and differentiation. Interpretation CDH1 was detected as a differentially expressed gene, and immunohistochemistry showed that cadherin 1 exists in the muscles of IBM, whereas it was rarely seen in those of other idiopathic inflammatory myopathies. Cadherin 1 upregulation in muscle could provide a valuable clue to the pathological mechanisms of IBM. ANN NEUROL 2022;91:317–328
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Affiliation(s)
- Chiseko Ikenaga
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
| | - Hidetoshi Date
- Department of Neurology, National Center Hospital National Center of Neurology and Psychiatry Tokyo Japan
| | - Motoi Kanagawa
- Division of Molecular Brain Science Kobe University Graduate School of Medicine Kobe Japan
- Department of Cell Biology and Molecular Medicine Ehime University Graduate School of Medicine Ehime Japan
| | - Jun Mitsui
- Department of Molecular Neurology, Graduate School of Medicine The University of Tokyo Tokyo Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences The University of Tokyo Chiba Japan
| | - Iago Pinal‐Fernandez
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Muscle Disease Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda MD US
- Faculty of Health Sciences and Faculty of Computer Science, Multimedia and Telecommunications Universitat Oberta de Catalunya Barcelona Spain
| | - Andrew L. Mammen
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Muscle Disease Unit National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health Bethesda MD US
| | - Thomas E. Lloyd
- Department of Neurology Johns Hopkins University School of Medicine Baltimore MD US
- Solomon H. Synder Department of Neuroscience Johns Hopkins University School of Medicine Baltimore MD US
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine The University of Tokyo Tokyo Japan
- Institute of Medical Genomics International University of Health and Welfare Chiba Japan
| | - Jun Shimizu
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Department of Physical Therapy Tokyo University of Technology Tokyo Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine the University of Tokyo Tokyo Japan
- Division of Molecular Brain Science Kobe University Graduate School of Medicine Kobe Japan
| | - Jun Goto
- Department of Neurology International University of Health and Welfare, Mita Hospital Tokyo Japan
- Department of Neurology International University of Health and Welfare, Ichikawa Hospital Chiba Japan
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5
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Ishino K, Hasuwa H, Yoshimura J, Iwasaki YW, Nishihara H, Seki NM, Hirano T, Tsuchiya M, Ishizaki H, Masuda H, Kuramoto T, Saito K, Sakakibara Y, Toyoda A, Itoh T, Siomi MC, Morishita S, Siomi H. Hamster PIWI proteins bind to piRNAs with stage-specific size variations during oocyte maturation. Nucleic Acids Res 2021; 49:2700-2720. [PMID: 33590099 PMCID: PMC7969018 DOI: 10.1093/nar/gkab059] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/18/2021] [Accepted: 01/23/2021] [Indexed: 12/27/2022] Open
Abstract
In animal gonads, transposable elements are actively repressed to preserve genome integrity through the PIWI-interacting RNA (piRNA) pathway. In mice, piRNAs are abundantly expressed in male germ cells, and form effector complexes with three distinct PIWIs. The depletion of individual Piwi genes causes male-specific sterility with no discernible phenotype in female mice. Unlike mice, most other mammals have four PIWI genes, some of which are expressed in the ovary. Here, purification of PIWI complexes from oocytes of the golden hamster revealed that the size of the PIWIL1-associated piRNAs changed during oocyte maturation. In contrast, PIWIL3, an ovary-specific PIWI in most mammals, associates with short piRNAs only in metaphase II oocytes, which coincides with intense phosphorylation of the protein. An improved high-quality genome assembly and annotation revealed that PIWIL1- and PIWIL3-associated piRNAs appear to share the 5′-ends of common piRNA precursors and are mostly derived from unannotated sequences with a diminished contribution from TE-derived sequences, most of which correspond to endogenous retroviruses. Our findings show the complex and dynamic nature of biogenesis of piRNAs in hamster oocytes, and together with the new genome sequence generated, serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes.
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Affiliation(s)
- Kyoko Ishino
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Hidetoshi Hasuwa
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yuka W Iwasaki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Naomi M Seki
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.,Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Takamasa Hirano
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.,National Institute of Genetics, Mishima 411-8540, Japan
| | - Marie Tsuchiya
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | | | - Harumi Masuda
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Tae Kuramoto
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Kuniaki Saito
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan.,National Institute of Genetics, Mishima 411-8540, Japan
| | - Yasubumi Sakakibara
- Department of Biosciences and Informatics, Keio University, Yokohama 223-8522, Japan
| | | | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Kanagawa 226-8501, Japan
| | - Mikiko C Siomi
- Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Haruhiko Siomi
- Department of Molecular Biology, Keio University School of Medicine, Tokyo 160-8582, Japan
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6
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Yoshimura J, Kimura M, Ikemura N, Sawada T. Optical Frequency Domain Images of 3 Unique Femoral Artery Stents at 5 Months After Implantation. JACC Cardiovasc Interv 2021; 14:e105-e106. [PMID: 33582085 DOI: 10.1016/j.jcin.2020.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 11/26/2022]
Affiliation(s)
- Jun Yoshimura
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Masayoshi Kimura
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan.
| | - Nariko Ikemura
- Department of Cardiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Takahisa Sawada
- Department of Cardiology, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
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7
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Shiraishi J, Ito F, Yoshimura J, Kirii Y, Kataoka E, Ozawa T, Ito D, Kojima A, Kimura M, Kishita E, Nakagawa Y, Hyogo M, Sawada T. Stentless Interventional Procedure Using Rotational Atherectomy and Drug-Coated Balloon for Noncalcified De Novo Lesions. CJC Open 2021; 3:714-722. [PMID: 34169250 PMCID: PMC8209394 DOI: 10.1016/j.cjco.2021.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Accepted: 01/12/2021] [Indexed: 11/18/2022] Open
Abstract
Background Several recent reports have shown that a stentless interventional procedure using rotational atherectomy followed by drug-coated balloon (DCB) treatment (RA/DCB) is a potent revascularization therapy for calcified de novo lesions even in the new-generation drug-eluting stent era; however, the role of the RA/DCB procedure for noncalcified de novo lesions remains unclear. Methods A total of 47 consecutive patients (53 lesions) who underwent RA/DCB for coronary de novo lesions were enrolled. According to the presence or absence of severe calcification at target lesions on fluoroscopy, the 47 patients were divided into the noncalcified cases (n = 12) and the calcified cases (n = 35), and the 53 lesions were divided into the noncalcified lesions (n = 14) and the calcified lesions (n = 39). Results The noncalcified cases tended to have a higher frequency of bleeding risk and had a significantly lower prevalence of dual antiplatelet therapy compared with the calcified cases. The main lesion-specific factors for the RA/DCB procedure among the noncalcified lesions were presence of left circumflex coronary artery ostial lesion. The final burr size, DCB diameter used, and angiographic success rate did not significantly differ between the 2 groups. The noncalcified lesions had a larger reference diameter and a shorter lesion length than the calcified lesions, whereas acute gain and late lumen loss did not differ between the 2 groups. Nine-month clinical outcomes were comparable between the 2 groups. Conclusions Under drug-eluting stent-unsuitable clinical or lesion conditions, acute and midterm outcomes of RA/DCB for noncalcified de novo lesions might be comparable with those for calcified de novo lesions.
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Affiliation(s)
- Jun Shiraishi
- Corresponding author: Dr Jun Shiraishi, Department of Cardiology, Kyoto First Red Cross Hospital, Honmachi, Higashiyama-ku, Kyoto 605-0981, Japan. Tel.: +81-75-561-1121; fax: +81-75-561-6308.
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8
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Hosoe J, Miya F, Kadowaki H, Fujiwara T, Suzuki K, Kato T, Waki H, Sasako T, Aizu K, Yamamura N, Sasaki F, Kurano M, Hara K, Tanaka M, Ishiura H, Tsuji S, Honda K, Yoshimura J, Morishita S, Matsuzawa F, Aikawa SI, Boroevich KA, Nangaku M, Okada Y, Tsunoda T, Shojima N, Yamauchi T, Kadowaki T. Clinical usefulness of multigene screening with phenotype-driven bioinformatics analysis for the diagnosis of patients with monogenic diabetes or severe insulin resistance. Diabetes Res Clin Pract 2020; 169:108461. [PMID: 32971154 DOI: 10.1016/j.diabres.2020.108461] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 08/29/2020] [Accepted: 09/16/2020] [Indexed: 11/29/2022]
Abstract
AIMS Monogenic diabetes is clinically heterogeneous and differs from common forms of diabetes (type 1 and 2). We aimed to investigate the clinical usefulness of a comprehensive genetic testing system, comprised of targeted next-generation sequencing (NGS) with phenotype-driven bioinformatics analysis in patients with monogenic diabetes, which uses patient genotypic and phenotypic data to prioritize potentially causal variants. METHODS We performed targeted NGS of 383 genes associated with monogenic diabetes or common forms of diabetes in 13 Japanese patients with suspected (n = 10) or previously diagnosed (n = 3) monogenic diabetes or severe insulin resistance. We performed in silico structural analysis and phenotype-driven bioinformatics analysis of candidate variants from NGS data. RESULTS Among the patients suspected having monogenic diabetes or insulin resistance, we diagnosed 3 patients as subtypes of monogenic diabetes due to disease-associated variants of INSR, LMNA, and HNF1B. Additionally, in 3 other patients, we detected rare variants with potential phenotypic effects. Notably, we identified a novel missense variant in TBC1D4 and an MC4R variant, which together may cause a mixed phenotype of severe insulin resistance. CONCLUSIONS This comprehensive approach could assist in the early diagnosis of patients with monogenic diabetes and facilitate the provision of tailored therapy.
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Affiliation(s)
- Jun Hosoe
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fuyuki Miya
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; CREST, JST, Tokyo, Japan
| | | | - Toyofumi Fujiwara
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Chiba, Japan
| | - Ken Suzuki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Takashi Kato
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hironori Waki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Sasako
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Katsuya Aizu
- Division of Endocrinology and Metabolism, Saitama Children's Medical Center, Saitama, Japan
| | - Natsumi Yamamura
- Department of Pediatric Nephrology and Metabolism, Osaka Medical Center and Research Institute for Maternal and Child Health, Izumi, Japan
| | - Fusako Sasaki
- Department of Pediatrics, School of Medicine, Fukuoka University, Fukuoka, Japan
| | - Makoto Kurano
- Department of Clinical Laboratory Medicine, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuo Hara
- Department of Endocrinology and Metabolism, Saitama Medical Center, Jichi Medical University, Saitama, Japan
| | - Masaki Tanaka
- Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, The University of Tokyo Hospital, Tokyo, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenjiro Honda
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | | | | | - Keith A Boroevich
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Masaomi Nangaku
- Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Tatsuhiko Tsunoda
- Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan; CREST, JST, Tokyo, Japan; Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuhiro Shojima
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Toshimasa Yamauchi
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Takashi Kadowaki
- Department of Diabetes and Metabolic Diseases, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Toranomon Hospital, Tokyo, Japan.
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9
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Teranishi Y, Miyawaki S, Hongo H, Dofuku S, Okano A, Takayanagi S, Ota T, Yoshimura J, Qu W, Mitsui J, Nakatomi H, Morishita S, Tsuji S, Saito N. Targeted deep sequencing of DNA from multiple tissue types improves the diagnostic rate and reveals a highly diverse phenotype of mosaic neurofibromatosis type 2. J Med Genet 2020; 58:701-711. [PMID: 33067351 DOI: 10.1136/jmedgenet-2020-106973] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Although 60% of patients with de novo neurofibromatosis type 2 (NF2) are presumed to have mosaic NF2, the actual diagnostic rate of this condition remains low at around 20% because of the existing difficulties in detecting NF2 variants with low variant allele frequency (VAF). Here, we examined the correlation between the genotype and phenotype of mosaic NF2 after improving the diagnostic rate of mosaic NF2. METHODS We performed targeted deep sequencing of 36 genes including NF2 using DNA samples from multiple tissues (blood, buccal mucosa, hair follicle and tumour) of 53 patients with de novo NF2 and elucidated their genotype-phenotype correlation. RESULTS Twenty-four patients (45.2%) had the NF2 germline variant, and 20 patients with NF2 (37.7%) had mosaic NF2. The mosaic NF2 phenotype was significantly different from that in patients with NF2 germline variant in terms of distribution of NF2-related disease, tumour growth rate and hearing outcome. The behaviour of schwannoma correlated to the extent of VAF with NF2 variant in normal tissues unlike meningioma. CONCLUSION We have improved the diagnostic rate of mosaic NF2 compared with that of previous studies by targeted deep sequencing of DNA from multiple tissues. Many atypical patients with NF2 diagnosed with 'unilateral vestibular schwannoma' or 'multiple meningiomas' presumably have mosaic NF2. Finally, we suggest that the highly diverse phenotype of NF2 could result not only from the type and location of NF2 variant but also the extent of VAF in the NF2 variant within normal tissue DNA.
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Affiliation(s)
- Yu Teranishi
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroki Hongo
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shogo Dofuku
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Atsushi Okano
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Takahiro Ota
- Department of Neurosurgery, Tokyo Metropolitan Tama Medical Center, Fuchu, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hirofumi Nakatomi
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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10
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Naruse H, Ishiura H, Mitsui J, Takahashi Y, Matsukawa T, Sakuishi K, Nakamagoe K, Miyake Z, Tamaoka A, Goto J, Yoshimura J, Doi K, Morishita S, Toda T, Tsuji S. Splice-site mutations in KIF5A in the Japanese case series of amyotrophic lateral sclerosis. Neurogenetics 2020; 22:11-17. [PMID: 32815063 DOI: 10.1007/s10048-020-00626-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/12/2020] [Indexed: 11/29/2022]
Abstract
Our objective was to investigate the frequency of KIF5A variants in amyotrophic lateral sclerosis (ALS) and the clinical characteristics of familial ALS (FALS) associated with variants in KIF5A. Whole-exome sequence analysis was performed for a Japanese series of 43 families with FALS and 444 patients with sporadic ALS (SALS), in whom causative variants had not been identified. We compared the frequencies of rare variants (MAF < 0.01) in KIF5A, including missense and loss of function (LoF) variants, between ALS and control subjects (n = 1163). Clinical characteristics of patients with FALS carrying pathogenic variants in KIF5A were also described. LoF variants were identified only in the probands of two families with FALS, both of which were 3' splice-site variants leading to exon skipping and an altered C-terminal domain, located in the mutational hotspot causing FALS, and were considered to be pathogenic for FALS. Rare missense variants in KIF5A were identified in five patients with SALS (1.13%) and 11 control subjects (0.95%, carrier frequency), which were not significantly different. Consequently, the pathogenic LoF variants in KIF5A accounted for 2.1% of all FALS families in this study. These patients suffered from ALS characteristically associated with the predominant involvement of upper motor neuron. In conclusion, we identified two pathogenic splice-site variants in KIF5A in the probands in two Japanese families with FALS, which altered the C-terminal region of KIF5A. Our findings broaden the phenotype spectrum of ALS associated with variants in KIF5A in the Japanese series.
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Affiliation(s)
- Hiroya Naruse
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8655, Japan
| | - Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takashi Matsukawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8655, Japan
| | - Kaori Sakuishi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyotaka Nakamagoe
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Zenshi Miyake
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Akira Tamaoka
- Department of Neurology, Division of Clinical Medicine, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Jun Goto
- Department of Neurology, International University of Health and Welfare Mita Hospital, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Koichiro Doi
- School of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo, 113-8655, Japan. .,Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan.
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11
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Hongo H, Miyawaki S, Imai H, Shimizu M, Yagi S, Mitsui J, Ishiura H, Yoshimura J, Doi K, Qu W, Teranishi Y, Okano A, Ono H, Nakatomi H, Shimizu T, Morishita S, Tsuji S, Saito N. Comprehensive investigation of RNF213 nonsynonymous variants associated with intracranial artery stenosis. Sci Rep 2020; 10:11942. [PMID: 32686731 PMCID: PMC7371676 DOI: 10.1038/s41598-020-68888-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 07/01/2020] [Indexed: 12/22/2022] Open
Abstract
Intracranial artery stenosis (ICAS) is the most common cause of ischemic stroke worldwide. RNF213 single nucleotide variant c.14429G > A (p.Arg4810Lys, rs112735431) was recently reported to be associated with ICAS in East Asians. However, the disease susceptibility of other RNF213 variants has not been clarified. This study comprehensively investigated ICAS-associated RNF213 variants in a pool of 168 Japanese ICAS patients and 1,194 control subjects. We found 138 nonsynonymous germline variants by target resequencing of all coding exons in RNF213. Association study between ICAS patients and control subjects revealed that only p.Arg4810Lys had significant association with ICAS (P = 1.5 × 10-28, odds ratio = 29.3, 95% confidence interval 15.31-56.2 [dominant model]). Fourteen of 138 variants were rare variants detected in ICAS patients not harboring p.Arg4810Lys variant. Two of these rare variants (p.Cys118Arg and p.Leu2356Phe) consistent with variants previously reported in moyamoya disease patients characterized by stenosis of intracranial artery and association with RNF213, and three rare variants (p.Ser193Gly, p.Val1817Leu, and p.Asp3329Tyr) were found neither in control subjects and Single Nucleotide Polymorphism Database. The present findings may improve our understanding of the genetic background of intracranial artery stenosis.
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Affiliation(s)
- Hiroki Hongo
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan.
| | - Hideaki Imai
- Department of Neurosurgery, Japan Community Healthcare Organization Tokyo Shinjuku Medical Center, Tokyo, Japan
| | | | - Shinichi Yagi
- Kanto Neurosurgical Hospital, Kumagaya, Saitama, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Faculty of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan.,School of Bioscience and Biotechnology, Tokyo University of Technology, Tokyo, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Yu Teranishi
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Atsushi Okano
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hideaki Ono
- Department of Neurosurgery, Fuji Brain Institute and Hospital, Fujinomiya, Shizuoka, Japan
| | - Hirofumi Nakatomi
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | | | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,International University of Health and Welfare, Narita, Chiba, Japan
| | - Nobuhito Saito
- Department of Neurosurgery, Faculty of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
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12
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Katoh K, Aiba K, Fukushi D, Yoshimura J, Suzuki Y, Mitsui J, Morishita S, Tuji S, Yamada K, Wakamatsu N. Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation. Hum Mutat 2020; 41:1447-1460. [PMID: 32485067 DOI: 10.1002/humu.24058] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 05/04/2020] [Accepted: 05/22/2020] [Indexed: 11/10/2022]
Abstract
A heterozygous deletion at Xq27.3q28 including FMR1, AFF2, and IDS causing intellectual disability and characteristic facial features is very rare in females, with only 10 patients having been reported. Here, we examined two female patients with different clinical features harboring the Xq27.3q28 deletion and determined the chromosomal breakpoints. Moreover, we assessed the X chromosome inactivation (XCI) in peripheral blood from both patients. Both patients had an almost overlapping deletion at Xq27.3q28, however, the more severe patient (Patient 1) showed skewed XCI of the normal X chromosome (79:21) whereas the milder patient (Patient 2) showed random XCI. Therefore, deletion at Xq27.3q28 critically affected brain development, and the ratio of XCI of the normal X chromosome greatly affected the clinical characteristics of patients with deletion at Xq27.3q28. As the chromosomal breakpoints were determined, we analyzed a change in chromatin domains termed topologically associated domains (TADs) using published Hi-C data on the Xq27.3q28 region, and found that only patient 1 had a possibility of a drastic change in TADs. The altered chromatin topologies on the Xq27.3q28 region might affect the clinical features of patient 1 by changing the expression of genes just outside the deletion and/or the XCI establishment during embryogenesis resulting in skewed XCI.
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Affiliation(s)
- Kimiko Katoh
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Kaori Aiba
- Department of Pediatrics, Toyohashi Municipal Hospital, Toyohashi, Aichi, Japan
| | - Daisuke Fukushi
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Yasuyo Suzuki
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shoji Tuji
- Department of Molecular Neurology, The University of Tokyo, Tokyo, Japan
| | - Kenichiro Yamada
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan
| | - Nobuaki Wakamatsu
- Department of Genetics, Institute for Developmental Research, Aichi Developmental Disability Center, Kasugai, Aichi, Japan.,Department of Neurology, Neurology and Stroke Center, Takamatsu Municipal Hospital, Takamatsu, Kagawa, Japan.,Department of Pathology and Host Defense, Faculty of Medicine, Kagawa University, Miki, Kagawa, Japan
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13
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Kurihara M, Ishiura H, Bannai T, Mitsui J, Yoshimura J, Morishita S, Hayashi T, Shimizu J, Toda T, Tsuji S. A Novel de novo KIF1A Mutation in a Patient with Autism, Hyperactivity, Epilepsy, Sensory Disturbance, and Spastic Paraplegia. Intern Med 2020; 59:839-842. [PMID: 31813911 PMCID: PMC7118386 DOI: 10.2169/internalmedicine.3661-19] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Heterozygous mutations in KIF1A have been reported to cause syndromic intellectual disability or pure spastic paraplegia. However, their genotype-phenotype correlations have not been fully elucidated. We herein report a man with autism and hyperactivity along with sensory disturbance and spastic paraplegia, carrying a novel de novo mutation in KIF1A [c.37C>T (p.R13C)]. Autism and hyperactivity have only previously been reported in a patient with c.38 G>A (R13H) mutation. This case suggests that alterations in this arginine at codon 13 might lead to a common clinical spectrum and further expand the genetic and clinical spectra associated with KIF1A mutations.
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Affiliation(s)
- Masanori Kurihara
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Taro Bannai
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Japan
| | - Toshihiro Hayashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Physiology, Teikyo University School of Medicine, Japan
| | - Jun Shimizu
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Japan
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14
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Suzuki Y, Nishijima S, Furuta Y, Yoshimura J, Suda W, Oshima K, Hattori M, Morishita S. Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut. Microbiome 2019; 7:119. [PMID: 31455406 PMCID: PMC6712665 DOI: 10.1186/s40168-019-0737-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/16/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Elucidating the ecological and biological identity of extrachromosomal mobile genetic elements (eMGEs), such as plasmids and bacteriophages, in the human gut remains challenging due to their high complexity and diversity. RESULTS Here, we show efficient identification of eMGEs as complete circular or linear contigs from PacBio long-read metagenomic data. De novo assembly of PacBio long reads from 12 faecal samples generated 82 eMGE contigs (2.5~666.7-kb), which were classified as 71 plasmids and 11 bacteriophages, including 58 novel plasmids and six bacteriophages, and complete genomes of five diverse crAssphages with terminal direct repeats. In a dataset of 413 gut metagenomes from five countries, many of the identified plasmids were highly abundant and prevalent. The ratio of gut plasmids by our plasmid data is more than twice that in the public database. Plasmids outnumbered bacterial chromosomes three to one on average in this metagenomic dataset. Host prediction suggested that Bacteroidetes-associated plasmids predominated, regardless of microbial abundance. The analysis found several plasmid-enriched functions, such as inorganic ion transport, while antibiotic resistance genes were harboured mostly in low-abundance Proteobacteria-associated plasmids. CONCLUSIONS Overall, long-read metagenomics provided an efficient approach for unravelling the complete structure of human gut eMGEs, particularly plasmids.
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Affiliation(s)
- Yoshihiko Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Suguru Nishijima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory, Tokyo, 169-8555 Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, Sapporo, 001-0020 Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Wataru Suda
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Kenshiro Oshima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
| | - Masahira Hattori
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
- Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, 169-8555 Japan
- Laboratory for Microbiome Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8568 Japan
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15
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Ishiura H, Shibata S, Yoshimura J, Suzuki Y, Qu W, Doi K, Almansour MA, Kikuchi JK, Taira M, Mitsui J, Takahashi Y, Ichikawa Y, Mano T, Iwata A, Harigaya Y, Matsukawa MK, Matsukawa T, Tanaka M, Shirota Y, Ohtomo R, Kowa H, Date H, Mitsue A, Hatsuta H, Morimoto S, Murayama S, Shiio Y, Saito Y, Mitsutake A, Kawai M, Sasaki T, Sugiyama Y, Hamada M, Ohtomo G, Terao Y, Nakazato Y, Takeda A, Sakiyama Y, Umeda-Kameyama Y, Shinmi J, Ogata K, Kohno Y, Lim SY, Tan AH, Shimizu J, Goto J, Nishino I, Toda T, Morishita S, Tsuji S. Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease. Nat Genet 2019; 51:1222-1232. [DOI: 10.1038/s41588-019-0458-z] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 05/29/2019] [Indexed: 11/09/2022]
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16
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Higuchi Y, Okunushi R, Hara T, Hashiguchi A, Yuan J, Yoshimura A, Murayama K, Ohtake A, Ando M, Hiramatsu Y, Ishihara S, Tanabe H, Okamoto Y, Matsuura E, Ueda T, Toda T, Yamashita S, Yamada K, Koide T, Yaguchi H, Mitsui J, Ishiura H, Yoshimura J, Doi K, Morishita S, Sato K, Nakagawa M, Yamaguchi M, Tsuji S, Takashima H. Mutations in COA7 cause spinocerebellar ataxia with axonal neuropathy. Brain 2019; 141:1622-1636. [PMID: 29718187 PMCID: PMC5972596 DOI: 10.1093/brain/awy104] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 02/20/2018] [Indexed: 11/13/2022] Open
Abstract
Several genes related to mitochondrial functions have been identified as causative genes of neuropathy or ataxia. Cytochrome c oxidase assembly factor 7 (COA7) may have a role in assembling mitochondrial respiratory chain complexes that function in oxidative phosphorylation. Here we identified four unrelated patients with recessive mutations in COA7 among a Japanese case series of 1396 patients with Charcot-Marie-Tooth disease (CMT) or other inherited peripheral neuropathies, including complex forms of CMT. We also found that all four patients had characteristic neurological features of peripheral neuropathy and ataxia with cerebellar atrophy, and some patients showed leukoencephalopathy or spinal cord atrophy on MRI scans. Validated mutations were located at highly conserved residues among different species and segregated with the disease in each family. Nerve conduction studies showed axonal sensorimotor neuropathy. Sural nerve biopsies showed chronic axonal degeneration with a marked loss of large and medium myelinated fibres. An immunohistochemical assay with an anti-COA7 antibody in the sural nerve from the control patient showed the positive expression of COA7 in the cytoplasm of Schwann cells. We also observed mildly elevated serum creatine kinase levels in all patients and the presence of a few ragged-red fibres and some cytochrome c oxidase-negative fibres in a muscle biopsy obtained from one patient, which was suggestive of subclinical mitochondrial myopathy. Mitochondrial respiratory chain enzyme assay in skin fibroblasts from the three patients showed a definitive decrease in complex I or complex IV. Immunocytochemical analysis of subcellular localization in HeLa cells indicated that mutant COA7 proteins as well as wild-type COA7 were localized in mitochondria, which suggests that mutant COA7 does not affect the mitochondrial recruitment and may affect the stability or localization of COA7 interaction partners in the mitochondria. In addition, Drosophila COA7 (dCOA7) knockdown models showed rough eye phenotype, reduced lifespan, impaired locomotive ability and shortened synaptic branches of motor neurons. Our results suggest that loss-of-function COA7 mutation is responsible for the phenotype of the presented patients, and this new entity of disease would be referred to as spinocerebellar ataxia with axonal neuropathy type 3.
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Affiliation(s)
- Yujiro Higuchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Ryuta Okunushi
- Department of Applied Biology and The Center for Advanced Insect Research, Kyoto Institute of Technology, Japan
| | - Taichi Hara
- Laboratory of Cellular Regulation, Faculty of Human Sciences, Waseda University, Mikajima, Tokorozawa, Saitama 359-1192, Japan.,Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Akihiro Hashiguchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Junhui Yuan
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Kei Murayama
- Department of Metabolism, Chiba Children's Hospital, Chiba, Japan
| | - Akira Ohtake
- Department of Pediatrics, Faculty of Medicine, Saitama Medical University, Saitama, Japan.,Center for Intractable Diseases, Saitama Medical University Hospital, Saitama, Japan
| | - Masahiro Ando
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yu Hiramatsu
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Satoshi Ishihara
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Cardiovascular medicine, Nephrology and Neurology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hajime Tanabe
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuji Okamoto
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Takehiro Ueda
- Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tatsushi Toda
- Division of Neurology/Molecular Brain Science, Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | - Kenichiro Yamada
- Department of Pediatrics, Hiratsuka City Hospital, Hiratsuka City, Kanagawa, Japan
| | - Takashi Koide
- Department of Neurology, Hiratsuka City Hospital, Hiratsuka City, Kanagawa, Japan
| | - Hiroaki Yaguchi
- Department of Neurology, Brain Center, Sapporo City General Hospital, Sapporo, Hokkaido, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Ken Sato
- Laboratory of Molecular Traffic, Institute for Molecular and Cellular Regulation, Gunma University, Gunma, Japan
| | - Masanori Nakagawa
- Director of North Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masamitsu Yamaguchi
- Department of Applied Biology and The Center for Advanced Insect Research, Kyoto Institute of Technology, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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17
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Hashiguchi S, Doi H, Kunii M, Nakamura Y, Shimuta M, Suzuki E, Koyano S, Okubo M, Kishida H, Shiina M, Ogata K, Hirashima F, Inoue Y, Kubota S, Hayashi N, Nakamura H, Takahashi K, Katsumoto A, Tada M, Tanaka K, Sasaoka T, Miyatake S, Miyake N, Saitsu H, Sato N, Ozaki K, Ohta K, Yokota T, Mizusawa H, Mitsui J, Ishiura H, Yoshimura J, Morishita S, Tsuji S, Takeuchi H, Ishikawa K, Matsumoto N, Ishikawa T, Tanaka F. Ataxic phenotype with altered Ca V3.1 channel property in a mouse model for spinocerebellar ataxia 42. Neurobiol Dis 2019; 130:104516. [PMID: 31229688 DOI: 10.1016/j.nbd.2019.104516] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/06/2019] [Accepted: 06/19/2019] [Indexed: 11/16/2022] Open
Abstract
Spinocerebellar ataxia 42 (SCA42) is a neurodegenerative disorder recently shown to be caused by c.5144G > A (p.Arg1715His) mutation in CACNA1G, which encodes the T-type voltage-gated calcium channel CaV3.1. Here, we describe a large Japanese family with SCA42. Postmortem pathological examination revealed severe cerebellar degeneration with prominent Purkinje cell loss without ubiquitin accumulation in an SCA42 patient. To determine whether this mutation causes ataxic symptoms and neurodegeneration, we generated knock-in mice harboring c.5168G > A (p.Arg1723His) mutation in Cacna1g, corresponding to the mutation identified in the SCA42 family. Both heterozygous and homozygous mutants developed an ataxic phenotype from the age of 11-20 weeks and showed Purkinje cell loss at 50 weeks old. Degenerative change of Purkinje cells and atrophic thinning of the molecular layer were conspicuous in homozygous knock-in mice. Electrophysiological analysis of Purkinje cells using acute cerebellar slices from young mice showed that the point mutation altered the voltage dependence of CaV3.1 channel activation and reduced the rebound action potentials after hyperpolarization, although it did not significantly affect the basic properties of synaptic transmission onto Purkinje cells. Finally, we revealed that the resonance of membrane potential of neurons in the inferior olivary nucleus was decreased in knock-in mice, which indicates that p.Arg1723His CaV3.1 mutation affects climbing fiber signaling to Purkinje cells. Altogether, our study shows not only that a point mutation in CACNA1G causes an ataxic phenotype and Purkinje cell degeneration in a mouse model, but also that the electrophysiological abnormalities at an early stage of SCA42 precede Purkinje cell loss.
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Affiliation(s)
- Shunta Hashiguchi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hiroshi Doi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Misako Kunii
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Yukihiro Nakamura
- Department of Pharmacology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Misa Shimuta
- Department of Pharmacology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Etsuko Suzuki
- Department of Pharmacology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan
| | - Shigeru Koyano
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Masaki Okubo
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hitaru Kishida
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Masaaki Shiina
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Fumiko Hirashima
- Department of Rehabilitation Medicine, Flower and Forest Tokyo Hospital, 2-3-6 Nishigahara, Kita-ku, Tokyo 114-0024, Japan
| | - Yukichi Inoue
- Department of Neurology, Toyama Prefectural Rehabilitation Hospital and Support Center for Children with Disabilities, 36 Shimoiino, Toyama 931-8517, Japan
| | - Shun Kubota
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Noriko Hayashi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Haruko Nakamura
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Keita Takahashi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Atsuko Katsumoto
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Mikiko Tada
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kenichi Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Toshikuni Sasaoka
- Department of Comparative and Experimental Medicine, Center for Bioresource-based Researches, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Hirotomo Saitsu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Nozomu Sato
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Kokoro Ozaki
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Kiyobumi Ohta
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Takanori Yokota
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Hidehiro Mizusawa
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Jun Yoshimura
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Shinichi Morishita
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8655, Japan
| | - Hideyuki Takeuchi
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Kinya Ishikawa
- Department of Neurology and Neurological Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-0034, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan
| | - Taro Ishikawa
- Department of Pharmacology, The Jikei University School of Medicine, 3-25-8 Nishi-shinbashi, Minato-ku, Tokyo 105-8461, Japan.
| | - Fumiaki Tanaka
- Department of Neurology and Stroke Medicine, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan.
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18
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Yoshimura J, Ichikawa K, Shoura MJ, Artiles KL, Gabdank I, Wahba L, Smith CL, Edgley ML, Rougvie AE, Fire AZ, Morishita S, Schwarz EM. Recompleting the Caenorhabditis elegans genome. Genome Res 2019; 29:1009-1022. [PMID: 31123080 PMCID: PMC6581061 DOI: 10.1101/gr.244830.118] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 03/11/2019] [Indexed: 01/14/2023]
Abstract
Caenorhabditis elegans was the first multicellular eukaryotic genome sequenced to apparent completion. Although this assembly employed a standard C. elegans strain (N2), it used sequence data from several laboratories, with DNA propagated in bacteria and yeast. Thus, the N2 assembly has many differences from any C. elegans available today. To provide a more accurate C. elegans genome, we performed long-read assembly of VC2010, a modern strain derived from N2. Our VC2010 assembly has 99.98% identity to N2 but with an additional 1.8 Mb including tandem repeat expansions and genome duplications. For 116 structural discrepancies between N2 and VC2010, 97 structures matching VC2010 (84%) were also found in two outgroup strains, implying deficiencies in N2. Over 98% of N2 genes encoded unchanged products in VC2010; moreover, we predicted ≥53 new genes in VC2010. The recompleted genome of C. elegans should be a valuable resource for genetics, genomics, and systems biology.
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Affiliation(s)
- Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Massa J Shoura
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Idan Gabdank
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Lamia Wahba
- Department of Pathology, Stanford University, Stanford, California 94305, USA
| | - Cheryl L Smith
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Mark L Edgley
- Department of Zoology and Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z3, British Columbia, Canada
| | - Ann E Rougvie
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, Minnesota 55454, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University, Stanford, California 94305, USA.,Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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19
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Naruse H, Ishiura H, Mitsui J, Takahashi Y, Matsukawa T, Tanaka M, Doi K, Yoshimura J, Morishita S, Goto J, Toda T, Tsuji S. Burden of rare variants in causative genes for amyotrophic lateral sclerosis (ALS) accelerates age at onset of ALS. J Neurol Neurosurg Psychiatry 2019; 90:537-542. [PMID: 30355605 DOI: 10.1136/jnnp-2018-318568] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 07/30/2018] [Accepted: 09/26/2018] [Indexed: 12/13/2022]
Abstract
OBJECTIVES To evaluate the burden of rare variants in the causative genes for amyotrophic lateral sclerosis (ALS) on the age at onset of ALS in a Japanese case series. METHODS We conducted whole-exome sequencing analysis of 89 families with familial ALS (FALS) and 410 patients with sporadic ALS (SALS) to identify known pathogenic mutations or rare functionally predicted deleterious variants in the causative genes for ALS. Rare variants (minor allele frequency <1%) with scaled Combined Annotation-Dependent Depletion score >20 were defined as rare functionally predicted deleterious variants. The patients with ALS were classified on the basis of the number of pathogenic and/or rare functionally predicted deleterious variants, and the age at onset was compared among the classified groups. RESULTS Whole-exome sequencing analysis revealed known pathogenic mutations or rare functionally predicted deleterious variants in causative genes for ALS in 56 families with FALS (62.9%) and 87 patients with SALS (21.2%). Such variants in multiple genes were identified in seven probands with FALS and eight patients with SALS. The ages at onset in the patients with ALS with multiple variants were significantly earlier than those in other patients with ALS. Even when the patients with known pathogenic mutations were excluded, a significantly earlier onset of the disease was still observed in patients with multiple rare functionally predicted deleterious variants. CONCLUSIONS A substantial number of patients carried rare variants in multiple genes, and the burden of rare variants in the known causative genes for ALS affects the age at onset in the Japanese ALS series.
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Affiliation(s)
- Hiroya Naruse
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuji Takahashi
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takashi Matsukawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Tanaka
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Goto
- Department of Neurology, International University of Health and Welfare Mita Hospital, Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan .,Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
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20
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Ichinose Y, Ishiura H, Tanaka M, Yoshimura J, Doi K, Umeda T, Yamauchi H, Tsuchiya M, Koh K, Yamashiro N, Mitsui J, Goto J, Onishi H, Ohtsuka T, Shindo K, Morishita S, Tsuji S, Takiyama Y. Neuroimaging, genetic, and enzymatic study in a Japanese family with a GBA gross deletion. Parkinsonism Relat Disord 2018; 61:57-63. [PMID: 30528172 DOI: 10.1016/j.parkreldis.2018.11.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/19/2018] [Accepted: 11/29/2018] [Indexed: 11/24/2022]
Abstract
INTRODUCTION Glucocerebrosidase gene (GBA) variants are associated with Parkinson's disease (PD) and dementia with Lewy bodies (DLB). The molecular mechanisms underlying these diseases with GBA variants, however, are not well understood. In order to determine the effect of a deletion mutation in GBA, we performed a neuroimaging, genetic, and enzymatic study in a Japanese family with a gross deletion of exons 3 to 11 in GBA. METHODS We performed [123I] FP-CIT SPECT and [123I] N-isopropyl-p-iodoamphetamine SPECT (IMP-SPECT), and determined GBA expression and glucocerebrosidase (GCase) activity in leukocytes in two GBA-associated PD patients and nine unaffected individuals (including four mutation carriers) in a Japanese family with a heterozygous gross deletion mutation in the GBA gene. RESULTS The two PD patients and two of the four clinically unaffected carriers showed decreased [123I] FP-CIT uptake. IMP-SPECT showed a pattern like that in DLB in one patient. When we compared PD patients with GBA mutations with clinically unaffected carriers, there was a poor correlation between the development of PD and the expression level of GBA or GCase activity. CONCLUSION We confirmed the gross deletion mutation in the GBA gene, which appeared to be associated with the PD or reduced [123I] FP-CIT in this family. However, since we cannot conclude whether a reduction of GCase activity is directly correlated with the pathogenesis of PD or not, longitudinal follow-up of this family is needed.
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Affiliation(s)
- Yuta Ichinose
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | | | - Masaki Tanaka
- Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan
| | - Jun Yoshimura
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Koichiro Doi
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takako Umeda
- Department of Radiology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Hajime Yamauchi
- Department of Biochemistry, Graduate School of Medical Sciences, University Of Yamanashi, Yamanashi, Japan
| | - Mai Tsuchiya
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Kishin Koh
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Nobuo Yamashiro
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Jun Mitsui
- Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Goto
- Department of Neurology, Mita Hospital, International University of Health and Welfare, Tokyo, Japan
| | - Hiroshi Onishi
- Department of Radiology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Toshihisa Ohtsuka
- Department of Biochemistry, Graduate School of Medical Sciences, University Of Yamanashi, Yamanashi, Japan
| | - Kazumasa Shindo
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan
| | - Shinichi Morishita
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shoji Tsuji
- Institute of Medical Genomics, International University of Health and Welfare, Chiba, Japan; Department of Molecular Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshihisa Takiyama
- Department of Neurology, Graduate School of Medical Sciences, University of Yamanashi, Yamanashi, Japan.
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21
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Tohnai G, Nakamura R, Sone J, Nakatochi M, Yokoi D, Katsuno M, Watanabe H, Watanabe H, Ito M, Li Y, Izumi Y, Morita M, Taniguchi A, Kano O, Oda M, Kuwabara S, Abe K, Aiba I, Okamoto K, Mizoguchi K, Hasegawa K, Aoki M, Hattori N, Onodera O, Naruse H, Mitsui J, Takahashi Y, Goto J, Ishiura H, Morishita S, Yoshimura J, Doi K, Tsuji S, Nakashima K, Kaji R, Atsuta N, Sobue G. Frequency and characteristics of the TBK1 gene variants in Japanese patients with sporadic amyotrophic lateral sclerosis. Neurobiol Aging 2018; 64:158.e15-158.e19. [DOI: 10.1016/j.neurobiolaging.2017.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 10/24/2017] [Accepted: 12/04/2017] [Indexed: 12/12/2022]
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22
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Ichikawa K, Tomioka S, Suzuki Y, Nakamura R, Doi K, Yoshimura J, Kumagai M, Inoue Y, Uchida Y, Irie N, Takeda H, Morishita S. Centromere evolution and CpG methylation during vertebrate speciation. Nat Commun 2017. [PMID: 29184138 DOI: 10.1038/s41467-017-01982-7.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Centromeres and large-scale structural variants evolve and contribute to genome diversity during vertebrate speciation. Here, we perform de novo long-read genome assembly of three inbred medaka strains that are derived from geographically isolated subpopulations and undergo speciation. Using single-molecule real-time (SMRT) sequencing, we obtain three chromosome-mapped genomes of length ~734, ~678, and ~744Mbp with a resource of twenty-two centromeric regions of length 20-345kbp. Centromeres are positionally conserved among the three strains and even between four pairs of chromosomes that were duplicated by the teleost-specific whole-genome duplication 320-350 million years ago. The centromeres do not all evolve at a similar pace; rather, centromeric monomers in non-acrocentric chromosomes evolve significantly faster than those in acrocentric chromosomes. Using methylation sensitive SMRT reads, we uncover centromeres are mostly hypermethylated but have hypomethylated sub-regions that acquire unique sequence compositions independently. These findings reveal the potential of non-acrocentric centromere evolution to contribute to speciation.
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Affiliation(s)
- Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Shingo Tomioka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan
| | - Masahiko Kumagai
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yusuke Inoue
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Yui Uchida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Naoki Irie
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| | - Shinich Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba, 277-8583, Japan.
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23
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Hatano K, Ishiura H, Date H, Tanaka M, Mitsui J, Goto J, Yoshimura J, Doi K, Morishita S, Tsuji S. Search for target genes of transcriptional regulation by Dentatorubral-pallidoluysian atrophy protein that acts as a transcriptional co-regulator. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.220] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Naruse H, Ishiura H, Mitsui J, Takahashi Y, Doi K, Yoshimura J, Morishita S, Goto J, Tsuji S. Mutational analysis of sporadic amyotrophic lateral sclerosis (ALS) with loss of function mutations in ALS-related genes in the Japanese population. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.1602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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25
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Koh K, Ishiura H, Ichikawa Y, Matsukawa T, Goto J, Mitsui J, Takahashi Y, Kawabe Matsukawa M, Doi K, Yoshimura J, Namekawa M, Morishita S, Ogawa T, Sunada Y, Kurisaki H, Hasegawa K, Tsuji S, Takiyama Y. Clinical characteristics and detailed haplotype analysis of patients with SCA36 in Japan. J Neurol Sci 2017. [DOI: 10.1016/j.jns.2017.08.3298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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26
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Eriguchi Y, Kuwabara H, Inai A, Kawakubo Y, Nishimura F, Kakiuchi C, Tochigi M, Ohashi J, Aoki N, Kato K, Ishiura H, Mitsui J, Tsuji S, Doi K, Yoshimura J, Morishita S, Shimada T, Furukawa M, Umekage T, Sasaki T, Kasai K, KanoMD PhD Y. Identification of candidate genes involved in the etiology of sporadic Tourette syndrome by exome sequencing. Am J Med Genet B Neuropsychiatr Genet 2017; 174:712-723. [PMID: 28608572 DOI: 10.1002/ajmg.b.32559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 05/15/2017] [Indexed: 01/01/2023]
Abstract
Tourette Syndrome (TS) is a neurodevelopmental disorder characterized by chronic motor and vocal tics. Although there is a large genetic contribution, the genetic architecture of TS remains unclear. Exome sequencing has successfully revealed the contribution of de novo mutations in sporadic cases with neuropsychiatric disorders such as autism and schizophrenia. Here, using exome sequencing, we investigated de novo mutations in individuals with sporadic TS to identify novel risk loci and elucidate the genetic background of TS. Exome analysis was conducted for sporadic TS cases: nine trio families and one quartet family with concordant twins were investigated. Missense mutations were evaluated using functional prediction algorithms, and their population frequencies were calculated based on three public databases. Gene expression patterns in the brain were analyzed using the BrainSpan Developmental Transcriptome. Thirty de novo mutations, including four synonymous and four missense mutations, were identified. Among the missense mutations, one in the rapamycin-insensitive companion of mammalian target of rapamycin (RICTOR)-coding gene (rs140964083: G > A, found in one proband) was predicted to be hazardous. In the three public databases analyzed, variants in the same SNP locus were absent, and variants in the same gene were either absent or present at an extremely low frequency (3/5,008), indicating the rarity of hazardous RICTOR mutations in the general population. The de novo variant of RICTOR may be implicated in the development of sporadic TS, and RICTOR is a novel candidate factor for TS etiology.
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Affiliation(s)
- Yosuke Eriguchi
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Neuropsychiatry, Sakura Hospital, Aomori, Japan
| | - Hitoshi Kuwabara
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Disability Services Office, The University of Tokyo, Tokyo, Japan
| | - Aya Inai
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuki Kawakubo
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Chihiro Kakiuchi
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mamoru Tochigi
- Department of Neuropsychiatry, Teikyo University School of Medicine, Tokyo, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Naoto Aoki
- Department of Neuropsychiatry, Sakura Hospital, Aomori, Japan
| | - Kayoko Kato
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Medical Genome Center, The University of Tokyo Hospital, The University of Tokyo, Tokyo, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Takafumi Shimada
- Division for Counseling and Support, The University of Tokyo, Tokyo, Japan
| | - Masaomi Furukawa
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tadashi Umekage
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Department of Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko KanoMD PhD
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Naruse H, Ishiura H, Mitsui J, Date H, Takahashi Y, Matsukawa T, Tanaka M, Ishii A, Tamaoka A, Hokkoku K, Sonoo M, Segawa M, Ugawa Y, Doi K, Yoshimura J, Morishita S, Goto J, Tsuji S. Molecular epidemiological study of familial amyotrophic lateral sclerosis in Japanese population by whole-exome sequencing and identification of novel HNRNPA1 mutation. Neurobiol Aging 2017; 61:255.e9-255.e16. [PMID: 29033165 DOI: 10.1016/j.neurobiolaging.2017.08.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Revised: 08/27/2017] [Accepted: 08/30/2017] [Indexed: 12/13/2022]
Abstract
To elucidate the genetic epidemiology of familial amyotrophic lateral sclerosis (FALS) in the Japanese population, we conducted whole-exome sequencing analysis of 30 FALS families in whom causative mutations have not been identified in previous studies. Consequently, whole-exome sequencing analysis revealed novel mutations in HNRNPA1, TBK1, and VCP. Taken together with our previous results of mutational analyses by direct nucleotide sequencing analysis, a microarray-based resequencing method, or repeat-primed PCR analysis, causative mutations were identified in 41 of the 68 families (60.3%) with SOD1 being the most frequent cause of FALS (39.7%). Of the mutations identified in this study, a novel c.862/1018C>G (p.P288A/340A) mutation in HNRNPA1 located in the nuclear localization signal domain of hnRNPA1, enhances the recruitment of mutant hnRNPA1 into stress granules, indicating that an altered nuclear localization signal activity plays an essential role in amyotrophic lateral sclerosis pathogenesis.
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Affiliation(s)
- Hiroya Naruse
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hidetoshi Date
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuji Takahashi
- Department of Neurology, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takashi Matsukawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Tanaka
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akiko Ishii
- Department of Neurology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Akira Tamaoka
- Department of Neurology, Faculty of Medicine, University of Tsukuba, Ibaraki, Japan
| | - Keiichi Hokkoku
- Department of Neurology, Teikyo University School of Medicine, Tokyo, Japan
| | - Masahiro Sonoo
- Department of Neurology, Teikyo University School of Medicine, Tokyo, Japan
| | - Mari Segawa
- Department of Neurology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Yoshikazu Ugawa
- Department of Neurology, School of Medicine, Fukushima Medical University, Fukushima, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Jun Goto
- Department of Neurology, International University of Health and Welfare Mita Hospital, Tokyo, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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28
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Kawazu M, Kojima S, Ueno T, Totoki Y, Nakamura H, Kunita A, Qu W, Yoshimura J, Soda M, Yasuda T, Hama N, Saito-Adachi M, Sato K, Kohsaka S, Sai E, Ikemura M, Yamamoto S, Ogawa T, Fukayama M, Tada K, Seto Y, Morishita S, Hazama S, Shibata T, Yamashita Y, Mano H. Integrative analysis of genomic alterations in triple-negative breast cancer in association with homologous recombination deficiency. PLoS Genet 2017. [PMID: 28636652 PMCID: PMC5500377 DOI: 10.1371/journal.pgen.1006853] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Triple-negative breast cancer (TNBC) cells do not express estrogen receptors, progesterone receptors, or human epidermal growth factor receptor 2. Currently, apart from poly ADP-ribose polymerase inhibitors, there are few effective therapeutic options for this type of cancer. Here, we present comprehensive characterization of the genetic alterations in TNBC performed by high coverage whole genome sequencing together with transcriptome and whole exome sequencing. Silencing of the BRCA1 gene impaired the homologous recombination pathway in a subset of TNBCs, which exhibited similar phenotypes to tumors with BRCA1 mutations; they harbored many structural variations (SVs) with relative enrichment for tandem duplication. Clonal analysis suggested that TP53 mutations and methylation of CpG dinucleotides in the BRCA1 promoter were early events of carcinogenesis. SVs were associated with driver oncogenic events such as amplification of MYC, NOTCH2, or NOTCH3 and affected tumor suppressor genes including RB1, PTEN, and KMT2C. Furthermore, we identified putative TGFA enhancer regions. Recurrent SVs that affected the TGFA enhancer region led to enhanced expression of the TGFA oncogene that encodes one of the high affinity ligands for epidermal growth factor receptor. We also identified a variety of oncogenes that could transform 3T3 mouse fibroblasts, suggesting that individual TNBC tumors may undergo a unique driver event that can be targetable. Thus, we revealed several features of TNBC with clinically important implications. Cancer can result from genetic alterations, some of which can be good drug targets. To reveal genetic alterations that provide important information for the development of ideal therapeutic strategies for triple-negative breast cancer (TNBC), TNBC tumor samples were subjected to comprehensive genomic analyses. We identified novel recurrent structural variations associated with enhanced expression of the TGFA gene that encodes one of the high affinity ligands for epidermal growth factor receptor (EGFR). Although TGFA expression is known to be elevated in a subset of TNBC tumors, this is the first report of the mechanistic basis of this phenomenon. It is of particular importance considering that anti-EGFR agents are possible therapeutic options for TNBC patients. Our study also revealed several features associated with “BRCAness”, which is critical for identification of patients who may be responsive to platinum agents and/or poly ADP-ribose polymerase inhibitors. Thus, the data presented in this report may advance our understanding of the pathogenesis of TNBC.
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Affiliation(s)
- Masahito Kawazu
- Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- * E-mail:
| | - Shinya Kojima
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshihide Ueno
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akiko Kunita
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Manabu Soda
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiko Yasuda
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Mihoko Saito-Adachi
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kazuhito Sato
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinji Kohsaka
- Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eirin Sai
- Department of Medical Genomics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masako Ikemura
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shigeru Yamamoto
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Tomoko Ogawa
- Department of Breast Surgery, Mie University Hospital, Mie, Japan
| | - Masashi Fukayama
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiichiro Tada
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyuki Seto
- Department of Breast and Endocrine Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shoichi Hazama
- Department of Gastroenterological, Breast and Endocrine Surgery, Yamaguchi University Graduate School of Medicine, Yamaguchi, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yoshihiro Yamashita
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Mano
- Department of Cellular Signaling, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- National Cancer Center Research Institute, Tokyo, Japan
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29
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Von Seth M, Hillered L, Otterbeck A, Hanslin K, Larsson A, Sjölin J, Lipcsey M, Cove ME, Chew NS, Vu LH, Lim RZ, Puthucheary Z, Hanslin K, Wilske F, Skorup P, Tano E, Sjölin J, Lipcsey M, Derese I, Thiessen S, Derde S, Dufour T, Pauwels L, Bekhuis Y, Van den Berghe G, Vanhorebeek I, Khan M, Dwivedi D, Zhou J, Prat A, Seidah NG, Liaw PC, Fox-Robichaud AE, Von Seth M, Skorup P, Hillered L, Larsson A, Sjölin J, Lipcsey M, Otterbeck A, Hanslin K, Lipcsey M, Larsson A, Von Seth M, Correa T, Pereira J, Takala J, Jakob S, Skorup P, Maudsdotter L, Tano E, Lipcsey M, Castegren M, Larsson A, Sjölin J, Xue M, Xu JY, Liu L, Huang YZ, Guo FM, Yang Y, Qiu HB, Kuzovlev A, Moroz V, Goloubev A, Myazin A, Chumachenko A, Pisarev V, Takeyama N, Tsuda M, Kanou H, Aoki R, Kajita Y, Hashiba M, Terashima T, Tomino A, Davies R, O’Dea KP, Soni S, Ward JK, O’Callaghan DJ, Takata M, Gordon AC, Wilson J, Zhao Y, Singer M, Spencer J, Shankar-Hari M, Genga KR, Lo C, Cirstea MS, Walley KR, Russell JA, Linder A, Boyd JH, Sedlag A, Riedel C, Georgieff M, Barth E, Debain A, Jonckheer J, Moeyersons W, Van zwam K, Puis L, Staessens K, Honoré PM, Spapen HD, De Waele E, de Garibay APR, Bracht H, Ende-Schneider B, Schreiber C, Kreymann B, Bini A, Votino E, Giuliano G, Steinberg I, Vetrugno L, Trunfio D, Sidoti A, Essig A, Brogi E, Forfori F, Conroy M, Marsh B, O’Flynn J, Henne-Bruns D, Gebhard F, Orend K, Halatsch M, Weiss M, Chase M, Freinkman E, Uber A, Liu X, Cocchi MN, Donnino MW, Peetermans M, Liesenborghs L, Claes J, Vanassche T, Hoylaerts M, Jacquemin M, Vanhoorelbeke K, De Meyer S, Verhamme P, Vögeli A, Ottiger M, Meier M, Steuer C, Bernasconi L, Huber A, Christ-Crain M, Henzen C, Hoess C, Thomann R, Zimmerli W, Müller B, Schütz P, Hoppensteadt D, Walborn A, Rondina M, Tsuruta K, Fareed J, Tachyla S, Ikeda T, Ono S, Ueno T, Suda S, Nagura T, Damiani E, Domizi R, Scorcella C, Tondi S, Pierantozzi S, Ciucani S, Mininno N, Adrario E, Pelaia P, Donati A, Andersen MS, Lu S, Lopez G, Lassen AT, Ghiran I, Shapiro NI, Trahtemberg U, Sviri S, Beil M, Agur Z, Van Heerden P, Jahaj E, Vassiliou A, Mastora Z, Orfanos SE, Kotanidou A, Wirz Y, Sager R, Amin D, Amin A, Haubitz S, Hausfater P, Huber A, Kutz A, Mueller B, Schuetz P, Sager RS, Wirz YW, Amin DA, Amin AA, Hausfater PH, Huber AH, Haubitz S, Kutz A, Mueller B, Schuetz P, Gottin L, Dell’amore C, Stringari G, Cogo G, Ceolagraziadei M, Sommavilla M, Soldani F, Polati E, Meier M, Baumgartner T, Zurauskaité G, Gupta S, Mueller B, Devendra A, Schuetz P, Mandaci D, Eren G, Ozturk F, Emir N, Hergunsel O, Azaiez S, Khedher S, Maaoui A, Salem M, Chernevskaya E, Beloborodova N, Bedova A, Sarshor YU, Pautova A, Gusarov V, Öveges N, László I, Forgács M, Kiss T, Hankovszky P, Palágyi P, Bebes A, Gubán B, Földesi I, Araczki Á, Telkes M, Ondrik Z, Helyes Z, Kemény Á, Molnár Z, Spanuth E, Ebelt H, Ivandic B, Thomae R, Werdan K, El-Shafie M, Taema K, El-Hallag M, Kandeel A, Tayeh O, Taema K, Eldesouky M, Omara A, Winkler MS, Holzmann M, Nierhaus A, Mudersbach E, Schwedhelm E, Daum G, Kluge S, Zoellner C, Greiwe G, Sawari H, Schwedhelm E, Nierhaus A, Kluge S, Kubitz J, Jung R, Daum G, Reichenspurner H, Zoellner C, Winkler MS, Groznik M, Ihan A, Andersen LW, Chase M, Holmberg MJ, Wulff A, Cocchi MN, Donnino MW, Balci C, Haliloglu M, Bilgili B, Bilgin H, Kasapoglu U, Sayan I, Süzer M, Mulazımoglu L, Cinel I, Patel V, Shah S, Parulekar P, Minton C, Patel J, Ejimofo C, Choi H, Costa R, Caruso P, Nassar P, Fu J, Jin J, Xu Y, Kong J, Wu D, Yaguchi A, Klonis A, Ganguly S, Kollef M, Burnham C, Fuller B, Mavrommati A, Chatzilia D, Salla E, Papadaki E, Kamariotis S, Christodoulatos S, Stylianakis A, Alamanos G, Simoes M, Trigo E, Silva N, Martins P, Pimentel J, Baily D, Curran LA, Ahmadnia E, Patel BV, Adukauskiene D, Cyziute J, Adukauskaite A, Pentiokiniene D, Righetti F, Colombaroli E, Castellano G, Wilske F, Skorup P, Lipcsey M, Hanslin K, Larsson A, Sjölin J, Man M, Shum HP, Chan YH, Chan KC, Yan WW, Lee RA, Lau SK, Dilokpattanamongkol P, Thirapakpoomanunt P, Anakkamaetee R, Montakantikul P, Tangsujaritvijit V, Sinha S, Pati J, Sahu S, Adukauskiene D, Valanciene D, Dambrauskiene A, Adukauskiene D, Valanciene D, Dambrauskiene A, Hernandez K, Lopez T, Saca D, Bello M, Mahmood W, Hamed K, Al Badi N, AlThawadi S, Al Hosaini S, Salahuddin N, Cilloniz CC, Ceccato AC, Bassi GLL, Ferrer MF, Gabarrus AG, Ranzani OR, Jose ASS, Vidal CGG, de la Bella Casa JPP, Blasi FB, Torres AT, Adukauskiene D, Ciginskiene A, Dambrauskiene A, Simoliuniene R, Giuliano G, Triunfio D, Sozio E, Taddei E, Brogi E, Sbrana F, Ripoli A, Bertolino G, Tascini C, Forfori F, Fleischmann C, Goldfarb D, Schlattmann P, Schlapbach L, Kissoon N, Baykara N, Akalin H, Arslantas MK, Gavrilovic SG, Vukoja MV, Hache MH, Kashyap RK, Dong YD, Gajic OG, Ranzani O, Shankar-Hari M, Harrison D, Rabello L, Rowan K, Salluh J, Soares M, Markota AM, Fluher JF, Kogler DK, Borovšak ZB, Sinkovic AS, László I, Öveges N, Forgács M, Kiss T, Hankovszky P, Palágyi P, Bebes A, Gubán B, Földesi I, Araczki Á, Telkes M, Ondrik Z, Helyes Z, Kemény Á, Molnár Z, Fareed J, Siddiqui Z, Aggarwal P, Iqbal O, Hoppensteadt D, Lewis M, Wasmund R, Abro S, Raghuvir S, Tsuruta K, Barie PS, Fineberg D, Radford A, Tsuruta K, Casazza A, Vilardo A, Bellazzi E, Boschi R, Ciprandi D, Gigliuto C, Preda R, Vanzino R, Vetere M, Carnevale L, Kyriazopoulou E, Pistiki A, Routsi C, Tsangaris I, Giamarellos-Bourboulis E, Kyriazopoulou E, Tsangaris I, Routsi C, Pnevmatikos I, Vlachogiannis G, Antoniadou E, Mandragos K, Armaganidis A, Giamarellos-Bourboulis E, Allan P, Oehmen R, Luo J, Ellis C, Latham P, Newman J, Pritchett C, Pandya D, Cripps A, Harris S, Jadav M, Langford R, Ko B, Park H, Beumer CM, Koch R, Beuningen DV, Oudelashof AM, Vd Veerdonk FL, Kolwijck E, VanderHoeven JG, Bergmans DC, Hoedemaekers C, Brandt JB, Golej J, Burda G, Mostafa G, Schneider A, Vargha R, Hermon M, Levin P, Broyer C, Assous M, Wiener-Well Y, Dahan M, Benenson S, Ben-Chetrit E, Faux A, Sherazi R, Sethi A, Saha S, Kiselevskiy M, Gromova E, Loginov S, Tchikileva I, Dolzhikova Y, Krotenko N, Vlasenko R, Anisimova N, Spadaro S, Fogagnolo A, Remelli F, Alvisi V, Romanello A, Marangoni E, Volta C, Degrassi A, Mearelli F, Casarsa C, Fiotti N, Biolo G, Cariqueo M, Luengo C, Galvez R, Romero C, Cornejo R, Llanos O, Estuardo N, Alarcon P, Magazi B, Khan S, Pasipanodya J, Eriksson M, Strandberg G, Lipsey M, Larsson A, Rajput Z, Hiscock F, Karadag T, Uwagwu J, Jain S, Molokhia A, Barrasa H, Soraluce A, Uson E, Rodriguez A, Isla A, Martin A, Fernández B, Fonseca F, Sánchez-Izquierdo JA, Maynar FJ, Kaffarnik M, Alraish R, Frey O, Roehr A, Stockmann M, Wicha S, Shortridge D, Castanheira M, Sader HS, Streit JM, Flamm RK, Falsetta K, Lam T, Reidt S, Jancik J, Kinoshita T, Yoshimura J, Yamakawa K, Fujimi S, Armaganidis A, Torres A, Zakynthinos S, Mandragos C, Giamarellos-Bourboulis E, Ramirez P, De la Torre-Prados M, Rodriguez A, Dale G, Wach A, Beni L, Hooftman L, Zwingelstein C, François B, Colin G, Dequin PF, Laterre PF, Perez A, Welte R, Lorenz I, Eller P, Joannidis M, Bellmann R, Lim S, Chana S, Patel S, Higuera J, Cabestrero D, Rey L, Narváez G, Blandino A, Aroca M, Saéz S, De Pablo R, Thiessen S, Vanhorebeek I, Derde S, Derese I, Dufour T, Albert CN, Langouche L, Goossens C, Peersman N, Vermeersch P, Vander Perre S, Holst J, Wouters P, Van den Berghe G, Liu X, Uber AU, Holmberg M, Konanki V, McNaughton M, Zhang J, Donnino MW, Demirkiran O, Byelyalov A, Luengo C, Guerrero J, Cariqueo M, Scorcella C, Domizi R, Damiani E, Tondi S, Pierantozzi S, Rossini N, Falanga U, Monaldi V, Adrario E, Pelaia P, Donati A, Cole O, Scawn N, Balciunas M, Blascovics I, Vuylsteke A, Salaunkey K, Omar A, Salama A, Allam M, Alkhulaifi A, Verstraete S, Vanhorebeek I, Van Puffelen E, Derese I, Ingels C, Verbruggen S, Wouters P, Joosten K, Hanot J, Guerra G, Vlasselaers D, Lin J, Van den Berghe G, Haines R, Zolfaghari P, Hewson R, Offiah C, Prowle J, Park H, Ko B, Buter H, Veenstra JA, Koopmans M, Boerma EC, Veenstra JA, Buter H, Koopmans M, Boerma EC, Taha A, Shafie A, Hallaj S, Gharaibeh D, Hon H, Bizrane M, El Khattate AA, Madani N, Abouqal R, Belayachi J, Kongpolprom N, Sanguanwong N, Sanaie S, Mahmoodpoor A, Hamishehkar H, Biderman P, Van Heerden P, Avitzur Y, Solomon S, Iakobishvili Z, Carmi U, Gorfil D, Singer P, Paisley C, Patrick-Heselton J, Mogk M, Humphreys J, Welters I, Pierantozzi S, Scorcella C, Domizi R, Damiani E, Tondi S, Casarotta E, Bolognini S, Adrario E, Pelaia P, Donati A, Holmberg MJ, Moskowitz A, Patel P, Grossestreuer A, Uber A, Andersen LW, Donnino MW, Malinverni S, Goedeme D, Mols P, Langlois PL, Szwec C, D’Aragon F, Heyland DK, Manzanares W, Manzanares W, Szwec C, Langlois P, Aramendi I, Heyland D, Stankovic N, Nadler J, Uber A, Holmberg M, Sanchez L, Wolfe R, Chase M, Donnino M, Cocchi M, Atalan HK, Gucyetmez B, Kavlak ME, Aslan S, Kargi A, Yazici S, Donmez R, Polat KY, Piechota M, Piechota A, Misztal M, Bernas S, Pietraszek-Grzywaczewska I, Saleh M, Hamdy A, Hamdy A, Elhallag M, Atar F, Kundakci A, Gedik E, Sahinturk H, Zeyneloglu P, Pirat A, Popescu M, Tomescu D, Van Gassel R, Baggerman M, Schaap F, Bol M, Nicolaes G, Beurskens D, Damink SO, Van de Poll M, Horibe M, Sasaki M, Sanui M, Iwasaki E, Sawano H, Goto T, Ikeura T, Hamada T, Oda T, Mayumi T, Kanai T, Kjøsen G, Horneland R, Rydenfelt K, Aandahl E, Tønnessen T, Haugaa H, Lockett P, Evans L, Somerset L, Ker-Reid F, Laver S, Courtney E, Dalton S, Georgiou A, Robinson K, Lam T, Haas B, Reidt S, Bartlett K, Jancik J, Bigwood M, Hanley R, Morgan P, Marouli D, Chatzimichali A, Kolyvaki S, Panteli A, Diamantaki E, Pediaditis E, Sirogianni P, Ginos P, Kondili E, Georgopoulos D, Askitopoulou H, Zampieri FG, Liborio AB, Besen BA, Cavalcanti AB, Dominedò C, Dell’Anna AM, Monayer A, Grieco DL, Barelli R, Cutuli SL, Maddalena AI, Picconi E, Sonnino C, Sandroni C, Antonelli M, Gucyetmez B, Atalan HK, Tuzuner F, Cakar N, Jacob M, Sahu S, Singh YP, Mehta Y, Yang KY, Kuo S, Rai V, Cheng T, Ertmer C, Czempik P, Hutchings S, Watts S, Wilson C, Burton C, Kirkman E, Drennan D, O’Prey A, MacKay A, Forrest R, Oglinda A, Ciobanu G, Casian M, Oglinda C, Lun CT, Yuen HJ, Ng G, Leung A, So SO, Chan HS, Lai KY, Sanguanwit P, Charoensuk W, Phakdeekitcharoen B, Batres-Baires G, Kammerzell I, Lahmer T, Mayr U, Schmid R, Huber W, Spanuth E, Bomberg H, Klingele M, Thomae R, Groesdonk H, Bernas S, Piechota M, Mirkiewicz K, Pérez AG, Silva J, Ramos A, Acharta F, Perezlindo M, Lovesio L, Antonelli PG, Dogliotti A, Lovesio C, Baron J, Schiefer J, Baron DM, Faybik P, Shum HP, Yan WW, Chan TM, Marouli D, Chatzimichali A, Kolyvaki S, Panteli A, Diamantaki E, Pediaditis E, Sirogianni P, Ginos P, Kondili E, Georgopoulos D, Askitopoulou H, Vicka V, Gineityte D, Ringaitiene D, Sipylaite J, Pekarskiene J, Beurskens DM, Van Smaalen TC, Hoogland P, Winkens B, Christiaans MH, Reutelingsperger CP, Van Heurn E, Nicolaes GA, Schmitt FS, Salgado ES, Friebe JF, Fleming TF, Zemva JZ, Schmoch TS, Uhle FU, Kihm LK, Morath CM, Nusshag CN, Zeier MZ, Bruckner TB, Mehrabi AM, Nawroth PN, Weigand MW, Hofer SH, Brenner TB, Fotopoulou G, Poularas I, Kokkoris S, Brountzos E, Zakynthinos S, Routsi C, Saleh M, Elghonemi M, Nilsson KF, Sandin J, Gustafsson L, Frithiof R, Skorniakov I, Varaksin A, Vikulova D, Shaikh O, Whiteley C, Ostermann M, Di Lascio G, Anicetti L, Bonizzoli M, Fulceri G, Migliaccio ML, Sentina P, Cozzolino M, Peris A, Khadzhynov D, Halleck F, Staeck O, Lehner L, Budde K, Slowinski T, Slowinski T, Kindgen-Milles D, Khadzhynov D, Huysmans N, Laenen MV, Helmschrodt A, Boer W. 37th International Symposium on Intensive Care and Emergency Medicine (part 3 of 3). Crit Care 2017. [PMCID: PMC5374592 DOI: 10.1186/s13054-017-1629-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Yamashita T, Mitsui J, Shimozawa N, Takashima S, Umemura H, Sato K, Takemoto M, Hishikawa N, Ohta Y, Matsukawa T, Ishiura H, Yoshimura J, Doi K, Morishita S, Tsuji S, Abe K. Ataxic form of autosomal recessive PEX10-related peroxisome biogenesis disorders with a novel compound heterozygous gene mutation and characteristic clinical phenotype. J Neurol Sci 2017; 375:424-429. [PMID: 28320181 DOI: 10.1016/j.jns.2017.02.058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2016] [Revised: 02/23/2017] [Accepted: 02/24/2017] [Indexed: 11/30/2022]
Abstract
Peroxisome biogenesis factor 10 (PEX10) is involved in the import of peroxisomal matrix proteins, and the mutation of this gene causes 3 subtypes of peroxisome biogenesis disorders, namely Zellweger syndrome (severe), neonatal adrenoleukodystrophy (moderate) and an ataxic form (mild). Here, we report 3 siblings of the ataxic form with cerebellar ataxia, mild mental retardation, and 3 additional characteristic features: mydriasis, hyperreflexia and involuntary head movement. All 3 siblings are compound heterozygous for a previously reported mutation, c.2T>C (p.M1T), and a novel mutation, c.920G>A, causing a missense change (p.C307Y) located in the RING finger domain of PEX10. The present cases suggest that these PEX10 mutations involve not only cerebellar but also more multiple nervous systems including pupillary autonomic, pyramidal and extrapyramidal systems.
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Affiliation(s)
- Toru Yamashita
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8655, Japan
| | - Nobuyuki Shimozawa
- Division of Genomic Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Shigeo Takashima
- Division of Genomic Research, Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Hiroshi Umemura
- Department of Dermatology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Kota Sato
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Mami Takemoto
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Nozomi Hishikawa
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Yasuyuki Ohta
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan
| | - Takashi Matsukawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8655, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-8655, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-8655, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-8655, Japan
| | - Koji Abe
- Department of Neurology, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikatacho, Okayama 700-8558, Japan..
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Matsukawa T, Koshi KM, Mitsui J, Bannai T, Kawabe M, Ishiura H, Terao Y, Shimizu J, Murayama K, Yoshimura J, Doi K, Morishita S, Tsuji S, Goto J. Slowly progressive d -bifunctional protein deficiency with survival to adulthood diagnosed by whole-exome sequencing. J Neurol Sci 2017; 372:6-10. [DOI: 10.1016/j.jns.2016.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 11/05/2016] [Accepted: 11/07/2016] [Indexed: 10/20/2022]
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Fujimori K, Tezuka T, Ishiura H, Mitsui J, Doi K, Yoshimura J, Tada H, Matsumoto T, Isoda M, Hashimoto R, Hattori N, Takahashi T, Morishita S, Tsuji S, Akamatsu W, Okano H. Modeling neurological diseases with induced pluripotent cells reprogrammed from immortalized lymphoblastoid cell lines. Mol Brain 2016; 9:88. [PMID: 27716287 PMCID: PMC5046991 DOI: 10.1186/s13041-016-0267-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/20/2016] [Indexed: 12/28/2022] Open
Abstract
Patient-specific induced pluripotent stem cells (iPSCs) facilitate understanding of the etiology of diseases, discovery of new drugs and development of novel therapeutic interventions. A frequently used starting source of cells for generating iPSCs has been dermal fibroblasts (DFs) isolated from skin biopsies. However, there are also numerous repositories containing lymphoblastoid B-cell lines (LCLs) generated from a variety of patients. To date, this rich bioresource of LCLs has been underused for generating iPSCs, and its use would greatly expand the range of targeted diseases that could be studied by using patient-specific iPSCs. However, it remains unclear whether patient’s LCL-derived iPSCs (LiPSCs) can function as a disease model. Therefore, we generated Parkinson’s disease patient-specific LiPSCs and evaluated their utility as tools for modeling neurological diseases. We established iPSCs from two LCL clones, which were derived from a healthy donor and a patient carrying PARK2 mutations, by using existing non-integrating episomal protocols. Whole genome sequencing (WGS) and comparative genomic hybridization (CGH) analyses showed that the appearance of somatic variations in the genomes of the iPSCs did not vary substantially according to the original cell types (LCLs, T-cells and fibroblasts). Furthermore, LiPSCs could be differentiated into functional neurons by using the direct neurosphere conversion method (dNS method), and they showed several Parkinson’s disease phenotypes that were similar to those of DF-iPSCs. These data indicate that the global LCL repositories can be used as a resource for generating iPSCs and disease models. Thus, LCLs are the powerful tools for generating iPSCs and modeling neurological diseases.
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Affiliation(s)
- Koki Fujimori
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Toshiki Tezuka
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan
| | - Hirobumi Tada
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan.,Department of Integrative Aging Neuroscience, Section of Neuroendocrinology, National Center for Geriatrics and Gerontology, Obu, Aichi, 474-8511, Japan
| | - Takuya Matsumoto
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.,Institute for Innovation, Ajinomoto Co., Inc., Kawasaki-ku, Kanagawa, 210-8681, Japan
| | - Miho Isoda
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan
| | - Ryota Hashimoto
- Molecular Research Center for Children's Mental Development, United Graduate School of Child Development, Osaka University, Suita-shi, Osaka, 565-0871, Japan.,Department of Psychiatry, Osaka University Graduate School of Medicine, Suita-shi, Osaka, 565-0871, Japan
| | - Nubutaka Hattori
- Department of Neurology, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan
| | - Takuya Takahashi
- Department of Physiology, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Kanagawa, 236-0027, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8655, Japan.,Medical Genome Center, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Wado Akamatsu
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan. .,Center for Genomic and Regenerative Medicine, Juntendo University, School of Medicine, Bunkyo-ku, Tokyo, 113-8431, Japan.
| | - Hideyuki Okano
- Department of Physiology, Keio University, School of Medicine, Shinjuku-ku, Tokyo, 160-8582, Japan.
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Suzuki Y, Korlach J, Turner SW, Tsukahara T, Taniguchi J, Qu W, Ichikawa K, Yoshimura J, Yurino H, Takahashi Y, Mitsui J, Ishiura H, Tsuji S, Takeda H, Morishita S. AgIn: measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics 2016; 32:2911-9. [PMID: 27318202 PMCID: PMC5039925 DOI: 10.1093/bioinformatics/btw360] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/03/2016] [Indexed: 12/18/2022] Open
Abstract
Motivation: Determining the methylation state of regions with high copy numbers is challenging for second-generation sequencing, because the read length is insufficient to map reads uniquely, especially when repetitive regions are long and nearly identical to each other. Single-molecule real-time (SMRT) sequencing is a promising method for observing such regions, because it is not vulnerable to GC bias, it produces long read lengths, and its kinetic information is sensitive to DNA modifications. Results: We propose a novel linear-time algorithm that combines the kinetic information for neighboring CpG sites and increases the confidence in identifying the methylation states of those sites. Using a practical read coverage of ∼30-fold from an inbred strain medaka (Oryzias latipes), we observed that both the sensitivity and precision of our method on individual CpG sites were ∼93.7%. We also observed a high correlation coefficient (R = 0.884) between our method and bisulfite sequencing, and for 92.0% of CpG sites, methylation levels ranging over [0,1] were in concordance within an acceptable difference 0.25. Using this method, we characterized the landscape of the methylation status of repetitive elements, such as LINEs, in the human genome, thereby revealing the strong correlation between CpG density and hypomethylation and detecting hypomethylation hot spots of LTRs and LINEs. We uncovered the methylation states for nearly identical active transposons, two novel LINE insertions of identity ∼99% and length 6050 base pairs (bp) in the human genome, and 16 Tol2 elements of identity >99.8% and length 4682 bp in the medaka genome. Availability and Implementation: AgIn (Aggregate on Intervals) is available at: https://github.com/hacone/AgIn Contact:ysuzuki@cb.k.u-tokyo.ac.jp or moris@cb.k.u-tokyo.ac.jp Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yuta Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | | | | | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Junko Taniguchi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Kazuki Ichikawa
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Hideaki Yurino
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
| | - Yuji Takahashi
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-8655, Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8583, Japan
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Higuchi Y, Hashiguchi A, Yuan J, Yoshimura A, Mitsui J, Ishiura H, Tanaka M, Ishihara S, Tanabe H, Nozuma S, Okamoto Y, Matsuura E, Ohkubo R, Inamizu S, Shiraishi W, Yamasaki R, Ohyagi Y, Kira JI, Oya Y, Yabe H, Nishikawa N, Tobisawa S, Matsuda N, Masuda M, Kugimoto C, Fukushima K, Yano S, Yoshimura J, Doi K, Nakagawa M, Morishita S, Tsuji S, Takashima H. Mutations in MME cause an autosomal-recessive Charcot-Marie-Tooth disease type 2. Ann Neurol 2016; 79:659-72. [PMID: 26991897 PMCID: PMC5069600 DOI: 10.1002/ana.24612] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 01/16/2016] [Accepted: 02/03/2016] [Indexed: 01/12/2023]
Abstract
Objective The objective of this study was to identify new causes of Charcot–Marie–Tooth (CMT) disease in patients with autosomal‐recessive (AR) CMT. Methods To efficiently identify novel causative genes for AR‐CMT, we analyzed 303 unrelated Japanese patients with CMT using whole‐exome sequencing and extracted recessive variants/genes shared among multiple patients. We performed mutation screening of the newly identified membrane metalloendopeptidase (MME) gene in 354 additional patients with CMT. We clinically, genetically, pathologically, and radiologically examined 10 patients with the MME mutation. Results We identified recessive mutations in MME in 10 patients. The MME gene encodes neprilysin (NEP), which is well known to be one of the most prominent beta‐amyloid (Aβ)‐degrading enzymes. All patients had a similar phenotype consistent with late‐onset axonal neuropathy. They showed muscle weakness, atrophy, and sensory disturbance in the lower extremities. All the MME mutations could be loss‐of‐function mutations, and we confirmed a lack/decrease of NEP protein expression in a peripheral nerve. No patients showed symptoms of dementia, and 1 patient showed no excess Aβ in Pittsburgh compound‐B positron emission tomography imaging. Interpretation Our results indicate that loss‐of‐function MME mutations are the most frequent cause of adult‐onset AR‐CMT2 in Japan, and we propose that this new disease should be termed AR‐CMT2T. A loss‐of‐function MME mutation did not cause early‐onset Alzheimer's disease. Identifying the MME mutation responsible for AR‐CMT could improve the rate of molecular diagnosis and the understanding of the molecular mechanisms of CMT. Ann Neurol 2016;79:659–672
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Affiliation(s)
- Yujiro Higuchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akihiro Hashiguchi
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Junhui Yuan
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Akiko Yoshimura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Ishiura
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Tanaka
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Satoshi Ishihara
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Cardiovascular medicine, Nephrology and Neurology, Graduate School of Medicine, University of the Ryukyus, Okinawa, Japan
| | - Hajime Tanabe
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Satoshi Nozuma
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Yuji Okamoto
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Eiji Matsuura
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
| | - Ryuichi Ohkubo
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan.,Department of Neurology, Fujimoto General Hospital, Miyazaki, Japan
| | - Saeko Inamizu
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Wataru Shiraishi
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Ryo Yamasaki
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasumasa Ohyagi
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Jun-ichi Kira
- Department of Neurology, Neurological Institute, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yasushi Oya
- Department of Neurology, National Center Hospital, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Hayato Yabe
- Department of Neurology and Clinical Pharmacology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Noriko Nishikawa
- Department of Neurology and Clinical Pharmacology, Ehime University Graduate School of Medicine, Ehime, Japan
| | - Shinsuke Tobisawa
- Department of Neurology, Tokyo Metropolitan Neurological Hospital, Tokyo, Japan
| | - Nozomu Matsuda
- Department of Neurology, Fukushima Medical University, Fukushima, Japan
| | - Masayuki Masuda
- Department of Neurology, Tokyo Medical University, Tokyo, Japan
| | - Chiharu Kugimoto
- Department of Neurology and Stroke Medicine, Yokohama City University, Yokohama, Japan
| | - Kazuhiro Fukushima
- Department of Home-Care Promotion, Shinshu University School of Medicine, Matsumoto, Japan
| | - Satoshi Yano
- Department of Neurology, Showa University School of Medicine, Tokyo, Japan
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Koichiro Doi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masanori Nakagawa
- Director of North Medical Center, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Shoji Tsuji
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Takashima
- Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences, Kagoshima, Japan
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Mano KK, Matsukawa T, Mitsui J, Ishiura H, Tokushige SI, Takahashi Y, Sato NS, Nakamoto FK, Ichikawa Y, Nagashima Y, Terao Y, Shimizu J, Hamada M, Uesaka Y, Oyama G, Ogawa G, Yoshimura J, Doi K, Morishita S, Tsuji S, Goto J. Atypical parkinsonism caused by Pro105Leu mutation of prion protein: A broad clinical spectrum. Neurol Genet 2016; 2:e48. [PMID: 27066585 PMCID: PMC4817902 DOI: 10.1212/nxg.0000000000000048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/23/2015] [Indexed: 11/17/2022]
Abstract
Objective: To delineate molecular and clinical characteristics of 3 families with PRNP P105L mutation, a variant of Gerstmann-Sträussler-Scheinker syndrome whose main motor symptoms were parkinsonism and/or involuntary movements. Methods: The causative mutation was first determined in the affected patients of family 1 using whole-exome sequencing, and then mutational analysis was extended to families 2 and 3. The clinical features of the patients of these 3 families were summarized. Haplotype analysis was performed using high-density single nucleotide polymorphism array. Results: The whole-exome sequencing revealed that the heterozygous mutation c.314C>T (p.P105L) in PRNP was the only known pathogenic mutation shared by the 3 patients of the family with autosomal dominant parkinsonism. We further identified the same mutation in patients of the other 2 families with autosomal dominant parkinsonism and/or involuntary movements. The clinical features of our patients with PRNP P105L mutation included various motor symptoms such as parkinsonism and involuntary movements in addition to progressive dementia. The clinical features in part overlapped with those of other forms of inherited prion diseases, such as fatal familial insomnia and Huntington disease-like type 1. The patients with PRNP P105L mutation shared a haplotype spanning 7.1 Mb around PRNP, raising the possibility that the mutations in the patients originated from a common founder. Conclusion: Most of the patients presented with parkinsonism in addition to progressive dementia. Although spastic paraparesis has been emphasized as the main clinical feature, the clinical spectrum of patients with PRNP P105L is broader than expected.
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Affiliation(s)
- Kagari Koshi Mano
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Takashi Matsukawa
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Jun Mitsui
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Hiroyuki Ishiura
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Shin-Ichi Tokushige
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Yuji Takahashi
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Naoko Saito Sato
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Fumiko Kusunoki Nakamoto
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Yaeko Ichikawa
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Yu Nagashima
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Yasuo Terao
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Jun Shimizu
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Masashi Hamada
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Yoshikazu Uesaka
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Genko Oyama
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Go Ogawa
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Jun Yoshimura
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Koichiro Doi
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Shinichi Morishita
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Shoji Tsuji
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
| | - Jun Goto
- Department of Neurology (K.K.M., T.M., J.M., H.I., S.-i.T., Y. Takahashi, N.S.S., F.K.N., Y.I., Y.N., Y. Terao, J.S., M.H., S.T., J.G.), Graduate School of Medicine, The University of Tokyo; Shonai Amarume Hospital (Y. Takahashi); Department of Neurology (Y.U.), Toranomon Hospital; Department of Neurology (G. Oyama), Juntendo University; Department of Neurology (G. Ogawa), Teikyo University; and Department of Computational Biology and Medical Sciences (J.Y., K.D., S.M.), Graduate School of Frontier Sciences, The University of Tokyo. Y. Takahashi is currently affiliated with the Department of Neurology, National Center of Psychiatry and Neurology. Y.I. is currently affiliated with the Department of Neurology, Kyorin University
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Yamashita S, Mori A, Nishida Y, Kurisaki R, Tawara N, Nishikami T, Misumi Y, Ueyama H, Imamura S, Higuchi Y, Hashiguchi A, Higuchi I, Morishita S, Yoshimura J, Uchino M, Takashima H, Tsuji S, Ando Y. Clinicopathological features of the first Asian family having vocal cord and pharyngeal weakness with distal myopathy due to a MATR3 mutation. Neuropathol Appl Neurobiol 2015; 41:391-8. [PMID: 25185957 DOI: 10.1111/nan.12179] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 08/13/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Satoshi Yamashita
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
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Nakatani Y, Mello CC, Hashimoto SI, Shimada A, Nakamura R, Tsukahara T, Qu W, Yoshimura J, Suzuki Y, Sugano S, Takeda H, Fire A, Morishita S. Associations between nucleosome phasing, sequence asymmetry, and tissue-specific expression in a set of inbred Medaka species. BMC Genomics 2015; 16:978. [PMID: 26584643 PMCID: PMC4653950 DOI: 10.1186/s12864-015-2198-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 11/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Transcription start sites (TSSs) with pronounced and phased nucleosome arrays downstream and nucleosome-depleted regions upstream of TSSs are observed in various species. RESULTS We have characterized sequence variation and expression properties of this set of TSSs (which we call "Nucleocyclic TSSs") using germline and somatic cells of three medaka (Oryzias latipes) inbred isolates from different locations. We found nucleocyclic TSSs in medaka to be associated with higher gene expression and characterized by a clear boundary in sequence composition with potentially-nucleosome-destabilizing A/T-enrichment upstream (p < 10(-60)) and nucleosome- accommodating C/G-enrichment downstream (p < 10(-40)) that was highly conserved from an ancestor. A substantial genetic distance between the strains facilitated the in-depth analysis of patterns of fixed mutations, revealing a localization-specific equilibrium between the rates of distinct mutation categories that would serve to maintain the conserved sequence anisotropy around TSSs. Downstream of nucleocyclic TSSs, C to T, T to C, and other mutation rates on the sense strand increased around first nucleosome dyads and decreased around first linkers, which contrasted with genomewide mutational patterns around nucleosomes (p < 5 %). C to T rates are higher than G to A rates around nucleosome associated with germline nucleocyclic TSS sites (p < 5 %), potentially due to the asymmetric effect of transcription-coupled repair. CONCLUSIONS Our results demonstrate an atypical evolutionary process surrounding nucleocyclic TSSs.
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Affiliation(s)
- Yoichiro Nakatani
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.
| | - Cecilia C Mello
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, 94305-5324, USA.
| | - Shin-Ichi Hashimoto
- Graduate School of Medical Sciences, Kanazawa University, Kanazawa, 920-1192, Japan.
| | - Atsuko Shimada
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Wei Qu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.
| | - Jun Yoshimura
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.
| | - Yutaka Suzuki
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan.
| | - Sumio Sugano
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan.
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
| | - Andrew Fire
- Departments of Pathology and Genetics, School of Medicine, Stanford University, Stanford, CA, 94305-5324, USA.
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-0882, Japan.
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Koyama T, Ito H, Kakishima S, Yoshimura J, Cooley JR, Simon C, Sota T. Geographic body size variation in the periodical cicadas Magicicada
: implications for life cycle divergence and local adaptation. J Evol Biol 2015; 28:1270-7. [DOI: 10.1111/jeb.12653] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 02/24/2015] [Accepted: 04/20/2015] [Indexed: 11/28/2022]
Affiliation(s)
- T. Koyama
- Department of Zoology; Graduate School of Science; Kyoto University; Kyoto Japan
| | - H. Ito
- Graduate School of Science and Technology; Shizuoka University; Hamamatsu Japan
| | - S. Kakishima
- Graduate School of Science and Technology; Shizuoka University; Hamamatsu Japan
| | - J. Yoshimura
- Graduate School of Science and Technology; Shizuoka University; Hamamatsu Japan
- Department of Environmental and Forest Biology; College of Environmental Science and Forestry; State University of New York; Syracuse NY USA
- Marine Biosystems Research Center; Chiba University; Uchiura Kamogawa Chiba Japan
| | - J. R. Cooley
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - C. Simon
- Department of Ecology and Evolutionary Biology; University of Connecticut; Storrs CT USA
| | - T. Sota
- Department of Zoology; Graduate School of Science; Kyoto University; Kyoto Japan
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Yoshimura J, Kiguchi T, Matsushima A, Fujimi S. Development of antibiotic treatment algorithms based on Gram stain to restrict use of broad-spectrum antibiotics in the treatment of ventilator-associated pneumonia: a retrospective analysis. Crit Care 2015. [PMCID: PMC4471268 DOI: 10.1186/cc14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Nishimura T, Herpin A, Kimura T, Hara I, Kawasaki T, Nakamura S, Yamamoto Y, Saito TL, Yoshimura J, Morishita S, Tsukahara T, Kobayashi S, Naruse K, Shigenobu S, Sakai N, Schartl M, Tanaka M. Analysis of a novel gene, Sdgc, reveals sex chromosome-dependent differences of medaka germ cells prior to gonad formation. Development 2014; 141:3363-9. [DOI: 10.1242/dev.106864] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In vertebrates that have been examined to date, the sexual identity of germ cells is determined by the sex of gonadal somatic cells. In the teleost fish medaka, a sex-determination gene on the Y chromosome, DMY/dmrt1bY, is expressed in gonadal somatic cells and regulates the sexual identity of germ cells. Here, we report a novel mechanism by which sex chromosomes cell-autonomously confer sexually different characters upon germ cells prior to gonad formation in a genetically sex-determined species. We have identified a novel gene, Sdgc (sex chromosome-dependent differential expression in germ cells), whose transcripts are highly enriched in early XY germ cells. Chimeric analysis revealed that sexually different expression of Sdgc is controlled in a germ cell-autonomous manner by the number of Y chromosomes. Unexpectedly, DMY/dmrt1bY was expressed in germ cells prior to gonad formation, but knockdown and overexpression of DMY/dmrt1bY did not affect Sdgc expression. We also found that XX and XY germ cells isolated before the onset of DMY/dmrt1bY expression in gonadal somatic cells behaved differently in vitro and were affected by Sdgc. Sdgc maps close to the sex-determination locus, and recombination around the two loci appears to be repressed. Our results provide important insights into the acquisition and plasticity of sexual differences at the cellular level even prior to the developmental stage of sex determination.
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Affiliation(s)
- Toshiya Nishimura
- Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
| | - Amaury Herpin
- Department of Physiological Chemistry, University of Würzburg, D-97074 Würzburg, Germany
- INRA, UR1037 Fish Physiology and Genomics, Rennes F-35000, France
| | - Tetsuaki Kimura
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Ikuyo Hara
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Toshihiro Kawasaki
- Genetic Strains Research Center, National institute of Genetics, Mishima 411-8540, Japan
| | - Shuhei Nakamura
- Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Yasuhiro Yamamoto
- Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Taro L. Saito
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Jun Yoshimura
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Shinichi Morishita
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 277-0882, Japan
| | - Tatsuya Tsukahara
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku 113-0033, Japan
| | - Satoru Kobayashi
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Kiyoshi Naruse
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
- Interuniversity Bio-Backup Project Center, National Institute for Basic Biology, Okazaki 444-8585, Japan
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Shuji Shigenobu
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
- Functional Genomics Facility, National Institute for Basic Biology, Okazaki 444-8585, Japan
| | - Noriyoshi Sakai
- Genetic Strains Research Center, National institute of Genetics, Mishima 411-8540, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Mishima 411-8540, Japan
| | - Manfred Schartl
- Department of Physiological Chemistry, University of Würzburg, D-97074 Würzburg, Germany
- Comprehensive Cancer Center Mainfranken, University Clinic Würzburg, D-97074 Würzburg, Germany
| | - Minoru Tanaka
- Laboratory of Molecular Genetics for Reproduction, National Institute for Basic Biology, Okazaki 444-8787, Japan
- The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8585, Japan
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Isojima T, Doi K, Mitsui J, Oda Y, Tokuhiro E, Yasoda A, Yorifuji T, Horikawa R, Yoshimura J, Ishiura H, Morishita S, Tsuji S, Kitanaka S. A recurrent de novo FAM111A mutation causes Kenny-Caffey syndrome type 2. J Bone Miner Res 2014; 29:992-8. [PMID: 23996431 DOI: 10.1002/jbmr.2091] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2013] [Revised: 08/21/2013] [Accepted: 08/27/2013] [Indexed: 11/08/2022]
Abstract
Kenny-Caffey syndrome (KCS) is a rare dysmorphologic syndrome characterized by proportionate short stature, cortical thickening and medullary stenosis of tubular bones, delayed closure of anterior fontanelle, eye abnormalities, and hypoparathyroidism. The autosomal dominant form of KCS (KCS type 2 [KCS2]) is distinguished from the autosomal recessive form of KCS (KCS type 1 [KCS1]), which is caused by mutations of the tubulin-folding cofactor E (TBCE) gene, by the absence of mental retardation. In this study, we recruited four unrelated Japanese patients with typical sporadic KCS2, and performed exome sequencing in three patients and their parents to elucidate the molecular basis of KCS2. The possible candidate genes were explored by a de novo mutation detection method. A single gene, FAM111A (NM_001142519.1), was shared among three families. An identical missense mutation, R569H, was heterozygously detected in all three patients but not in the unaffected family members. This mutation was also found in an additional unrelated patient. These findings are in accordance with those of a recent independent report by a Swiss group that KCS2 is caused by a de novo mutation of FAM111A, and R569H is a hot spot mutation for KCS2. Although the function of FAM111A is not known, this study would provide evidence that FAM111A is a key molecule for normal bone development, height gain, and parathyroid hormone development and/or regulation.
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Affiliation(s)
- Tsuyoshi Isojima
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Doi K, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, Ishiura H, Takahashi Y, Ichikawa Y, Goto J, Tsuji S, Morishita S. Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing. ACTA ACUST UNITED AC 2013; 30:815-22. [PMID: 24215022 PMCID: PMC3957077 DOI: 10.1093/bioinformatics/btt647] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Motivation: Long expansions of short tandem repeats (STRs), i.e. DNA repeats of 2–6 nt, are associated with some genetic diseases. Cost-efficient high-throughput sequencing can quickly produce billions of short reads that would be useful for uncovering disease-associated STRs. However, enumerating STRs in short reads remains largely unexplored because of the difficulty in elucidating STRs much longer than 100 bp, the typical length of short reads. Results: We propose ab initio procedures for sensing and locating long STRs promptly by using the frequency distribution of all STRs and paired-end read information. We validated the reproducibility of this method using biological replicates and used it to locate an STR associated with a brain disease (SCA31). Subsequently, we sequenced this STR site in 11 SCA31 samples using SMRTTM sequencing (Pacific Biosciences), determined 2.3–3.1 kb sequences at nucleotide resolution and revealed that (TGGAA)- and (TAAAATAGAA)-repeat expansions determined the instability of the repeat expansions associated with SCA31. Our method could also identify common STRs, (AAAG)- and (AAAAG)-repeat expansions, which are remarkably expanded at four positions in an SCA31 sample. This is the first proposed method for rapidly finding disease-associated long STRs in personal genomes using hybrid sequencing of short and long reads. Availability and implementation: Our TRhist software is available at http://trhist.gi.k.u-tokyo.ac.jp/. Contact:moris@cb.k.u-tokyo.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Koichiro Doi
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Department of Information and Communication Engineering, Faculty of Engineering and Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo 113-8655, Japan
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Takahashi Y, Fukuda Y, Yoshimura J, Toyoda A, Kurppa K, Moritoyo H, Belzil V, Dion P, Higasa K, Doi K, Ishiura H, Mitsui J, Date H, Ahsan B, Matsukawa T, Ichikawa Y, Moritoyo T, Ikoma M, Hashimoto T, Kimura F, Murayama S, Onodera O, Nishizawa M, Yoshida M, Atsuta N, Sobue G, Fifita J, Williams K, Blair I, Nicholson G, Gonzalez-Perez P, Brown R, Nomoto M, Elenius K, Rouleau G, Fujiyama A, Morishita S, Goto J, Tsuji S, Tsuji S. ERBB4 mutations that disrupt the neuregulin-ErbB4 pathway cause amyotrophic lateral sclerosis type 19. Am J Hum Genet 2013; 93:900-5. [PMID: 24119685 DOI: 10.1016/j.ajhg.2013.09.008] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 08/26/2013] [Accepted: 09/13/2013] [Indexed: 12/20/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating neurological disorder characterized by the degeneration of motor neurons and typically results in death within 3-5 years from onset. Familial ALS (FALS) comprises 5%-10% of ALS cases, and the identification of genes associated with FALS is indispensable to elucidating the molecular pathogenesis. We identified a Japanese family affected by late-onset, autosomal-dominant ALS in which mutations in genes known to be associated with FALS were excluded. A whole- genome sequencing and parametric linkage analysis under the assumption of an autosomal-dominant mode of inheritance with incomplete penetrance revealed the mutation c.2780G>A (p. Arg927Gln) in ERBB4. An extensive mutational analysis revealed the same mutation in a Canadian individual with familial ALS and a de novo mutation, c.3823C>T (p. Arg1275Trp), in a Japanese simplex case. These amino acid substitutions involve amino acids highly conserved among species, are predicted as probably damaging, and are located within a tyrosine kinase domain (p. Arg927Gln) or a C-terminal domain (p. Arg1275Trp), both of which mediate essential functions of ErbB4 as a receptor tyrosine kinase. Functional analysis revealed that these mutations led to a reduced autophosphorylation of ErbB4 upon neuregulin-1 (NRG-1) stimulation. Clinical presentations of the individuals with mutations were characterized by the involvement of both upper and lower motor neurons, a lack of obvious cognitive dysfunction, and relatively slow progression. This study indicates that disruption of the neuregulin-ErbB4 pathway is involved in the pathogenesis of ALS and potentially paves the way for the development of innovative therapeutic strategies such using NRGs or their agonists to upregulate ErbB4 functions.
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Ichikawa Y, Ishiura H, Mitsui J, Takahashi Y, Kobayashi S, Takuma H, Kanazawa I, Doi K, Yoshimura J, Morishita S, Goto J, Tsuji S. Exome analysis reveals a Japanese family with spinocerebellar ataxia, autosomal recessive 1. J Neurol Sci 2013; 331:158-60. [PMID: 23786967 DOI: 10.1016/j.jns.2013.05.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Revised: 04/17/2013] [Accepted: 05/13/2013] [Indexed: 11/28/2022]
Abstract
Spinocerebellar ataxia autosomal recessive 1 (SCAR1/AOA2) is clinically characterized by an early-onset progressive cerebellar ataxia with axonal neuropathy, ocular motor apraxia, and elevation of serum alpha-fetoprotein level. The disorder is caused by mutations in senataxin (SETX) gene. Here, we report a Japanese SCAR1/AOA2 family with a homozygous nonsense mutation (p.Q1441X) of SETX that was identified by exome sequencing. The family was previously reported as early-onset ataxia of undetermined cause. The present study emphasized the role of whole exome-sequence analysis to establish the molecular diagnosis of neurodegenerative disease presenting with diverse clinical presentations.
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Affiliation(s)
- Yaeko Ichikawa
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Japan
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Ishikawa T, Okada T, Ishikawa-Fujiwara T, Todo T, Kamei Y, Shigenobu S, Tanaka M, Saito TL, Yoshimura J, Morishita S, Toyoda A, Sakaki Y, Taniguchi Y, Takeda S, Mori K. ATF6α/β-mediated adjustment of ER chaperone levels is essential for development of the notochord in medaka fish. Mol Biol Cell 2013; 24:1387-95. [PMID: 23447699 PMCID: PMC3639050 DOI: 10.1091/mbc.e12-11-0830] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
ATF6α and ATF6β are membrane-bound transcription factors activated by regulated intramembrane proteolysis in response to endoplasmic reticulum (ER) stress to induce various ER quality control proteins. ATF6α- and ATF6β single-knockout mice develop normally, but ATF6α/β double knockout causes embryonic lethality, the reason for which is unknown. Here we show in medaka fish that ATF6α is primarily responsible for transcriptional induction of the major ER chaperone BiP and that ATF6α/β double knockout, but not ATF6α- or ATF6β single knockout, causes embryonic lethality, as in mice. Analyses of ER stress reporters reveal that ER stress occurs physiologically during medaka early embryonic development, particularly in the brain, otic vesicle, and notochord, resulting in ATF6α- and ATF6β-mediated induction of BiP, and that knockdown of the α1 chain of type VIII collagen reduces such ER stress. The absence of transcriptional induction of several ER chaperones in ATF6α/β double knockout causes more profound ER stress and impaired notochord development, which is partially rescued by overexpression of BiP. Thus ATF6α/β-mediated adjustment of chaperone levels to increased demands in the ER is essential for development of the notochord, which synthesizes and secretes large amounts of extracellular matrix proteins to serve as the body axis before formation of the vertebra.
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Affiliation(s)
- Tokiro Ishikawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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Mitsui J, Matsukawa T, Ishiura H, Higasa K, Yoshimura J, Saito TL, Ahsan B, Takahashi Y, Goto J, Iwata A, Niimi Y, Riku Y, Goto Y, Mano K, Yoshida M, Morishita S, Tsuji S. CSF1R mutations identified in three families with autosomal dominantly inherited leukoencephalopathy. Am J Med Genet B Neuropsychiatr Genet 2012; 159B:951-7. [PMID: 23038421 DOI: 10.1002/ajmg.b.32100] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 09/06/2012] [Indexed: 11/11/2022]
Abstract
Genetic and phenotypic heterogeneities are considerably high in adult-onset leukoencephalopathy, in which comprehensive mutational analyses of the candidate genes by conventional methods are too laborious. We applied exome sequencing to conduct a comprehensive mutational analysis of genes for autosomal dominant leukoencephalopathies. Genomic DNA samples from four patients of three families with autosomal dominantly inherited adult-onset leukodystrophy were subjected to exome sequencing. On the basis of the results, 21 patients with adult-onset sporadic leukodystrophy and one patient with pathologically proven HDLS were additionally screened for CSF1R mutations. Exome sequencing identified heterozygous CSF1R mutations (p.I794T and p.R777W) in two families. I794T has recently been reported as a causative mutation for hereditary diffuse leukoencephalopathy with spheroids (HDLS), and R777W is a novel mutation. Although mutational analysis of CSF1R in 21 sporadic cases revealed no mutations, another novel CSF1R mutation, p.C653Y, was identified in one patient with autopsy-proven HDSL. These variants were located in the PTK domain where the causative mutations cluster. Functional prediction of the mutant CSF1R as well as cross-species conservation of the affected amino acids supports the notion that these variants are pathogenic for HDLS. Exome sequencing is useful for a comprehensive mutational analysis of causative genes for hereditary leukoencephalopathies, and CSF1R should be considered a candidate gene for patients with autosomal dominant leukoencephalopathies.
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Affiliation(s)
- Jun Mitsui
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Naito Y, Yoshimura J, Morishita S, Ui-Tei K. siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. BMC Bioinformatics 2009; 10:392. [PMID: 19948054 PMCID: PMC2791777 DOI: 10.1186/1471-2105-10-392] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 11/30/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND RNA interference (RNAi), mediated by 21-nucleotide (nt)-length small interfering RNAs (siRNAs), is a powerful tool not only for studying gene function but also for therapeutic applications. RNAi, requiring perfect complementarity between the siRNA guide strand and the target mRNA, was believed to be extremely specific. However, a recent growing body of evidence has suggested that siRNA could down-regulate unintended genes whose transcripts possess complementarity to the 7-nt siRNA seed region. This off-target gene silencing may often provide incongruous results obtained from knockdown experiments, leading to misinterpretation. Thus, an efficient algorithm for designing functional siRNAs with minimal off-target effect based on the mechanistic features is considered of value. RESULTS We present siDirect 2.0, an update of our web-based software siDirect, which provides functional and off-target minimized siRNA design for mammalian RNAi. The previous version of our software designed functional siRNAs by considering the relationship between siRNA sequence and RNAi activity, and provided them along with the enumeration of potential off-target gene candidates by using a fast and sensitive homology search algorithm. In the new version, the siRNA design algorithm is extensively updated to eliminate off-target effects by reflecting our recent finding that the capability of siRNA to induce off-target effect is highly correlated to the thermodynamic stability, or the melting temperature (Tm), of the seed-target duplex, which is formed between the nucleotides positioned at 2-8 from the 5' end of the siRNA guide strand and its target mRNA. Selection of siRNAs with lower seed-target duplex stabilities (benchmark Tm < 21.5 degrees C) followed by the elimination of unrelated transcripts with nearly perfect match should minimize the off-target effects. CONCLUSION siDirect 2.0 provides functional, target-specific siRNA design with the updated algorithm which significantly reduces off-target silencing. When the candidate functional siRNAs could form seed-target duplexes with Tm values below 21.5 degrees C, and their 19-nt regions spanning positions 2-20 of both strands have at least two mismatches to any other non-targeted transcripts, siDirect 2.0 can design at least one qualified siRNA for >94% of human mRNA sequences in RefSeq. siDirect 2.0 is available at http://siDirect2.RNAi.jp/.
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Affiliation(s)
- Yuki Naito
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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Saito TL, Yoshimura J, Sasaki S, Ahsan B, Sasaki A, Kuroshu R, Morishita S. UTGB toolkit for personalized genome browsers. Bioinformatics 2009; 25:1856-61. [PMID: 19497937 PMCID: PMC2712345 DOI: 10.1093/bioinformatics/btp350] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 05/27/2009] [Accepted: 05/30/2009] [Indexed: 11/12/2022] Open
Abstract
UNLABELLED The advent of high-throughput DNA sequencers has increased the pace of collecting enormous amounts of genomic information, yielding billions of nucleotides on a weekly basis. This advance represents an improvement of two orders of magnitude over traditional Sanger sequencers in terms of the number of nucleotides per unit time, allowing even small groups of researchers to obtain huge volumes of genomic data over fairly short period. Consequently, a pressing need exists for the development of personalized genome browsers for analyzing these immense amounts of locally stored data. The UTGB (University of Tokyo Genome Browser) Toolkit is designed to meet three major requirements for personalization of genome browsers: easy installation of the system with minimum efforts, browsing locally stored data and rapid interactive design of web interfaces tailored to individual needs. The UTGB Toolkit is licensed under an open source license. AVAILABILITY The software is freely available at http://utgenome.org/.
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Affiliation(s)
- Taro L Saito
- Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa City, Chiba 277-0882, Japan
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