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Takada K, Orba Y, Kida Y, Wu J, Ono C, Matsuura Y, Nakagawa S, Sawa H, Watanabe T. Genes involved in the limited spread of SARS-CoV-2 in the lower respiratory airways of hamsters may be associated with adaptive evolution. J Virol 2024; 98:e0178423. [PMID: 38624229 DOI: 10.1128/jvi.01784-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/17/2024] [Indexed: 04/17/2024] Open
Abstract
Novel respiratory viruses can cause a pandemic and then evolve to coexist with humans. The Omicron strain of severe acute respiratory syndrome coronavirus 2 has spread worldwide since its emergence in late 2021, and its sub-lineages are now established in human society. Compared to previous strains, Omicron is markedly less invasive in the lungs and causes less severe disease. One reason for this is that humans are acquiring immunity through previous infection and vaccination, but the nature of the virus itself is also changing. Using our newly established low-volume inoculation system, which reflects natural human infection, we show that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain. Furthermore, by characterizing chimeric viruses with the Omicron gene in the Wuhan strain genetic background and vice versa, we found that viral genes downstream of ORF3a, but not the S gene, were responsible for the limited spread of the Omicron strain in the lower airways of the virus-infected hamsters. Moreover, molecular evolutionary analysis of SARS-CoV-2 revealed a positive selection of genes downstream of ORF3a (M and E genes). Our findings provide insight into the adaptive evolution of the virus in humans during the pandemic convergence phase.IMPORTANCEThe severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has spread worldwide since its emergence in late 2021, and its sub-lineages are established in human society. Compared to previous strains, the Omicron strain is less invasive in the lower respiratory tract, including the lungs, and causes less severe disease; however, the mechanistic basis for its restricted replication in the lower airways is poorly understood. In this study, using a newly established low-volume inoculation system that reflects natural human infection, we demonstrated that the Omicron strain spreads less efficiently into the lungs of hamsters compared with an earlier Wuhan strain and found that viral genes downstream of ORF3a are responsible for replication restriction in the lower respiratory tract of Omicron-infected hamsters. Furthermore, we detected a positive selection of genes downstream of ORF3a (especially the M and E genes) in SARS-CoV-2, suggesting that these genes may undergo adaptive changes in humans.
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Grants
- 16H06429, 16K21723, 16H06434, JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP16K21723, JP16H06432 MEXT | Japan Society for the Promotion of Science (JSPS)
- 22K15469, 21J01036 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20fk0108281, JP19fk0108113, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP23wm0125008, JP223fa627005 Japan Agency for Medical Research and Development (AMED)
- JP19fk018113, JP223fa627002h, 22gm1610010h0001 Japan Agency for Medical Research and Development (AMED)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
- JPMJCR20H6 MEXT | Japan Science and Technology Agency (JST)
- Takeda Science Foundation (TSF)
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Affiliation(s)
- Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yurie Kida
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
| | - Chikako Ono
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, Japan
| | - Hirofumi Sawa
- One Health Research Center, Hokkaido University, Sapporo, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Sapporo, Hokkaido, Japan
- Global Virus Network, Baltimore, Maryland, USA
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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2
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Vuleta S, Nakagawa S, Ainsworth TD. The global significance of Scleractinian corals without photoendosymbiosis. Sci Rep 2024; 14:10161. [PMID: 38698199 PMCID: PMC11066124 DOI: 10.1038/s41598-024-60794-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 11/21/2023] [Accepted: 04/26/2024] [Indexed: 05/05/2024] Open
Abstract
Globally tropical Scleractinian corals have been a focal point for discussions on the impact of a changing climate on marine ecosystems and biodiversity. Research into tropical Scleractinian corals, particularly the role and breakdown of photoendosymbiosis in response to warming, has been prolific in recent decades. However, research into their subtropical, temperate, cold- and deep-water counterparts, whose number is dominated by corals without photoendosymbiosis, has not been as prolific. Approximately 50% of Scleractinian corals (> 700 species) do not maintain photoendosymbiosis and as such, do not rely upon the products of photosynthesis for homeostasis. Some species also have variable partnerships with photendosymbionts depending on life history and ecological niche. Here we undertake a systematic map of literature on Scleractinian corals without, or with variable, photoendosymbiosis. In doing so we identify 482 publications spanning 5 decades. In mapping research effort, we find publications have been sporadic over time, predominately focusing on a limited number of species, with greater research effort directed towards deep-water species. We find only 141 species have been studied, with approximately 30% of the total identified research effort directed toward a single species, Desmophyllum pertusum, highlighting significant knowledge gaps into Scleractinian diversity. We find similar limitations to studied locations, with 78 identified from the global data, of which only few represent most research outputs. We also identified inconsistencies with terminology used to describe Scleractinia without photoendosymbiosis, likely contributing to difficulties in accounting for their role and contribution to marine ecosystems. We propose that the terminology requires re-evaluation to allow further systematic assessment of literature, and to ensure it's consistent with changes implemented for photoendosymbiotic corals. Finally, we find that knowledge gaps identified over 20 years ago are still present for most aphotoendosymbiotic Scleractinian species, and we show data deficiencies remain regarding their function, biodiversity and the impacts of anthropogenic stressors.
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Affiliation(s)
- S Vuleta
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences (BEES), The University of New South Wales, Sydney, NSW, 2033, Australia.
| | - S Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences (BEES), The University of New South Wales, Sydney, NSW, 2033, Australia
| | - T D Ainsworth
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences (BEES), The University of New South Wales, Sydney, NSW, 2033, Australia
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3
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Oka A, Hadano S, Ueda MT, Nakagawa S, Komaki G, Ando T. Rare CRHR2 and GRM8 variants identified as candidate factors associated with eating disorders in Japanese patients by whole exome sequencing. Heliyon 2024; 10:e28643. [PMID: 38644811 PMCID: PMC11031761 DOI: 10.1016/j.heliyon.2024.e28643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/11/2023] [Revised: 03/15/2024] [Accepted: 03/21/2024] [Indexed: 04/23/2024] Open
Abstract
Eating disorders (EDs) are a type of psychiatric disorder characterized by pathological eating and related behavior and considered to be highly heritable. The purpose of this study was to explore rare variants expected to display biological functions associated with the etiology of EDs. We performed whole exome sequencing (WES) of affected sib-pairs corresponding to disease subtype through their lifetime and their parents. From those results, rare single nucleotide variants (SNVs) concordant with sib-pairs were extracted and estimated to be most deleterious in the examined families. Two non-synonymous SNVs located on corticotropin-releasing hormone receptor 2 (CRHR2) and glutamate metabotropic receptor 8 (GRM8) were identified as candidate disease susceptibility factors. The SNV of CRHR2 was included within the cholesterol binding motif of the transmembrane helix region, while the SNV of GRM8 was found to contribute to hydrogen bonds for an α-helix structure. CRHR2 plays important roles in the serotoninergic system of dorsal raphe nuclei, which is involved with feeding and stress-coping behavior, whereas GRM8 modulates glutamatergic neurotransmission. Moreover, GRM8 modulates glutamatergic neurotransmission, and is also considered to have effects on dopaminergic and adrenergic neurotransmission. Thus, identification of rare and deleterious variants in this study is expected to increase understanding and treatment of affected individuals. Further investigation regarding the biological function of these variants may provide an opportunity to elucidate the pathogenesis of EDs.
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Affiliation(s)
- Akira Oka
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Shinji Hadano
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Department of Physiology, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo, 113-8510, Japan
| | - So Nakagawa
- Department of Molecular Life Sciences, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- The Institute of Medical Sciences, Tokai University, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa, 259-1292, Japan
| | - Gen Komaki
- Faculty of Medical Science, Fukuoka International University of Health and Welfare, Momochihama, Sawara-ku, Fukuoka, 814-0001, Japan
| | - Tetsuya Ando
- Department of Psychosomatic Medicine, Faculty of Medicine, School of Medicine, International University of Health and Welfare, 4-3 Kozunomori, Narita, Chiba, 286-8686, Japan
- Department of Behavioral Medicine, National Institute of Mental Health, National Center of Neurology and Psychiatry, 4-1-1 Ogawa-higashi, Kodaira, Tokyo, 187-8553, Japan
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4
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Konno Y, Uriu K, Chikata T, Takada T, Kurita JI, Ueda MT, Islam S, Yang Tan BJ, Ito J, Aso H, Kumata R, Williamson C, Iwami S, Takiguchi M, Nishimura Y, Morita E, Satou Y, Nakagawa S, Koyanagi Y, Sato K. Two-step evolution of HIV-1 budding system leading to pandemic in the human population. Cell Rep 2024; 43:113697. [PMID: 38294901 DOI: 10.1016/j.celrep.2024.113697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/04/2023] [Revised: 11/19/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
The pandemic HIV-1, HIV-1 group M, emerged from a single spillover event of its ancestral lentivirus from a chimpanzee. During human-to-human spread worldwide, HIV-1 diversified into multiple subtypes. Here, our interdisciplinary investigation mainly sheds light on the evolutionary scenario of the viral budding system of HIV-1 subtype C (HIV-1C), a most successfully spread subtype. Of the two amino acid motifs for HIV-1 budding, the P(T/S)AP and YPxL motifs, HIV-1C loses the YPxL motif. Our data imply that HIV-1C might lose this motif to evade immune pressure. Additionally, the P(T/S)AP motif is duplicated dependently of the level of HIV-1 spread in the human population, and >20% of HIV-1C harbored the duplicated P(T/S)AP motif. We further show that the duplication of the P(T/S)AP motif is caused by the expansion of the CTG triplet repeat. Altogether, our results suggest that HIV-1 has experienced a two-step evolution of the viral budding process during human-to-human spread worldwide.
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Affiliation(s)
- Yoriyuki Konno
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Takayuki Chikata
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Toru Takada
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan
| | - Jun-Ichi Kurita
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Saiful Islam
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Benjy Jek Yang Tan
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Hirofumi Aso
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Ryuichi Kumata
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Carolyn Williamson
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Shingo Iwami
- Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 8128581, Japan; MIRAI, Japan Science and Technology Agency, Kawaguchi 3320012, Japan
| | - Masafumi Takiguchi
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - Yoshifumi Nishimura
- Graduate School of Medical Life Science, Yokohama City University, Kanagawa 2300045, Japan
| | - Eiji Morita
- Department of Biochemistry and Molecular Biology, Faculty of Agriculture and Life Science, Hirosaki University, Aomori 0368561, Japan
| | - Yorifumi Satou
- Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8608556, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan
| | - Yoshio Koyanagi
- Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, the University of Tokyo, Tokyo 1130033, Japan; International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa 2778561, Japan; CREST, Japan Science and Technology Agency, Kawaguchi 3320012, Japan.
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5
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Nakagawa S, Katayama T, Jin L, Wu J, Kryukov K, Oyachi R, Takeuchi JS, Fujisawa T, Asano S, Komatsu M, Onami JI, Abe T, Arita M. SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan. Genes Genet Syst 2023; 98:221-237. [PMID: 37839865 DOI: 10.1266/ggs.23-00085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 10/17/2023] Open
Abstract
Since the early phase of the coronavirus disease 2019 (COVID-19) pandemic, a number of research institutes have been sequencing and sharing high-quality severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes to trace the route of infection in Japan. To provide insight into the spread of COVID-19, we developed a web platform named SARS-CoV-2 HaploGraph to visualize the emergence timing and geographical transmission of SARS-CoV-2 haplotypes. Using data from the GISAID EpiCoV database as of June 4, 2022, we created a haplotype naming system by determining the ancestral haplotype for each epidemic wave and showed prefecture- or region-specific haplotypes in each of four waves in Japan. The SARS-CoV-2 HaploGraph allows for interactive tracking of virus evolution and of geographical prevalence of haplotypes, and aids in developing effective public health control strategies during the global pandemic. The code and the data used for this study are publicly available at: https://github.com/ktym/covid19/.
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Affiliation(s)
- So Nakagawa
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Molecular Life Science, Tokai University School of Medicine
- Micro/Nano Technology Center, Tokai University
- Institute of Medical Sciences, Tokai University
| | | | | | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Kirill Kryukov
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
| | - Rise Oyachi
- Department of Molecular Life Science, Tokai University School of Medicine
| | - Junko S Takeuchi
- Center for Clinical Sciences, National Center for Global Health and Medicine
| | | | - Satomi Asano
- Department of Informatics, National Institute of Genetics
| | - Momoka Komatsu
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Jun-Ichi Onami
- Research Center for Open Science and Data Platform, National Institute of Informatics
| | - Takashi Abe
- Bioinformation and DDBJ Center, National Institute of Genetics
- Smart Information Systems, Faculty of Engineering, Niigata University
| | - Masanori Arita
- Bioinformation and DDBJ Center, National Institute of Genetics
- Department of Informatics, National Institute of Genetics
- RIKEN Center for Sustainable Resource Science
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6
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Kimura I, Yamasoba D, Nasser H, Ito H, Zahradnik J, Wu J, Fujita S, Uriu K, Sasaki J, Tamura T, Suzuki R, Deguchi S, Plianchaisuk A, Yoshimatsu K, Kazuma Y, Mitoma S, Schreiber G, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Takaori-Kondo A, Ito J, Shirakawa K, Takayama K, Irie T, Hashiguchi T, Nakagawa S, Fukuhara T, Saito A, Ikeda T, Sato K. Multiple mutations of SARS-CoV-2 Omicron BA.2 variant orchestrate its virological characteristics. J Virol 2023; 97:e0101123. [PMID: 37796123 PMCID: PMC10781145 DOI: 10.1128/jvi.01011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 10/06/2023] Open
Abstract
IMPORTANCE Most studies investigating the characteristics of emerging SARS-CoV-2 variants have been focusing on mutations in the spike proteins that affect viral infectivity, fusogenicity, and pathogenicity. However, few studies have addressed how naturally occurring mutations in the non-spike regions of the SARS-CoV-2 genome impact virological properties. In this study, we proved that multiple SARS-CoV-2 Omicron BA.2 mutations, one in the spike protein and another downstream of the spike gene, orchestrally characterize this variant, shedding light on the importance of Omicron BA.2 mutations out of the spike protein.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Hayato Ito
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Shigeru Fujita
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jiei Sasaki
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Tomokazu Tamura
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Rigel Suzuki
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
| | - Sayaka Deguchi
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Arnon Plianchaisuk
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | | | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shuya Mitoma
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Mami Nagashima
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Kenji Sadamasu
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - The Genotype to Phenotype Japan (G2P-Japan) Consortium
MisawaNaoko1KosugiYusuke1PanLin1SuganamiMai1ChibaMika1YoshimuraRyo1YasudaKyoko1IidaKeiko1OhsumiNaomi1StrangeAdam P.1KakuYu1PlianchaisukArnon1GuoZiyi1HinayAlfredo Jr. Amolong1Mendoza TolentinoJarel Elgin1ChenLuo1ShimizuRyo2Monira BegumM. S. T.2TakahashiOtowa2IchiharaKimiko2JonathanMichael2MugitaYuka2SuzukiSaori3SuzukiTateki4KimuraKanako4NakajimaYukari4YajimaHisano4HashimotoRina4WatanabeYukio4SakamotoAyaka4YasuharaNaoko4NagataKayoko4NomuraRyosuke4HorisawaYoshihito4TashiroYusuke4KawaiYugo4ShibataniYuki5NishiuchiTomoko5YoshidaIsao6KawabataRyoko7MatsunoKeita8NaoNaganori9SawaHirofumi9TanakaShinya10TsudaMasumi10WangLei10OdaYoshikata10FerdousZannatul10ShishidoKenji10MotozonoChihiro11ToyodaMako11UenoTakamasa11TabataKaori12Institute of Medical Science, University of Tokyo, Tokyo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, JapanHokkaido University, Sapporo, JapanKyoto University, Kyoto, JapanUniversity of Miyazaki, Miyazaki, JapanTokyo Metropolitan Institute of Public Health, Tokyo, JapanHiroshima University, Hiroshima, JapanOne Health Research Center, Hokkaido University, Sapporo, JapanInternational Institute for Zoonosis Control, Hokkaido University, Sapporo, JapanHokkaido University, Sapporo, JapanJoint Research Center for Human Retrovirus infection, Kumamoto, JapanKyushu University, Fukuoka, Japan
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Faculty of Medicine, Kobe University, Kobe, Japan
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
- Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
- First Medical Faculty at Biocev, Charles University, Vestec-Prague, Czechia
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
| | - Takashi Irie
- Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takao Hashiguchi
- Laboratory of Medical Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Faculty of Medicine, Hokkaido University, Sapporo, Japan
- Institute for Vaccine Research and Development (HU-IVReD), Hokkaido University, Sapporo, Japan
- AMED-CREST, Japan Agency for Medical Research and Development (AMED), Tokyo, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
- Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
- Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Microbiology and Immunology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
- International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
- International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- Collaboration Unit for Infection, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan
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7
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Takeuchi K, Senda M, Ikeda Y, Okuwaki K, Fukuzawa K, Nakagawa S, Sasaki M, Sasaki AT, Senda T. Functional molecular evolution of a GTP sensing kinase: PI5P4Kβ. FEBS J 2023; 290:4419-4428. [PMID: 36856076 PMCID: PMC10471773 DOI: 10.1111/febs.16763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/02/2023]
Abstract
Over 4 billion years of evolution, multiple mutations, including nucleotide substitutions, gene and genome duplications and recombination, have established de novo genes that translate into proteins with novel properties essential for high-order cellular functions. However, molecular processes through which a protein evolutionarily acquires a novel function are mostly speculative. Recently, we have provided evidence for a potential evolutionary mechanism underlying how, in mammalian cells, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) evolved into a GTP sensor from ATP-utilizing kinase. Mechanistically, PI5P4Kβ has acquired the guanine efficient association (GEA) motif by mutating its nucleotide base recognition sequence, enabling the evolutionary transition from an ATP-dependent kinase to a distinct GTP/ATP dual kinase with its KM for GTP falling into physiological GTP concentrations-the genesis of GTP sensing activity. Importantly, the GTP sensing activity of PI5P4Kβ is critical for the manifestation of cellular metabolism and tumourigenic activity in the multicellular organism. The combination of structural, biochemical and biophysical analyses used in our study provides a novel framework for analysing how a protein can evolutionarily acquire a novel activity, which potentially introduces a critical function to the cell.
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Affiliation(s)
- Koh Takeuchi
- Graduate School of Pharmacological Sciences, The University of Tokyo, Japan
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan
| | - Koji Okuwaki
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - Kaori Fukuzawa
- Graduate School of Pharmaceutical Sciences, Osaka University, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, OH, USA
- Department of Cancer Biology, University of Cincinnati College of Medicine, OH, USA
- Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH, USA
- Institute for Advanced Biosciences, Keio University, Yamagata, Japan
- Department of Clinical and Molecular Genetics, Hiroshima University Hospital, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Ibaraki, Japan
- Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Ibaraki, Japan
- Faculty of Pure and Applied Sciences, University of Tsukuba, Ibaraki, Japan
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8
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Kose E, Nakagawa S, Niki K, Hashizume J, Kawazoe T, Suzuki N, Uchida M, Takase H. Pharmacist Interventions for Adverse Drug Reactions in Palliative Care: A Multicentre Pilot Study. Pharmazie 2023; 78:141-149. [PMID: 37592417 DOI: 10.1691/ph.2023.3554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
This study aimed to investigate adverse reactions to medications administered during palliative care and compare the responses of Board-Certified Pharmacists in Palliative Pharmacy (BCPPP) and non-BCPPP professionals. Methods: This multicentre prospective survey included hospital and community pharmacists who are members of the Japanese Society for Pharmaceutical Palliative Care and Sciences. Study participants included patients who experienced new drug reactions during the study period and responded to the requested survey items. The follow-up period for each eligible patient began on the day the pharmacists initiated the intervention and ended at discharge, death, or after one month of intervention. The primary endpoint was the impact of pharmacist intervention on adverse drug reactions. The pharmacists included in the study evaluated the severity of adverse drug reactions to assess the effect of their intervention using an integrated palliative care outcome scale before and after the intervention. Key findings: During the survey period, 79 adverse drug reaction intervention reports from 69 patients were obtained from 54 pharmacists (28 certified and 26 non-certified). The response rate was 1.62% (54/3,343). The management of palliative pharmacotherapy side effects by BCPPP and non-BCPPP significantly improved the patients' activities of daily living (P < 0.001). The BCPPP group intervened for significantly more patients with adverse drug reactions and overall adverse drug reactions than the non-BCPPP group (P < 0.023 and P < 0.013, respectively). Conclusion: BCPPP interventions can improve symptom management.
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Affiliation(s)
- E Kose
- Department of Pharmacy; These authors contributed equally to this work
| | - S Nakagawa
- Department of Clinical Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee; These authors contributed equally to this work; Corresponding author: Sari Nakagawa, Department of Clinical Pharmacy, Faculty of Pharmaceutical Sciences, Kobe Gakuin University, 1-1-3 Minatojima, Chuo-ku, Kobe-shi, Hyogo 650-8586, Japan,
| | - K Niki
- Faculty of Pharmaceutical Sciences, Kobe Gakuin University; Department of Clinical Pharmacy Research and Education; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - J Hashizume
- Graduate School of Pharmaceutical Sciences, Osaka University; Department of Hospital Pharmacy
| | - T Kawazoe
- Nagasaki University Hospital; Department of Clinical Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - N Suzuki
- Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University; Department of Pharmacy
| | - M Uchida
- National Hospital Organization Sendai Medical Center; Department of Education and Research Center for Pharmacy Practice; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
| | - H Takase
- Faculty of Pharmaceutical Sciences, Doshisha Women's College of Liberal Arts; Department of Pharmacy; Nippon Medical School Tamanagayama Hospital; Research Promotion Committee
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9
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Kameda K, Yanagiya R, Miyatake Y, Carreras J, Higuchi H, Murayama H, Ishida T, Ito A, Iida S, Fukuhara N, Harigae H, Fujioka Y, Takahashi N, Wada H, Ishida F, Nakazawa H, Ishihara R, Murakami Y, Tagawa H, Matsuura T, Nakagawa S, Iwabuchi S, Hashimoto S, Imadome KI, Nakamura N, Ishizawa K, Kanda Y, Ando K, Kotani A. The hepatic niche leads to aggressive natural killer cell leukemia proliferation through the transferrin-transferrin receptor 1 axis. Blood 2023; 142:352-364. [PMID: 37146246 DOI: 10.1182/blood.2022018597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/28/2023] [Accepted: 03/13/2023] [Indexed: 05/07/2023] Open
Abstract
Aggressive natural killer cell leukemia (ANKL) is a rare lymphoid neoplasm frequently associated with Epstein-Barr virus, with a disastrously poor prognosis. Owing to the lack of samples from patients with ANKL and relevant murine models, comprehensive investigation of its pathogenesis including the tumor microenvironment (TME) has been hindered. Here we established 3 xenograft mice derived from patients with ANKL (PDXs), which enabled extensive analysis of tumor cells and their TME. ANKL cells primarily engrafted and proliferated in the hepatic sinusoid. Hepatic ANKL cells were characterized by an enriched Myc-pathway and proliferated faster than those in other organs. Interactome analyses and in vivo CRISPR-Cas9 analyses revealed transferrin (Tf)-transferrin receptor 1 (TfR1) axis as a potential molecular interaction between the liver and ANKL. ANKL cells were rather vulnerable to iron deprivation. PPMX-T003, a humanized anti-TfR1 monoclonal antibody, showed remarkable therapeutic efficacy in a preclinical setting using ANKL-PDXs. These findings indicate that the liver, a noncanonical hematopoietic organ in adults, serves as a principal niche for ANKL and the inhibition of the Tf-TfR1 axis is a promising therapeutic strategy for ANKL.
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Affiliation(s)
- Kazuaki Kameda
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Isehara, Japan
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
| | - Ryo Yanagiya
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Isehara, Japan
- Department of Neurology, Hematology, Diabetology, Endocrinology, and Metabolism (3rd Department of Internal Medicine), Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yuji Miyatake
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Isehara, Japan
| | - Joaquim Carreras
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Hiroshi Higuchi
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Isehara, Japan
- Department of Dermatology, Center for Cancer Immunology and Cutaneous Biology Research Center, Center for Cancer Research, Massachusetts General Hospital Cancer Center, Massachusetts General Hospital and Harvard Medical School, Boston, MA
| | - Hiromichi Murayama
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Takashi Ishida
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Asahi Ito
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Noriko Fukuhara
- Department of Hematology, Tohoku University Hospital, Sendai, Japan
| | - Hideo Harigae
- Department of Hematology, Tohoku University Hospital, Sendai, Japan
| | - Yuki Fujioka
- Department of Hematology, Nephrology and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Naoto Takahashi
- Department of Hematology, Nephrology and Rheumatology, Akita University Graduate School of Medicine, Akita, Japan
| | - Hidenori Wada
- Department of Hematology, Saitama Citizens Medical Center, Saitama, Japan
| | - Fumihiro Ishida
- Department of Biomedical Laboratory Sciences, Shinshu University School of Medicine, Matsumoto, Japan
| | - Hideyuki Nakazawa
- Division of Hematology, Department of Internal Medicine, Shinshu University School of Medicine, Matsumoto, Japan
| | - Rei Ishihara
- Department of Laboratory Science, Gunma University Graduate School of Health Science, Maebashi, Japan
| | - Yuki Murakami
- Department of Laboratory Science, Gunma University Graduate School of Health Science, Maebashi, Japan
| | - Hiroyuki Tagawa
- Department of Hematology, Hiraka General Hospital, Yokote, Japan
| | | | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Sadahiro Iwabuchi
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Shinichi Hashimoto
- Department of Molecular Pathophysiology, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | - Ken-Ichi Imadome
- Department of Advanced Medicine for Infections, National Center for Child Health and Development, Tokyo, Japan
| | - Naoya Nakamura
- Department of Pathology, Tokai University School of Medicine, Isehara, Japan
| | - Kenichi Ishizawa
- Department of Neurology, Hematology, Diabetology, Endocrinology, and Metabolism (3rd Department of Internal Medicine), Faculty of Medicine, Yamagata University, Yamagata, Japan
| | - Yoshinobu Kanda
- Division of Hematology, Jichi Medical University Saitama Medical Center, Saitama, Japan
- Division of Hematology, Department of Medicine, Jichi Medical University, Shimotsuke, Japan
| | - Kiyoshi Ando
- Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Japan
| | - Ai Kotani
- Department of Innovative Medical Science, Tokai University School of Medicine, Isehara, Japan
- Department of Hematological Malignancy, Institute of Medical Sciences, Tokai University, Isehara, Japan
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10
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Nakagawa S, Sakaguchi S, Ogura A, Mineta K, Endo T, Suzuki Y, Gojobori T. Current trends in RNA virus detection through metatranscriptome sequencing data. FEBS Open Bio 2023. [PMID: 37163224 DOI: 10.1002/2211-5463.13626] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/01/2023] [Accepted: 05/08/2023] [Indexed: 05/11/2023] Open
Abstract
With advances in sequencing technology, metatranscriptome sequencing from a variety of environmental and biological sources has revealed the existence of various previously unknown RNA viruses. This review presents recent major RNA virome studies sampled from invertebrate and vertebrate species as well as aquatic environments. In particular, we focus on severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and related RNA virus identification through metatranscriptome sequencing analyses. Recently developed bioinformatics software and databases for RNA virus identification are introduced. A relationship between newly identified RNA viruses and endogenous viral elements in host genomes is also discussed.
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Affiliation(s)
- So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, 259-1193, Japan
- Division of Genome Sciences, Institute of Medical Sciences, Tokai University, Kanagawa, 259-1193, Japan
- Division of Interdisciplinary Merging of Health Research, Micro/Nano Technology Center, Tokai University, Kanagawa, 259-1292, Japan
- Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University, Osaka, 569-8686, Japan
| | - Atsushi Ogura
- Graduate School of Bioscience, Nagahama Institute of Bioscience and Technology, Nagahama, Shiga, 526-0829, Japan
| | - Katsuhiko Mineta
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Toshinori Endo
- Faculty of Information Science and Technology, Hokkaido University, Sapporo, 060-0814, Japan
| | - Yoshiyuki Suzuki
- Graduate School of Science, Nagoya City University, Nagoya, 467-8501, Japan
| | - Takashi Gojobori
- Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
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11
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Kitao K, Shoji H, Miyazawa T, Nakagawa S. Dynamic evolution of retroviral envelope genes in egg-laying mammalian genomes. Mol Biol Evol 2023; 40:7124362. [PMID: 37062963 PMCID: PMC10152393 DOI: 10.1093/molbev/msad090] [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] [Received: 01/05/2023] [Revised: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 04/18/2023] Open
Abstract
Independently acquired envelope (env) genes from endogenous retroviruses have contributed to the placental trophoblast cell-cell fusion in therian mammals. Egg-laying mammals (monotremes) are an important sister clade for understanding mammalian placental evolution, but the env genes in their genomes have yet to be investigated. Here, env-derived open reading frames (env-ORFs) encoding more than 400 amino-acid lengths were searched in the genomes of two monotremes: platypus and echidna. Only two env-ORFs were present in the platypus genome, whereas 121 env-ORFs were found in the echidna genome. The echidna env-ORFs were phylogenetically classified into seven groups named env-Tac1 to -Tac7. Among them, the env-Tac1 group contained only a single gene, and its amino acid sequence showed high similarity to those of the RD114/simian type D retroviruses. Using the pseudotyped virus assay, we demonstrated that the Env-Tac1 protein utilizes echidna sodium-dependent neutral amino acid transporter type 1 and 2 (ASCT1 and ASCT2) as entry receptors. Moreover, the Env-Tac1 protein caused cell-cell fusion in human 293T cells depending on the expression of ASCT1 and ASCT2. These results illustrate that fusogenic env genes are not restricted to placental mammals, providing insights into the evolution of retroviral genes and the placenta.
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Affiliation(s)
- Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hiyori Shoji
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
- Division of Genome Sciences, Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan
- Division of Interdisciplinary Merging of Health Research, Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
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12
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Ohkura S, Horie M, Shimizu M, Nakagawa S, Osanai H, Miyagawa Y, Morita R. Characterization of Megabat-Favored, CA-Dependent Susceptibility to Retrovirus Infection. J Virol 2023; 97:e0180322. [PMID: 36779757 PMCID: PMC10062173 DOI: 10.1128/jvi.01803-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/21/2022] [Indexed: 02/14/2023] Open
Abstract
The isolation of the Koala retrovirus-like virus from Australian megabats and the identification of endogenous retroviruses in the bat genome have raised questions on bat susceptibility to retroviruses in general. To answer this, we studied the susceptibility of 12 cell lines from 11 bat species to four well-studied retroviruses (human and simian immunodeficiency viruses [HIV and SIV] and murine leukemia viruses [B- and N-MLV]). Systematic comparison of retroviral susceptibility among bats revealed that megabat cell lines were overall less susceptible to the four retroviruses than microbat cell lines, particularly to HIV-1 infection, whereas lineage-specific differences were observed for MLV susceptibility. Quantitative PCR of reverse transcription (RT) products, infection in heterokaryon cells, and point mutation analysis of the capsid (CA) revealed that (i) HIV-1 and MLV replication were blocked at the nuclear transport of the pre-integration complexes and before and/or during RT, respectively, and (ii) the observed lineage-specific restriction can be attributed to a dominant cellular factor constrained by specific positions in CA. Investigation of bat homologs of the three previously reported post-entry restriction factors constrained by the same residues in CA, tripartite motif-protein 5α (TRIM5α), myxovirus resistance 2/B (Mx2/MxB), and carboxy terminus-truncated cleavage and polyadenylation factor 6 (CPSF6-358), demonstrated poor anti-HIV-1 activity in megabat cells, whereas megabat TRIM5α restricted MLV infection, suggesting that the major known CA-dependent restriction factors were not dominant in the observed lineage-specific susceptibility to HIV-1 in bat cells. Therefore, HIV-1 susceptibility of megabat cells may be determined in a manner distinct from that of primate cells. IMPORTANCE Recent studies have demonstrated the circulation of gammaretroviruses among megabats in Australia and the bats' resistance to HIV-1 infection; however, the origins of these viruses in megabats and the contribution of bats to retrovirus spread to other mammalian species remains unclear. To determine the intrinsic susceptibility of bat cells to HIV-1 infection, we investigated 12 cell lines isolated from 11 bat species. We report that lineage-specific retrovirus restriction in the bat cell lines can be attributed to CA-dependent factors. However, in the megabat cell lines examined, factors known to bind capsid and block infection in primate cell culture, including homologs of TRIM5α, Mx2/MxB, and CPSF6, failed to exhibit significant anti-HIV-1 activities. These results suggested that the HIV-1 susceptibility of megabat cells occurs in a manner distinct from that of primate cells, where cellular factors, other than major known CA-dependent restriction factors, with lineage-specific functions could recognize retroviral proteins in megabats.
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Affiliation(s)
- Sadayuki Ohkura
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
| | - Masayuki Horie
- Graduate School of Veterinary Science, Osaka Metropolitan University, Osaka, Japan
- Osaka International Research Center for Infectious Diseases, Osaka Metropolitan University, Osaka, Japan
| | - Masumi Shimizu
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Haruka Osanai
- Department of Medicine, Nippon Medical School, Tokyo, Japan
| | - Yoshitaka Miyagawa
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo, Japan
| | - Rimpei Morita
- Department of Microbiology and Immunology, Nippon Medical School, Tokyo, Japan
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13
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Fujiwara N, Kubota N, Zhu S, Nakagawa S, Baba H, Hoshida Y. Disseminative Recurrence Signature for Hepatocellular Carcinoma From Nonalcoholic Fatty Liver Disease. Gastro Hep Adv 2023; 2:681-683. [PMID: 37621719 PMCID: PMC10448704 DOI: 10.1016/j.gastha.2023.03.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Affiliation(s)
- N Fujiwara
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
- Department of Gastroenterology and Hepatology, Mie University, Tsu, Mie, Japan
| | - N Kubota
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - S Zhu
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
| | - S Nakagawa
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - H Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Y Hoshida
- Division of Digestive and Liver Diseases, Department of Internal Medicine, Liver Tumor Translational Research Program, Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas
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14
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Shoji H, Kitao K, Miyazawa T, Nakagawa S. Potentially reduced fusogenicity of syncytin-2 in New World monkeys. FEBS Open Bio 2023; 13:459-467. [PMID: 36647789 PMCID: PMC9989925 DOI: 10.1002/2211-5463.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 12/08/2022] [Revised: 01/04/2023] [Accepted: 01/12/2023] [Indexed: 01/18/2023] Open
Abstract
Syncytin-2 is a membrane fusion protein involved in placenta development that is derived from the endogenous retrovirus envelope gene acquired in the common ancestral lineage of New World and Old World monkeys (OWMs). It is known that syncytin-2 is conserved between apes and OWMs, suggesting its functional importance; however, syncytin-2 of common marmosets (Callithrix jacchus) exhibits lower fusogenic activity than those of humans and OWMs in human cell lines. To obtain insight into the functional diversity of syncytin-2 genes in primates, we examined the syncytin-2 gene in New World monkeys (NWMs). We experimentally evaluated the cell fusion ability of syncytin-2 in humans, C. jacchus, and tufted capuchins (Sapajus apella). We found that the cell fusion ability of S. apella was lower than that of human syncytin-2. Chimeric syncytin-2 constructs revealed that the amino acid differences in the surface unit of S. apella syncytin-2 were responsible for the weak cell fusion activity. In addition, genomic sequence analyses of syncytin-2 revealed that the open reading frames (ORFs) of syncytin-2 were highly conserved in seven apes and 22 OWMs; however, the syncytin-2 ORFs of three of 12 NWM species were truncated. Our results suggest that syncytin-2 in several NWMs may be of less importance than in OWMs and apes, and other syncytin-like genes may be required for placental development in various NWM species.
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Affiliation(s)
- Hiyori Shoji
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
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15
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Ohtsuka M, Imafuku J, Hori S, Kurosaki A, Nakamura A, Nakahara T, Yahata T, Bhat K, Papastefan ST, Nakagawa S, Quadros RM, Miura H, Gurumurthy CB. Delivering mRNAs to mouse tissues using the SEND system. bioRxiv 2023:2023.01.28.522652. [PMID: 36747769 PMCID: PMC9900891 DOI: 10.1101/2023.01.28.522652] [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: 01/31/2023]
Abstract
mRNAs produced in a cell are almost always translated within the same cell. Some mRNAs are transported to other cells of the organism through processes involving membrane nanotubes or extracellular vesicles. A recent report describes a surprising new phenomenon of encapsulating mRNAs inside virus-like particles (VLPs) to deliver them to other cells in a process that was named SEND (Selective Endogenous eNcapsidation for cellular Delivery). Although the seminal work demonstrates the SEND process in cultured cells, it is unknown whether this phenomenon occurs in vivo . Here, we demonstrate the SEND process in living organisms using specially designed genetically engineered mouse models. Our proof of principle study lays a foundation for the SEND-VLP system to potentially be used as a gene therapy tool to deliver therapeutically important mRNAs to tissues.
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16
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Kryukov K, Imanishi T, Nakagawa S. Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System. Methods Mol Biol 2023; 2632:215-226. [PMID: 36781731 DOI: 10.1007/978-1-0716-2996-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 04/27/2023]
Abstract
With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.
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Affiliation(s)
- Kirill Kryukov
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan.
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17
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Kitao K, Miyazawa T, Nakagawa S. Monotreme-Specific Conserved Putative Proteins Derived from Retroviral Reverse Transcriptase. Virus Evol 2022; 8:veac084. [PMID: 36176487 PMCID: PMC9514029 DOI: 10.1093/ve/veac084] [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: 03/30/2022] [Revised: 08/02/2022] [Accepted: 09/02/2022] [Indexed: 12/04/2022] Open
Abstract
Endogenous retroviruses (ERVs) have played an essential role in the evolution of mammals. ERV-derived genes are reported in the therians, many of which are involved in placental development; however, the contribution of the ERV-derived genes in monotremes, which are oviparous mammals, remains to be uncovered. Here, we conducted a comprehensive search for possible ERV-derived genes in platypus and echidna genomes and identified three reverse transcriptase-like genes named RTOM1, RTOM2, and RTOM3 clustered in the GRIP2 intron. Comparative genomic analyses revealed that RTOM1, RTOM2, and RTOM3 are strongly conserved and are under purifying selection between these species. These could be generated by tandem duplications before the divergence of platypus and echidna. All RTOM transcripts were specifically expressed in the testis, possibly suggesting their physiological importance. This is the first study reporting monotreme-specific de novo gene candidates derived from ERVs, which provides new insights into the unique evolution of monotremes.
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Affiliation(s)
- Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University , Sakyo-ku, Kyoto 606-8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University , Sakyo-ku, Kyoto 606-8507, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine , Isehara, Kanagawa 259-1193, Japan
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18
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Kryukov K, Jin L, Nakagawa S. Efficient compression of SARS-CoV-2 genome data using Nucleotide Archival Format. Patterns 2022; 3:100562. [PMID: 35818472 PMCID: PMC9259476 DOI: 10.1016/j.patter.2022.100562] [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] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Sakaguchi S, Urayama SI, Takaki Y, Hirosuna K, Wu H, Suzuki Y, Nunoura T, Nakano T, Nakagawa S. NeoRdRp: A Comprehensive Dataset for Identifying RNA-dependent RNA Polymerases of Various RNA Viruses from Metatranscriptomic Data. Microbes Environ 2022; 37. [PMID: 36002304 PMCID: PMC9530720 DOI: 10.1264/jsme2.me22001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Indexed: 11/12/2022] Open
Abstract
RNA viruses are distributed throughout various environments, and most have recently been identified by metatranscriptome sequencing. However, due to the high nucleotide diversity of RNA viruses, it is still challenging to identify novel RNA viruses from metatranscriptome data. To overcome this issue, we created a dataset of RNA-dependent RNA polymerase (RdRp) domains that are essential for all RNA viruses belonging to Orthornavirae. Genes with RdRp domains from various RNA viruses were clustered based on amino acid sequence similarities. A multiple sequence alignment was generated for each cluster, and a hidden Markov model (HMM) profile was created when the number of sequences was greater than three. We further refined 426 HMM profiles by detecting RefSeq RNA virus sequences and subsequently combined the hit sequences with the RdRp domains. As a result, 1,182 HMM profiles were generated from 12,502 RdRp domain sequences, and the dataset was named NeoRdRp. The majority of NeoRdRp HMM profiles successfully detected RdRp domains, specifically in the UniProt dataset. Furthermore, we compared the NeoRdRp dataset with two previously reported methods for RNA virus detection using metatranscriptome sequencing data. Our methods successfully identified the majority of RNA viruses in the datasets; however, some RNA viruses were not detected, similar to the other two methods. NeoRdRp may be repeatedly improved by the addition of new RdRp sequences and is applicable as a system for detecting various RNA viruses from diverse metatranscriptome data.
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Affiliation(s)
- Shoichi Sakaguchi
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Syun-Ichi Urayama
- Laboratory of Fungal Interaction and Molecular Biology (donated by IFO), Department of Life and Environmental Sciences, University of Tsukuba
| | - Yoshihiro Takaki
- Super-cuttingedge Grand and Advanced Research (SUGAR) Program, Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | | | - Hong Wu
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Youichi Suzuki
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - Takuro Nunoura
- Research Center for Bioscience and Nanoscience (CeBN), Japan Agency for Marine-Earth Science and Technology (JAMSTEC)
| | - Takashi Nakano
- Department of Microbiology and Infection Control, Faculty of Medicine, Osaka Medical and Pharmaceutical University
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine
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20
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Imakawa K, Kusama K, Kaneko-Ishino T, Nakagawa S, Kitao K, Miyazawa T, Ishino F. Endogenous Retroviruses and Placental Evolution, Development, and Diversity. Cells 2022; 11:cells11152458. [PMID: 35954303 PMCID: PMC9367772 DOI: 10.3390/cells11152458] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/01/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
The main roles of placentas include physical protection, nutrient and oxygen import, export of gasses and fetal waste products, and endocrinological regulation. In addition to physical protection of the fetus, the placentas must provide immune protection throughout gestation. These basic functions are well-conserved; however, placentas are undoubtedly recent evolving organs with structural and cellular diversities. These differences have been explained for the last two decades through co-opting genes and gene control elements derived from transposable elements, including endogenous retroviruses (ERVs). However, the differences in placental structures have not been explained or characterized. This manuscript addresses the sorting of ERVs and their integration into the mammalian genomes and provides new ways to explain why placental structures have diverged.
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Affiliation(s)
- Kazuhiko Imakawa
- Research Institute of Agriculture, Tokai University, Kumamoto 862-8652, Japan
- Correspondence: ; Tel.: +81-96-386-2652
| | - Kazuya Kusama
- Department of Endocrine Pharmacology, Tokyo University of Pharmacy and Life Sciences, Tokyo 192-0392, Japan
| | | | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Nakagawa 259-1193, Japan
| | - Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Life and Medical Sciences, Kyoto University, Kyoto 606-8507, Japan
| | - Fumitoshi Ishino
- Institute of Research, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
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21
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Kawata A, Imai K, Tamura Y, Kaida T, Mima K, Nakagawa S, Hayashi H, Yamashita Y, Ikeda O, Baba H. Gastrointestinal: Superior mesenteric vein aneurysm treated using interventional radiology. J Gastroenterol Hepatol 2022; 37:1209. [PMID: 35018662 DOI: 10.1111/jgh.15755] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/23/2021] [Accepted: 12/05/2021] [Indexed: 12/09/2022]
Affiliation(s)
- A Kawata
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - K Imai
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Y Tamura
- Department of Diagnostic Radiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - T Kaida
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - K Mima
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - S Nakagawa
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - H Hayashi
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Y Yamashita
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - O Ikeda
- Department of Diagnostic Radiology, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - H Baba
- Department of Gastroenterological Surgery, Graduate School of Life Sciences, Kumamoto University, Kumamoto, Japan
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22
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Takeuchi K, Ikeda Y, Senda M, Harada A, Okuwaki K, Fukuzawa K, Nakagawa S, Yu HY, Nagase L, Imai M, Sasaki M, Lo YH, Ito D, Osaka N, Fujii Y, Sasaki AT, Senda T. The GTP responsiveness of PI5P4Kβ evolved from a compromised trade-off between activity and specificity. Structure 2022; 30:886-899.e4. [PMID: 35504278 PMCID: PMC9177683 DOI: 10.1016/j.str.2022.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/22/2021] [Accepted: 04/06/2022] [Indexed: 10/18/2022]
Abstract
Unlike most kinases, phosphatidylinositol 5-phosphate 4-kinase β (PI5P4Kβ) utilizes GTP as a physiological phosphate donor and regulates cell growth under stress (i.e., GTP-dependent stress resilience). However, the genesis and evolution of its GTP responsiveness remain unknown. Here, we reveal that PI5P4Kβ has acquired GTP preference by generating a short dual-nucleotide-recognizing motif called the guanine efficient association (GEA) motif. Comparison of nucleobase recognition with 660 kinases and 128 G proteins has uncovered that most kinases and PI5P4Kβ use their main-chain atoms for adenine recognition, while the side-chain atoms are required for guanine recognition. Mutational analysis of the GEA motif revealed that the acquisition of GTP reactivity is accompanied by an extended activity toward inosine triphosphate (ITP) and xanthosine triphosphate (XTP). Along with the evolutionary analysis data that point to strong negative selection of the GEA motif, these results suggest that the GTP responsiveness of PI5P4Kβ has evolved from a compromised trade-off between activity and specificity, underpinning the development of the GTP-dependent stress resilience.
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Affiliation(s)
- Koh Takeuchi
- Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan.
| | - Yoshiki Ikeda
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Miki Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Ayaka Harada
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Koji Okuwaki
- Department of Chemistry and Research Center for Smart Molecules, Rikkyo University, Toshima, Tokyo 171-8501, Japan
| | - Kaori Fukuzawa
- School of Pharmacy and Pharmaceutical Sciences, Hoshi University, Shinagawa, Tokyo 142-8501, Japan
| | - So Nakagawa
- Department of Molecular Life Sciences, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Hong Yang Yu
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Lisa Nagase
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Misaki Imai
- Molecular Profiling Research Center for Drug Discovery and Cellular Molecular Biotechnology Research Institute, National Institute of Advanced Science and Technology, Aomi, Koto, Tokyo 135-0063, Japan; Graduate School of Pharmacological Sciences, The University of Tokyo, Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Mika Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Yu-Hua Lo
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Doshun Ito
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan
| | - Natsuki Osaka
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Yuki Fujii
- Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585, Japan
| | - Atsuo T Sasaki
- Division of Hematology and Oncology, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA; Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan; Department of Neurosurgery, Brain Tumor Center at UC Gardner Neuroscience Institute, Cincinnati, OH 45267, USA.
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Tsukuba, Ibaraki 305-0801, Japan; Department of Accelerator Science, School of High Energy Accelerator Science, SOKENDAI (The Graduate University for Advanced Studies), Oho, Tsukuba, Ibaraki 305-0801, Japan; Faculty of Pure and Applied Sciences, University of Tsukuba, Tennodai, Ibaraki 305-8571, Japan.
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23
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Komiya S, Matsuo Y, Nakagawa S, Morimoto Y, Kryukov K, Okada H, Hirota K. MinION, a portable long-read sequencer, enables rapid vaginal microbiota analysis in a clinical setting. BMC Med Genomics 2022; 15:68. [PMID: 35337329 PMCID: PMC8953062 DOI: 10.1186/s12920-022-01218-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [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: 08/14/2021] [Accepted: 02/14/2022] [Indexed: 01/13/2023] Open
Abstract
Background It has been suggested that the local microbiota in the reproductive organs is relevant to women's health and may also affect pregnancy outcomes. Analysis of partial 16S ribosomal RNA (rRNA) gene sequences generated by short-read sequencers has been used to identify vaginal and endometrial microbiota, but it requires a long time to obtain the results, making it unsuitable for rapid bacterial identification from a small specimen amount in a clinical context. Methods We developed a simple workflow using the nanopore sequencer MinION that allows high-resolution and rapid differentiation of vaginal microbiota. Vaginal samples collected from 18 participants were subjected to DNA extraction and full-length 16S rRNA gene sequencing with MinION. Results The principal coordinate analysis showed no differences in the bacterial compositions regardless of the sample collection method. The analysis of vaginal microbiota could be completed with a total analysis time of approximately four hours, allowing same-day results. Taxonomic profiling by MinION sequencing revealed relatively low diversity of the vaginal bacterial community, identifying the prevailing Lactobacillus species and several causative agents of bacterial vaginosis. Conclusions Full-length 16S rRNA gene sequencing analysis with MinION provides a rapid means for identifying vaginal bacteria with higher resolution. Species-level profiling of human vaginal microbiota by MinION sequencing can allow the analysis of associations with conditions such as genital infections, endometritis, and threatened miscarriage. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01218-8.
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Affiliation(s)
- Shinnosuke Komiya
- Department of Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Osaka, Japan.,HORAC Grand Front Osaka Clinic, Osaka, Japan
| | - Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | | | - Kirill Kryukov
- Department of Informatics, National Institute of Genetics, Shizuoka, Japan
| | - Hidetaka Okada
- Department of Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Osaka, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan
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24
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Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y. Uhrf1 governs the proliferation and differentiation of muscle satellite cells. iScience 2022; 25:103928. [PMID: 35243267 PMCID: PMC8886052 DOI: 10.1016/j.isci.2022.103928] [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: 04/20/2021] [Revised: 12/06/2021] [Accepted: 02/10/2022] [Indexed: 11/19/2022] Open
Abstract
DNA methylation is an essential form of epigenetic regulation responsible for cellular identity. In muscle stem cells, termed satellite cells, DNA methylation patterns are tightly regulated during differentiation. However, it is unclear how these DNA methylation patterns affect the function of satellite cells. We demonstrate that a key epigenetic regulator, ubiquitin like with PHD and RING finger domains 1 (Uhrf1), is activated in proliferating myogenic cells but not expressed in quiescent satellite cells or differentiated myogenic cells in mice. Ablation of Uhrf1 in mouse satellite cells impairs their proliferation and differentiation, leading to failed muscle regeneration. Uhrf1-deficient myogenic cells exhibited aberrant upregulation of transcripts, including Sox9, with the reduction of DNA methylation level of their promoter and enhancer region. These findings show that Uhrf1 is a critical epigenetic regulator of proliferation and differentiation in satellite cells, by controlling cell-type-specific gene expression via maintenance of DNA methylation. Uhrf1 is activated in proliferating myogenic cells Uhrf1 in satellite cells is required for muscle regeneration Ablation of Uhrf1 in satellite cells impairs their proliferation and differentiation Uhrf1 controls cell-type-specific transcripts via maintenance of DNA methylation
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Affiliation(s)
- Hiroshi Sakai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
| | - Yuichiro Sawada
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Naohito Tokunaga
- Division of Analytical Bio-Medicine, Advanced Research Support Center, Ehime University, Toon, Ehime 791-0295, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Iori Sakakibara
- Department of Nutritional Physiology, Institute of Medical Nutrition, Tokushima University Graduate School, Kuramoto-cho, Tokushima 770-8503, Japan
| | - Yusuke Ono
- Department of Muscle Development and Regeneration, Institute of Molecular Embryology and Genetics, Kumamoto University, Honjo, Kumamoto 860-0811, Japan
| | - So-ichiro Fukada
- Project for Muscle Stem Cell Biology, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-0054, Japan
| | - Tadahiko Kikugawa
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Takashi Saika
- Department of Urology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, Ehime 791-0295, Japan
- Department of Pathophysiology, Ehime University Graduate School of Medicine, Toon, Ehime 791-0295, Japan
- Corresponding author
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25
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Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, Motozono C, Saito A, Nakagawa S, Sato K. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep 2022; 38:110218. [PMID: 34968415 DOI: 10.1101/2021.07.28.454085] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [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: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 05/22/2023] Open
Abstract
SARS-CoV-2 Lambda, a variant of interest, has spread in some South American countries; however, its virological features and evolutionary traits remain unclear. In this study, we use pseudoviruses and reveal that the spike protein of the Lambda variant is more infectious than that of other variants due to the T76I and L452Q mutations. The RSYLTPGD246-253N mutation, a unique 7-amino acid deletion in the N-terminal domain of the Lambda spike protein, is responsible for evasion from neutralizing antibodies and further augments antibody-mediated enhancement of infection. Although this mutation generates a nascent N-linked glycosylation site, the additional N-linked glycan is dispensable for the virological property conferred by this mutation. Since the Lambda variant has dominantly spread according to the increasing frequency of the isolates harboring the RSYLTPGD246-253N mutation, our data suggest that the RSYLTPGD246-253N mutation is closely associated with the substantial spread of the Lambda variant in South America.
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Laboratory of Systems Virology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto 6068507, Japan; Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 6068501, Japan
| | - Jiaqi Wu
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
| | - Jiri Zahradnik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Daichi Yamasoba
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Faculty of Medicine, Kobe University, Hyogo 6500017, Japan
| | - Erika P Butlertanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Yuri L Tanaka
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan
| | - Yafei Liu
- Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Laboratory of Immunochemistry, World Premier International Immunology Frontier Research Centre, Osaka University, Osaka 5650871, Japan
| | - Nanami Morizako
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan
| | - Kotaro Shirakawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Yasuhiro Kazuma
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Ryosuke Nomura
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Yoshihito Horisawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Kenzo Tokunaga
- Department of Pathology, National Institute of Infectious Diseases, Tokyo 1628640, Japan
| | - Takamasa Ueno
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto 6068507, Japan
| | - Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Hisashi Arase
- Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan; Department of Immunochemistry, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Center for Infectious Disease Education and Research, Osaka University, Osaka 5650871, Japan
| | - Chihiro Motozono
- Division of Infection and immunity, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan; Bioinformation and DDBJ Center, National Institute of Genetics, Mishima, Shizuoka 4118540, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan; Graduate School of Medicine, The University of Tokyo, 1130033 Tokyo, Japan.
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26
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Saito A, Irie T, Suzuki R, Maemura T, Nasser H, Uriu K, Kosugi Y, Shirakawa K, Sadamasu K, Kimura I, Ito J, Wu J, Iwatsuki-Horimoto K, Ito M, Yamayoshi S, Loeber S, Tsuda M, Wang L, Ozono S, Butlertanaka EP, Tanaka YL, Shimizu R, Shimizu K, Yoshimatsu K, Kawabata R, Sakaguchi T, Tokunaga K, Yoshida I, Asakura H, Nagashima M, Kazuma Y, Nomura R, Horisawa Y, Yoshimura K, Takaori-Kondo A, Imai M, Tanaka S, Nakagawa S, Ikeda T, Fukuhara T, Kawaoka Y, Sato K. Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature 2022; 602:300-306. [PMID: 34823256 PMCID: PMC8828475 DOI: 10.1038/s41586-021-04266-9] [Citation(s) in RCA: 330] [Impact Index Per Article: 165.0] [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: 07/22/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022]
Abstract
During the current coronavirus disease 2019 (COVID-19) pandemic, a variety of mutations have accumulated in the viral genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and, at the time of writing, four variants of concern are considered to be potentially hazardous to human society1. The recently emerged B.1.617.2/Delta variant of concern is closely associated with the COVID-19 surge that occurred in India in the spring of 2021 (ref. 2). However, the virological properties of B.1.617.2/Delta remain unclear. Here we show that the B.1.617.2/Delta variant is highly fusogenic and notably more pathogenic than prototypic SARS-CoV-2 in infected hamsters. The P681R mutation in the spike protein, which is highly conserved in this lineage, facilitates cleavage of the spike protein and enhances viral fusogenicity. Moreover, we demonstrate that the P681R-bearing virus exhibits higher pathogenicity compared with its parental virus. Our data suggest that the P681R mutation is a hallmark of the virological phenotype of the B.1.617.2/Delta variant and is associated with enhanced pathogenicity.
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Affiliation(s)
- Akatsuki Saito
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan ,grid.410849.00000 0001 0657 3887Center for Animal Disease Control, University of Miyazaki, Miyazaki, Japan ,grid.410849.00000 0001 0657 3887Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takashi Irie
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Rigel Suzuki
- grid.39158.360000 0001 2173 7691Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Tadashi Maemura
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.14003.360000 0001 2167 3675Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI USA
| | - Hesham Nasser
- grid.274841.c0000 0001 0660 6749Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan ,grid.33003.330000 0000 9889 5690Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt
| | - Keiya Uriu
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Kosugi
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kotaro Shirakawa
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenji Sadamasu
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Izumi Kimura
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jumpei Ito
- grid.26999.3d0000 0001 2151 536XDivision of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Jiaqi Wu
- grid.265061.60000 0001 1516 6626Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan ,grid.419082.60000 0004 1754 9200CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Kiyoko Iwatsuki-Horimoto
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Mutsumi Ito
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Seiya Yamayoshi
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.45203.300000 0004 0489 0290The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | - Samantha Loeber
- grid.28803.310000 0001 0701 8607Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI USA
| | - Masumi Tsuda
- grid.39158.360000 0001 2173 7691Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan ,grid.39158.360000 0001 2173 7691Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan
| | - Lei Wang
- grid.39158.360000 0001 2173 7691Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan ,grid.39158.360000 0001 2173 7691Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan
| | - Seiya Ozono
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Erika P. Butlertanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Yuri L. Tanaka
- grid.410849.00000 0001 0657 3887Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki, Japan
| | - Ryo Shimizu
- grid.274841.c0000 0001 0660 6749Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan ,grid.274841.c0000 0001 0660 6749Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kenta Shimizu
- grid.39158.360000 0001 2173 7691Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan
| | - Kumiko Yoshimatsu
- grid.39158.360000 0001 2173 7691Institute for Genetic Medicine, Hokkaido University, Hokkaido, Japan
| | - Ryoko Kawabata
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- grid.257022.00000 0000 8711 3200Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenzo Tokunaga
- grid.410795.e0000 0001 2220 1880Department of Pathology, National Institute of Infectious Diseases, Tokyo, Japan
| | - Isao Yoshida
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Hiroyuki Asakura
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Mami Nagashima
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Yasuhiro Kazuma
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Ryosuke Nomura
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yoshihito Horisawa
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kazuhisa Yoshimura
- grid.417096.dTokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | - Akifumi Takaori-Kondo
- grid.258799.80000 0004 0372 2033Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masaki Imai
- grid.26999.3d0000 0001 2151 536XDivision of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan ,grid.45203.300000 0004 0489 0290The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan
| | | | - Shinya Tanaka
- Department of Cancer Pathology, Faculty of Medicine, Hokkaido University, Hokkaido, Japan. .,Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Hokkaido, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan. .,CREST, Japan Science and Technology Agency, Saitama, Japan.
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto, Japan.
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido, Japan.
| | - Yoshihiro Kawaoka
- Division of Virology, Institute of Medical Science, University of Tokyo, Tokyo, Japan. .,Influenza Research Institute, Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA. .,The Research Center for Global Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan. .,CREST, Japan Science and Technology Agency, Saitama, Japan.
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27
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Bouquet J, Auberger N, Ashmus R, King D, Bordes A, Fontelle N, Nakagawa S, Madden Z, Proceviat C, Kato A, Désiré J, Vocadlo DJ, Blériot Y. Structural variation of the 3-acetamido-4,5,6-trihydroxyazepane iminosugar through epimerization and C-alkylation leads to low micromolar HexAB and NagZ inhibitors. Org Biomol Chem 2021; 20:619-629. [PMID: 34940771 DOI: 10.1039/d1ob02280f] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of seven-membered iminosugars derived from a 3S-acetamido-4R,5R,6S-trihydroxyazepane scaffold and their evaluation as inhibitors of functionally related exo-N-acetylhexosaminidases including human O-GlcNAcase (OGA), human lysosomal β-hexosaminidase (HexAB), and Escherichia coli NagZ. Capitalizing on the flexibility of azepanes and the active site tolerances of hexosaminidases, we explore the effects of epimerization of stereocenters at C-3, C-5 and C-6 and C-alkylation at the C-2 or C-7 positions. Accordingly, epimerization at C-6 (L-ido) and at C-5 (D-galacto) led to selective HexAB inhibitors whereas introduction of a propyl group at C-7 on the C-3 epimer furnished a potent NagZ inhibitor.
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Affiliation(s)
- J Bouquet
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - N Auberger
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - R Ashmus
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - D King
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - A Bordes
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - N Fontelle
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - S Nakagawa
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - Z Madden
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - C Proceviat
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - A Kato
- Department of Hospital Pharmacy, University of Toyama, 2630 Sugitani, Toyama 930-0194, Japan.
| | - J Désiré
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
| | - D J Vocadlo
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia, V5S 1P6, Canada.
| | - Y Blériot
- Université de Poitiers, IC2MP, UMR CNRS 7285, OrgaSynth Team, Glyco group, 4 rue Michel Brunet, 86073 Poitiers cedex 09, France.
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28
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Uriu K, Kimura I, Shirakawa K, Takaori-Kondo A, Nakada TA, Kaneda A, Nakagawa S, Sato K. Neutralization of the SARS-CoV-2 Mu Variant by Convalescent and Vaccine Serum. N Engl J Med 2021; 385:2397-2399. [PMID: 34731554 DOI: 10.1101/2021.09.06.459005] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
AbstractOn August 30, 2021, the WHO classified the SARS-CoV-2 Mu variant (B.1.621 lineage) as a new variant of interest. The WHO defines “comparative assessment of virus characteristics and public health risks” as primary action in response to the emergence of new SARS-CoV-2 variants. Here, we demonstrate that the Mu variant is highly resistant to sera from COVID-19 convalescents and BNT162b2-vaccinated individuals. Direct comparison of different SARS-CoV-2 spike proteins revealed that Mu spike is more resistant to serum-mediated neutralization than all other currently recognized variants of interest (VOI) and concern (VOC). This includes the Beta variant (B.1.351) that has been suggested to represent the most resistant variant to convalescent and vaccinated sera to date (e.g., Collier et al, Nature, 2021; Wang et al, Nature, 2021). Since breakthrough infection by newly emerging variants is a major concern during the current COVID-19 pandemic (Bergwerk et al., NEJM, 2021), we believe that our findings are of significant public health interest. Our results will help to better assess the risk posed by the Mu variant for vaccinated, previously infected and naïve populations.
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Affiliation(s)
| | | | | | | | | | | | | | - Kei Sato
- University of Tokyo, Tokyo, Japan
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29
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Affiliation(s)
| | | | | | | | | | | | | | - Kei Sato
- University of Tokyo, Tokyo, Japan
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30
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Kimura I, Kosugi Y, Wu J, Zahradnik J, Yamasoba D, Butlertanaka EP, Tanaka YL, Uriu K, Liu Y, Morizako N, Shirakawa K, Kazuma Y, Nomura R, Horisawa Y, Tokunaga K, Ueno T, Takaori-Kondo A, Schreiber G, Arase H, Motozono C, Saito A, Nakagawa S, Sato K. The SARS-CoV-2 Lambda variant exhibits enhanced infectivity and immune resistance. Cell Rep 2021; 38:110218. [PMID: 34968415 PMCID: PMC8683271 DOI: 10.1016/j.celrep.2021.110218] [Citation(s) in RCA: 91] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022] Open
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31
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Kitao K, Nakagawa S, Miyazawa T. An ancient retroviral RNA element hidden in mammalian genomes and its involvement in co-opted retroviral gene regulation. Retrovirology 2021; 18:36. [PMID: 34753509 PMCID: PMC8579622 DOI: 10.1186/s12977-021-00580-2] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 01/19/2023] Open
Abstract
Background Retroviruses utilize multiple unique RNA elements to control RNA processing and translation. However, it is unclear what functional RNA elements are present in endogenous retroviruses (ERVs). Gene co-option from ERVs sometimes entails the conservation of viral cis-elements required for gene expression, which might reveal the RNA regulation in ERVs. Results Here, we characterized an RNA element found in ERVs consisting of three specific sequence motifs, called SPRE. The SPRE-like elements were found in different ERV families but not in any exogenous viral sequences examined. We observed more than a thousand of copies of the SPRE-like elements in several mammalian genomes; in human and marmoset genomes, they overlapped with lineage-specific ERVs. SPRE was originally found in human syncytin-1 and syncytin-2. Indeed, several mammalian syncytin genes: mac-syncytin-3 of macaque, syncytin-Ten1 of tenrec, and syncytin-Car1 of Carnivora, contained the SPRE-like elements. A reporter assay revealed that the enhancement of gene expression by SPRE depended on the reporter genes. Mutation of SPRE impaired the wild-type syncytin-2 expression while the same mutation did not affect codon-optimized syncytin-2, suggesting that SPRE activity depends on the coding sequence. Conclusions These results indicate multiple independent invasions of various mammalian genomes by retroviruses harboring SPRE-like elements. Functional SPRE-like elements are found in several syncytin genes derived from these retroviruses. This element may facilitate the expression of viral genes, which were suppressed due to inefficient codon frequency or repressive elements within the coding sequences. These findings provide new insights into the long-term evolution of RNA elements and molecular mechanisms of gene expression in retroviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s12977-021-00580-2.
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Affiliation(s)
- Koichi Kitao
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan.
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32
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Ishimoto K, Hatanaka N, Otani S, Maeda S, Xu B, Yasugi M, Moore JE, Suzuki M, Nakagawa S, Yamasaki S. Tea crude extracts effectively inactivate severe acute respiratory syndrome coronavirus 2. Lett Appl Microbiol 2021; 74:2-7. [PMID: 34695222 PMCID: PMC8661916 DOI: 10.1111/lam.13591] [Citation(s) in RCA: 3] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 10/03/2021] [Accepted: 10/19/2021] [Indexed: 12/29/2022]
Abstract
It is well known that black and green tea extracts, particularly polyphenols, have antimicrobial activity against various pathogenic microbes including viruses. However, there is limited data on the antiviral activity against severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), which emerged rapidly in China in late 2019 and which has been responsible for coronavirus disease 2019 (COVID‐19) pandemic globally. In this study, 20 compounds and three extracts were obtained from black and green tea and found that three tea extracts showed significant antiviral activity against SARS‐CoV‐2, whereby the viral titre decreased about 5 logs TCID50 per ml by 1·375 mg ml−1 black tea extract and two‐fold diluted tea bag infusion obtained from black tea when incubated at 25°C for 10 s. However, when concentrations of black and green tea extracts were equally adjusted to 344 µg ml−1, green tea extracts showed more antiviral activity against SARS‐CoV‐2. This simple and highly respected beverage may be a cheap and widely acceptable means to reduce SARS‐CoV‐2 viral burden in the mouth and upper gastrointestinal and respiratory tracts in developed as well as developing countries.
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Affiliation(s)
- K Ishimoto
- Laboratory of Innovative Food Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,Global Center for Medical Engineering and Informatic, Osaka University, Osaka, Japan
| | - N Hatanaka
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Izumisano, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - S Otani
- Laboratory of Innovative Food Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,R&D Group, Mitsui Norin Co. Ltd, Fujieda, Shizuoka, Japan
| | - S Maeda
- Laboratory of Innovative Food Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,R&D Group, Mitsui Norin Co. Ltd, Fujieda, Shizuoka, Japan
| | - B Xu
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - M Yasugi
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Izumisano, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Izumisano, Osaka, Japan
| | - J E Moore
- Northern Ireland Public Health Laboratory, Nightingale (Belfast City) Hospital, Belfast, UK
| | - M Suzuki
- Laboratory of Innovative Food Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,R&D Group, Mitsui Norin Co. Ltd, Fujieda, Shizuoka, Japan
| | - S Nakagawa
- Laboratory of Innovative Food Science, Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan.,Global Center for Medical Engineering and Informatic, Osaka University, Osaka, Japan.,Laboratory of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Osaka University, Osaka, Japan
| | - S Yamasaki
- Department of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Izumisano, Osaka, Japan.,Asian Health Science Research Institute, Osaka Prefecture University, Izumisano, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Izumisano, Osaka, Japan
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33
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Poller C, Nageswaran V, Kuss A, Gast M, Tzvetkova A, Wang X, Weiss S, Mochmann L, Zeller T, Beling A, Nakagawa S, Landmesser U, Rauch B, Klingel K, Haghikia A. A novel class of small tRNA-like noncoding transcripts arising from the human NEAT1-MALAT1 region critically influences innate immunity and angiogenesis. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3357] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
The evolutionary conserved NEAT1-MALAT1 gene cluster encounters high interest in cardiovascular medicine and oncology. The cluster generates large primary transcripts which remain nuclear, whereas novel tRNA-like transcripts (mascRNA, menRNA) enzymatically generated from these precursors translocate to the cytosol. We previously found that NEAT1 and MALAT1 deficient mice display accelerated atherosclerosis and vascular inflammation due to immune dysfunctions.
Methods
While the previously investigated mice were deficient in the entire NEAT1 or MALAT1 locus, here we aimed to selectively disrupt only tRNA-like transcripts “menRNA” arising from NEAT1, or “mascRNA” arising from MALAT1. To none of these a biological function has been assigned so far. Both lncRNAs give rise to transcripts of vastly different size (NEAT1: 23kb MENb, 3.7kb MENe, 59nt “menRNA”; MALAT1: 8.3 kb primary, 59nt “mascRNA”), and traditional knockout methods are unable to selectively inactivate one of the small transcripts only. Through CRISPR/Cas9 editing we therefore developed human monocyte-macrophage cell lines with short deletions in the respective tRNA-encoding sequences to disrupt normal menRNA or mascRNA formation, respectively. These editing procedures do not affect transcription of the respective lncRNA parent transcripts, and also not disturb regular formation of the triple-helix structures at their 3'-ends which support stabilization of the respective lncRNAs (Fig. 1).
Results
We found the tRNA-like transcripts menRNA and mascRNA critically influence innate immunity and angiogenesis. In addition to common anomalies resulting from their selective CRISPR-Cas9 mediated deletion (Fig. 1), there are specific disturbances associated with either Δmasc or Δmen cells (Fig. 2).
Both ΔmascRNA and ΔmenRNA human monocytes show profoundly altered ribosomal RNA/protein and tRNA-modifying enzyme expression, display anomalous growth/ angiogenetic factor expression, fundamentally change angiogenetic patterns in co-cultures with human endothelial cells, and have gravely disturbed innate immune responses (LPS, DNA and RNA viruses) (Fig. 1).
CRISPR-engineered ΔmenRNA cells share remakable similarities with human post-MI PBMCs, suggesting the NEAT1-menRNA system may significantly contribute to post-MI residual inflammatory risk despite optimal standard therapy (Fig. 2).
Conclusions
Beyond prior work in knockout mice documenting immune function of the NEAT1-MALAT1 cluster, the current study identifies menRNA and mascRNA as important novel components of human innate immunity with relevance for angiogenetic processes. These data provide a second mechanistic link for the apparent relevance of the NEAT1-MALAT1 gene cluster in cardiovascular and malignant diseases. As prototypes of a novel class of small noncoding RNAs (distinct from miRNAs and siRNAs) they may constitute cytosolic therapeutic targets.
Funding Acknowledgement
Type of funding sources: Other. Main funding source(s): DZHK Shared Expertise Project/B19-006_SE/FKZ 81X2100257/Transcriptome analysis of circulating immune cells to improve the assessment of prognosis and the response to novel anti-inflammatory treatments after myocardial infarction Figure 1. Common anomaliesFigure 2. Specific anomalies
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Affiliation(s)
- C Poller
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - V Nageswaran
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - A Kuss
- University of Greifswald, Department of Functional Genomics, Greifswald, Germany
| | - M Gast
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - A Tzvetkova
- University of Greifswald, Department of Functional Genomics, Greifswald, Germany
| | - X Wang
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - S Weiss
- University of Greifswald, Department of Functional Genomics, Greifswald, Germany
| | - L Mochmann
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - T Zeller
- University Heart Center Hamburg, General and interventional cardiology, Hamburg, Germany
| | - A Beling
- Charite University Hospital, Institute of Biochemistry, Berlin, Germany
| | - S Nakagawa
- Hokkaido University, Faculty of Pharmaceutical Sciences, Sapporo, Japan
| | - U Landmesser
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
| | - B Rauch
- Universitaetsmedizin Greifswald, Department of Pharmacology, Greifswald, Germany
| | - K Klingel
- University Hospital, Department of Pathology, Tübingen, Germany
| | - A Haghikia
- Charite - Campus Benjamin Franklin, Cardiology CC11 Cardiovascular Medicine, Berlin, Germany
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Foo YZ, Sutherland CAM, Burton NS, Nakagawa S, Rhodes G. Accuracy in Facial Trustworthiness Impressions: Kernel of Truth or Modern Physiognomy? A Meta-Analysis. Pers Soc Psychol Bull 2021; 48:1580-1596. [PMID: 34609231 DOI: 10.1177/01461672211048110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Being able to identify trustworthy strangers is a critical social skill. However, whether such impressions are accurate is debatable. Critically, the field currently lacks a quantitative summary of the evidence. To address this gap, we conducted two meta-analyses. We tested whether there is a correlation between perceived and actual trustworthiness across faces, and whether perceivers show above-chance accuracy at assessing trustworthiness. Both meta-analyses revealed significant, modest accuracy (face level, r = .14; perceiver level, r = .27). Perceiver-level effects depended on domain, with aggressiveness and sexual unfaithfulness having stronger effects than agreeableness, criminality, financial reciprocity, and honesty. We also applied research weaving to map the literature, revealing potential biases, including a preponderance of Western studies, a lack of "cross-talk" between research groups, and clarity issues. Overall, this modest accuracy is unlikely to be of practical utility. Moreover, we strongly urge the field to improve reporting standards and generalizability of the results.
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Affiliation(s)
- Y Z Foo
- University of Western Australia, Crawley, Australia.,University of New South Wales, Randwick, Australia
| | - C A M Sutherland
- University of Western Australia, Crawley, Australia.,University of Aberdeen, UK
| | - N S Burton
- University of Western Australia, Crawley, Australia
| | - S Nakagawa
- University of New South Wales, Randwick, Australia
| | - G Rhodes
- University of Western Australia, Crawley, Australia
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Kryukov K, Ueda MT, Nakagawa S, Imanishi T. Sequence Compression Benchmark (SCB) database-A comprehensive evaluation of reference-free compressors for FASTA-formatted sequences. Gigascience 2021; 9:5867695. [PMID: 32627830 PMCID: PMC7336184 DOI: 10.1093/gigascience/giaa072] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/01/2020] [Accepted: 06/15/2020] [Indexed: 01/22/2023] Open
Abstract
Background Nearly all molecular sequence databases currently use gzip for data compression. Ongoing rapid accumulation of stored data calls for a more efficient compression tool. Although numerous compressors exist, both specialized and general-purpose, choosing one of them was difficult because no comprehensive analysis of their comparative advantages for sequence compression was available. Findings We systematically benchmarked 430 settings of 48 compressors (including 29 specialized sequence compressors and 19 general-purpose compressors) on representative FASTA-formatted datasets of DNA, RNA, and protein sequences. Each compressor was evaluated on 17 performance measures, including compression strength, as well as time and memory required for compression and decompression. We used 27 test datasets including individual genomes of various sizes, DNA and RNA datasets, and standard protein datasets. We summarized the results as the Sequence Compression Benchmark database (SCB database, http://kirr.dyndns.org/sequence-compression-benchmark/), which allows custom visualizations to be built for selected subsets of benchmark results. Conclusion We found that modern compressors offer a large improvement in compactness and speed compared to gzip. Our benchmark allows compressors and their settings to be compared using a variety of performance measures, offering the opportunity to select the optimal compressor on the basis of the data type and usage scenario specific to a particular application.
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Affiliation(s)
- Kirill Kryukov
- Correspondence address. Kirill Kryukov, Department of Genomics and Evolutionary Biology, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan. E-mail:
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
- Current address: Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Bunkyo, Tokyo 113-8510, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259–1193, Japan
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Hirabayashi A, Yahara K, Mitsuhashi S, Nakagawa S, Imanishi T, Ha VTT, Nguyen AV, Nguyen ST, Shibayama K, Suzuki M. Plasmid analysis of NDM metallo-β-lactamase-producing Enterobacterales isolated in Vietnam. PLoS One 2021; 16:e0231119. [PMID: 34319973 PMCID: PMC8318238 DOI: 10.1371/journal.pone.0231119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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] [Received: 03/12/2020] [Accepted: 06/21/2021] [Indexed: 11/19/2022] Open
Abstract
Carbapenem-resistant Enterobacterales (CRE) represent a serious threat to public health due to the lack of treatment and high mortality. The rate of antimicrobial resistance of Enterobacterales isolates to major antimicrobials, including carbapenems, is much higher in Vietnam than in Western countries, but the reasons remain unknown due to the lack of genomic epidemiology research. A previous study suggested that carbapenem resistance genes, such as the carbapenemase gene blaNDM, spread via plasmids among Enterobacterales in Vietnam. In this study, we characterized blaNDM-carrying plasmids in Enterobacterales isolated in Vietnam, and identified several possible cases of horizontal transfer of plasmids both within and among species of bacteria. Twenty-five carbapenem-nonsusceptible isolates from a medical institution in Hanoi were sequenced on Illumina short-read sequencers, and 13 blaNDM-positive isolates, including isolates of Klebsiella pneumoniae, Escherichia coli, Citrobacter freundii, Morganella morganii, and Proteus mirabilis, were further sequenced on an Oxford Nanopore Technologies long-read sequencer to obtain complete plasmid sequences. Almost identical 73 kb IncFII(pSE11)::IncN hybrid plasmids carrying blaNDM-1 were found in a P. mirabilis isolate and an M. morganii isolate. A 112 kb IncFII(pRSB107)::IncN hybrid plasmid carrying blaNDM-1 in an E. coli isolate had partially identical sequences with a 39 kb IncR plasmid carrying blaNDM-1 and an 88 kb IncFII(pHN7A8)::IncN hybrid plasmid in a C. freundii isolate. 148-149 kb IncFIA(Hl1)::IncA/C2 plasmids and 75-76 kb IncFII(Yp) plasmids, both carrying blaNDM-1 were shared among three sequence type 11 (ST11) isolates and three ST395 isolates of K. pneumoniae, respectively. Most of the plasmids co-carried genes conferring resistance to clinically relevant antimicrobials, including third-generation cephalosporins, aminoglycosides, and fluoroquinolones, in addition to blaNDM-1. These results provide insight into the genetic basis of CRE in Vietnam, and could help control nosocomial infections.
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Affiliation(s)
- Aki Hirabayashi
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Koji Yahara
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Satomi Mitsuhashi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Van Thi Thu Ha
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - An Van Nguyen
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - Son Thai Nguyen
- Microbiology Department, Hospital 103, Military Medical University, Hanoi, Vietnam
| | - Keigo Shibayama
- Department of Bacteriology II, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (KS); (MS)
| | - Masato Suzuki
- AMR Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail: (KS); (MS)
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Motozono C, Toyoda M, Zahradnik J, Saito A, Nasser H, Tan TS, Ngare I, Kimura I, Uriu K, Kosugi Y, Yue Y, Shimizu R, Ito J, Torii S, Yonekawa A, Shimono N, Nagasaki Y, Minami R, Toya T, Sekiya N, Fukuhara T, Matsuura Y, Schreiber G, Ikeda T, Nakagawa S, Ueno T, Sato K. SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe 2021; 29:1124-1136.e11. [PMID: 34171266 PMCID: PMC8205251 DOI: 10.1016/j.chom.2021.06.006] [Citation(s) in RCA: 325] [Impact Index Per Article: 108.3] [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: 04/13/2021] [Revised: 05/22/2021] [Accepted: 06/09/2021] [Indexed: 01/15/2023]
Abstract
Many SARS-CoV-2 variants with naturally acquired mutations have emerged. These mutations can affect viral properties such as infectivity and immune resistance. Although the sensitivity of naturally occurring SARS-CoV-2 variants to humoral immunity has been investigated, sensitivity to human leukocyte antigen (HLA)-restricted cellular immunity remains largely unexplored. Here, we demonstrate that two recently emerging mutations in the receptor-binding domain of the SARS-CoV-2 spike protein, L452R (in B.1.427/429 and B.1.617) and Y453F (in B.1.1.298), confer escape from HLA-A24-restricted cellular immunity. These mutations reinforce affinity toward the host entry receptor ACE2. Notably, the L452R mutation increases spike stability, viral infectivity, viral fusogenicity, and thereby promotes viral replication. These data suggest that HLA-restricted cellular immunity potentially affects the evolution of viral phenotypes and that a further threat of the SARS-CoV-2 pandemic is escape from cellular immunity.
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Affiliation(s)
- Chihiro Motozono
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Mako Toyoda
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jiri Zahradnik
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Akatsuki Saito
- Department of Veterinary Science, Faculty of Agriculture, University of Miyazaki, Miyazaki 8892192, Japan; Center for Animal Disease Control, University of Miyazaki, Miyazaki 8892192, Japan; Graduate School of Medicine and Veterinary Medicine, University of Miyazaki, Miyazaki 8892192, Japan
| | - Hesham Nasser
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan; Department of Clinical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41511, Egypt
| | - Toong Seng Tan
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Isaac Ngare
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yusuke Kosugi
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yuan Yue
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Ryo Shimizu
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan
| | - Jumpei Ito
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Shiho Torii
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Akiko Yonekawa
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Nobuyuki Shimono
- Department of Medicine and Biosystemic Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka 8128582, Japan
| | - Yoji Nagasaki
- Division of Infectious Diseases, Clinical Research Institute, National Hospitalization Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Rumi Minami
- Internal Medicine, Clinical Research Institute, National Hospital Organization, Kyushu Medical Center, Fukuoka 8108563, Japan
| | - Takashi Toya
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Noritaka Sekiya
- Department of Infection Prevention and Control, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan; Department of Clinical Laboratory, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo 1138677, Japan
| | - Takasuke Fukuhara
- Department of Microbiology and Immunology, Graduate School of Medicine, Hokkaido University, Hokkaido 0608638, Japan
| | - Yoshiharu Matsuura
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan; Division of Microbiology and Immunology, Center for Infectious Diseases Education and Research, Osaka University, Osaka 5650871, Japan; Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Osaka 5650871, Japan
| | - Gideon Schreiber
- Department of Biological Chemistry, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
| | - Takamasa Ueno
- Division of Infection and Immunity, Joint Research Center for Human Retrovirus Infection, Kumamoto University, Kumamoto 8600811, Japan.
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, The Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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Kimura Y, Yamashita T, Seto R, Imanishi M, Honda M, Nakagawa S, Saga Y, Takenaka S, Yu LJ, Madigan MT, Wang-Otomo ZY. Circular dichroism and resonance Raman spectroscopies of bacteriochlorophyll b-containing LH1-RC complexes. Photosynth Res 2021; 148:77-86. [PMID: 33834357 DOI: 10.1007/s11120-021-00831-5] [Citation(s) in RCA: 7] [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] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
The core light-harvesting complexes (LH1) in bacteriochlorophyll (BChl) b-containing purple phototrophic bacteria are characterized by a near-infrared absorption maximum around 1010 nm. The determinative cause for this ultra-redshift remains unclear. Here, we present results of circular dichroism (CD) and resonance Raman measurements on the purified LH1 complexes in a reaction center-associated form from a mesophilic and a thermophilic Blastochloris species. Both the LH1 complexes displayed purely positive CD signals for their Qy transitions, in contrast to those of BChl a-containing LH1 complexes. This may reflect differences in the conjugation system of the bacteriochlorin between BChl b and BChl a and/or the differences in the pigment organization between the BChl b- and BChl a-containing LH1 complexes. Resonance Raman spectroscopy revealed remarkably large redshifts of the Raman bands for the BChl b C3-acetyl group, indicating unusually strong hydrogen bonds formed with LH1 polypeptides, results that were verified by a published structure. A linear correlation was found between the redshift of the Raman band for the BChl C3-acetyl group and the change in LH1-Qy transition for all native BChl a- and BChl b-containing LH1 complexes examined. The strong hydrogen bonding and π-π interactions between BChl b and nearby aromatic residues in the LH1 polypeptides, along with the CD results, provide crucial insights into the spectral and structural origins for the ultra-redshift of the long-wavelength absorption maximum of BChl b-containing phototrophs.
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Affiliation(s)
- Y Kimura
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan.
| | - T Yamashita
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - R Seto
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - M Imanishi
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - M Honda
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan
| | - S Nakagawa
- Department of Chemistry, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - Y Saga
- Department of Chemistry, Kindai University, Higashi-Osaka, 577-8502, Japan
| | - S Takenaka
- Department of Agrobioscience, Graduate School of Agriculture, Kobe University, Nada, Kobe, 657-8501, Japan
| | - L-J Yu
- Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - M T Madigan
- Department of Microbiology, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Z-Y Wang-Otomo
- Faculty of Science, Ibaraki University, Mito, 310-8512, Japan.
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Matsuzawa A, Lee J, Nakagawa S, Itoh J, Takahashi Ueda M, Mitsuhashi S, Kochi Y, Kaneko-Ishino T, Ishino F. HERV-Derived Ervpb1 Is Conserved in Simiiformes, Exhibiting Expression in Hematopoietic Cell Lineages Including Macrophages. Int J Mol Sci 2021; 22:ijms22094504. [PMID: 33925887 PMCID: PMC8123466 DOI: 10.3390/ijms22094504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 11/16/2022] Open
Abstract
(1) Background: The ERVPb1 gene in humans is derived from an envelope (Env) gene of a human endogenous retrovirus group, HERV-P(b). The ERVPb1 gene reportedly has a conserved open reading frame (ORF) in Old World monkeys. Although its forced expression led to cell-fusion in an ex vivo cell culture system, like other Env-derived genes such as syncytin-1 and -2, its mRNA expression is not placenta-specific, but almost ubiquitous, albeit being quite low in human tissues and organs, implying a distinct role for ERVPb1. (2) Methods: To elucidate the cell lineage(s) in which the ERVPb1 protein is translated in human development, we developed a novel, highly sensitive system for detecting HERV-derived proteins/peptides expressed in the tissue differentiation process of human induced pluripotent stem cells (iPSCs). (3) Results: We first determined that ERVPb1 is also conserved in New World monkeys. Then, we showed that the ERVPb1 protein is translated from a uniquely spliced ERVPb1 transcript in hematopoietic cell lineages, including a subset of macrophages, and further showed that its mRNA expression is upregulated by lipopolysaccharide (LPS) stimulation in primary human monocytes. (4) Conclusions: ERVPb1 is unique to Simiiformes and actually translated in hematopoietic cell lineages, including a subset of macrophages.
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Affiliation(s)
- Ayumi Matsuzawa
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
| | - Jiyoung Lee
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan;
| | - Johbu Itoh
- Department of Pathology, School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan;
| | - Mahoko Takahashi Ueda
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (M.T.U.); (S.M.); (Y.K.)
| | - Tomoko Kaneko-Ishino
- Department of Nursing, School of Medicine, Tokai University, 143 Shimokasuya, Isehara 259-1193, Kanagawa, Japan
- Correspondence: (T.K.-I.); (F.I.)
| | - Fumitoshi Ishino
- Department of Epigenetics, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan; (A.M.); (J.L.)
- Correspondence: (T.K.-I.); (F.I.)
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Kimura I, Konno Y, Uriu K, Hopfensperger K, Sauter D, Nakagawa S, Sato K. Sarbecovirus ORF6 proteins hamper induction of interferon signaling. Cell Rep 2021; 34:108916. [PMID: 33765414 PMCID: PMC7953434 DOI: 10.1016/j.celrep.2021.108916] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 01/24/2021] [Accepted: 03/08/2021] [Indexed: 12/11/2022] Open
Abstract
The presence of an ORF6 gene distinguishes sarbecoviruses such as severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 from other betacoronaviruses. Here we show that ORF6 inhibits induction of innate immune signaling, including upregulation of type I interferon (IFN) upon viral infection as well as type I and III IFN signaling. Intriguingly, ORF6 proteins from SARS-CoV-2 lineages are more efficient antagonists of innate immunity than their orthologs from SARS-CoV lineages. Mutational analyses identified residues E46 and Q56 as important determinants of the antagonistic activity of SARS-CoV-2 ORF6. Moreover, we show that the anti-innate immune activity of ORF6 depends on its C-terminal region and that ORF6 inhibits nuclear translocation of IRF3. Finally, we identify naturally occurring frameshift/nonsense mutations that result in an inactivating truncation of ORF6 in approximately 0.2% of SARS-CoV-2 isolates. Our findings suggest that ORF6 contributes to the poor IFN activation observed in individuals with coronavirus disease 2019 (COVID-19).
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Affiliation(s)
- Izumi Kimura
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Yoriyuki Konno
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan
| | - Keiya Uriu
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; Graduate School of Medicine, The University of Tokyo, Tokyo 1130033, Japan
| | - Kristina Hopfensperger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany; Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tübingen, Tübingen 72076, Germany
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 2591193, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan
| | - Kei Sato
- Division of Systems Virology, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, The University of Tokyo, Tokyo 1088639, Japan; CREST, Japan Science and Technology Agency, Saitama 3220012, Japan.
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Hadley G, Billingsley S, Nakagawa S, Durkin C. 51 CT Head and Cervical Spine Audit in Patients Over the Age of 65: A District General Hospital Perspective. Age Ageing 2021. [DOI: 10.1093/ageing/afab030.12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Cervical spine (c-spine) injury has a high morbidity and mortality in patients over the age of 65; more than 60% result from falls from standing height (Beedham et al., 2019).
The Canadian Cervical Spine Rule (Stiell et al., 2001) deems that there is a high risk of c-spine fracture if any of the following apply:
The c-spine cannot be cleared clinically if the patient fits any of the above criteria. Imaging should be considered. As a result of recent clinical experiences Trust Guidelines at Stoke Mandeville Hospital now reflect this evidence (Hadley et al., 2019).
Methods
Fifty patients over the age of 65 who had a computerised tomography (CT) head scan in the Emergency Department (ED) following a traumatic head injury were randomly selected over a 1 month period. Cases were checked for examination of c-spine and/or CT c-spine. Results of the first cycle of the audit were presented at an ED Education Meeting. Indications for CT c-spine were displayed in poster format around the ED. Following these interventions, a re-audit was carried out using the same methodology.
Results
In fifty patients aged over 65 attending ED during one month, 16% had a CT c-spine in addition to a CT head. There was documented c-spine examination of 16% of those without CT c-spine on admission. In the re-audit 38% of the fifty patients who had a CT head underwent CT c-spine. In the group that did not have imaging of the c-spine, the proportion with documented cervical spine examination on admission remained the same (16%).
Conclusion
There was a 137.5% increase in the number of patients aged over 65 who appropriately underwent a CT c-spine as per Trust and National guidelines. Simple interventions (staff education and posters within the ED) were sufficient to significantly alter practice. Current trauma triage is not optimal for older patients who are reviewed by more junior doctors, less likely to be transferred to Major Trauma Centres and more likely to die than younger patients with similar injuries (Major Trauma In Older People 2017 Report). An older person’s trauma team in ED with age-appropriate triage would lead to appropriate imaging in a timely fashion, potentially improving the morbidity and mortality of these vulnerable patients.
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Affiliation(s)
- G Hadley
- Stoke Mandeville Hospital, Aylesbury, UK
| | | | - S Nakagawa
- Stoke Mandeville Hospital, Aylesbury, UK
| | - C Durkin
- Stoke Mandeville Hospital, Aylesbury, UK
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Shiraishi Y, Kryukov K, Tomomatsu K, Sakamaki F, Inoue S, Nakagawa S, Imanishi T, Asano K. Diagnosis of pleural empyema/parapneumonic effusion by next-generation sequencing. Infect Dis (Lond) 2021; 53:450-459. [PMID: 33689538 DOI: 10.1080/23744235.2021.1892178] [Citation(s) in RCA: 9] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
BACKGROUND Although a microbiological diagnosis of pleural infection is clinically important, it is often complicated by prior antibiotic treatment and/or difficulties with culturing some bacterial species. Therefore, we aimed to identify probable causative bacteria in pleural empyema/parapneumonic effusions by combining 16S ribosomal RNA (rRNA) gene amplification and next-generation sequencing (NGS). METHODS Pleural fluids were collected from 19 patients with infectious effusions and nine patients with non-infectious malignant effusions. We analysed DNA extracted from the pleural fluid supernatant by NGS using the Genome Search Toolkit and GenomeSync database, either directly or after PCR amplification of the 16S rRNA gene. Infectious and non-infectious effusions were distinguished by semi-quantitative PCR of the 16S rRNA gene. RESULTS Only 8 (42%) effusions were culture-positive, however, NGS of the 16S rRNA gene amplicon identified 14 anaerobes and 7 aerobes/facultative anaerobes in all patients, including Streptococcus sp. (n = 6), Fusobacterium sp. (n = 5), Porphyromonas sp. (n = 5), and Prevotella sp. (n = 4), accounting for >10% of the total genomes. The culture and NGS results were discordant for 3 out of 8 patients, all of whom had previously been treated with antibiotics. Total (2ΔCT value in semi-quantitative PCR of the 16S rRNA gene) and specific (total bacterial load multiplied by the proportion of primary bacteria in NGS) bacterial loads could efficiently distinguish empyema/parapneumonic effusion from non-infectious effusion. CONCLUSION Combining NGS with semi-quantitative PCR can facilitate the diagnosis of pleural empyema/parapneumonic effusion and its causal bacteria.
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Affiliation(s)
- Yoshiki Shiraishi
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.,Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | - Katsuyoshi Tomomatsu
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
| | - Fumio Sakamaki
- Division of Respiratory Disease, Department of Medicine, Tokai University Hachioji Hospital, Tokyo, Japan
| | - Shigeaki Inoue
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Koichiro Asano
- Division of Pulmonary Medicine, Department of Medicine, Tokai University School of Medicine, Isehara, Japan
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Mitsuhashi S, Nakagawa S, Sasaki-Honda M, Sakurai H, Frith MC, Mitsuhashi H. Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells. Hum Mol Genet 2021; 30:552-563. [PMID: 33693705 PMCID: PMC8120133 DOI: 10.1093/hmg/ddab063] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 01/27/2021] [Accepted: 02/23/2021] [Indexed: 01/11/2023] Open
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle. DUX4 is a transcription factor, which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent long terminal repeat (LTR)-retrotransposons and pericentromeric satellite repeats (Human Satellite II). DUX4-bound ERV sequences also create alternative promoters for genes or long non-coding RNAs, producing fusion transcripts. To further understand transcriptional regulation by DUX4, we performed nanopore long-read direct RNA sequencing (dRNA-seq) of human muscle cells induced by DUX4, because long reads show whole isoforms with greater confidence. We successfully detected differential expression of known DUX4-induced genes and discovered 61 differentially expressed repeat loci, which are near DUX4–ChIP peaks. We also identified 247 gene–ERV fusion transcripts, of which 216 were not reported previously. In addition, long-read dRNA-seq clearly shows that RNA splicing is a common event in DUX4-activated ERV transcripts. Long-read analysis showed non-LTR transposons including Alu elements are also transcribed from LTRs. Our findings revealed further complexity of DUX4-induced ERV transcripts. This catalogue of DUX4-activated repetitive elements may provide useful information to elucidate the pathology of FSHD. Also, our results indicate that nanopore dRNA-seq has complementary strengths to conventional short-read complementary DNA sequencing.
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Affiliation(s)
- Satomi Mitsuhashi
- Department of Genomic Function and Diversity, Tokyo Medical and Dental University, Tokyo 113-8510, Japan.,Department of Human Genetics, Yokohama City University, Yokohama, Kanagawa 236-0004, Japan
| | - So Nakagawa
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan.,Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Mitsuru Sasaki-Honda
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Hidetoshi Sakurai
- Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin Kawahara-cho, Sakyo-ku, Kyoto 606-8507, Japan
| | - Martin C Frith
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan.,Graduate School of Frontier Sciences, University of Tokyo, Chiba 277-8561, Japan.,Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 169-8555, Japan
| | - Hiroaki Mitsuhashi
- Micro/Nano Technology Center, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan.,Department of Applied Biochemistry, School of Engineering, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
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Chikuma S, Yamanaka S, Nakagawa S, Ueda MT, Hayabuchi H, Tokifuji Y, Kanayama M, Okamura T, Arase H, Yoshimura A. TRIM28 Expression on Dendritic Cells Prevents Excessive T Cell Priming by Silencing Endogenous Retrovirus. J Immunol 2021; 206:1528-1539. [PMID: 33619215 DOI: 10.4049/jimmunol.2001003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]
Abstract
Acquired immune reaction is initiated by dendritic cells (DCs), which present Ags to a few naive Ag-specific T cells. Deregulation of gene expression in DCs may alter the outcome of the immune response toward immunodeficiency and/or autoimmune diseases. Expression of TRIM28, a nuclear protein that mediates gene silencing through heterochromatin, decreased in DCs from old mice, suggesting alteration of gene regulation. Mice specifically lacking TRIM28 in DCs show increased DC population in the spleen and enhanced T cell priming toward inflammatory effector T cells, leading to acceleration and exacerbation in experimental autoimmune encephalomyelitis. TRIM28-deficient DCs were found to ectopically transcribe endogenous retrovirus (ERV) elements. Combined genome-wide analysis revealed a strong colocalization among the decreased repressive histone mark H3K9me3-transcribed ERV elements and the derepressed host genes that were related to inflammation in TRIM28-deficient DCs. This suggests that TRIM28 occupancy of ERV elements critically represses expression of proximal inflammatory genes on the genome. We propose that gene silencing through repressive histone modification by TRIM28 plays a role in maintaining the integrity of precise gene regulation in DCs, which prevents aberrant T cell priming to inflammatory effector T cells.
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Affiliation(s)
- Shunsuke Chikuma
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan;
| | - Soichiro Yamanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0032, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan
| | - Mahoko Takahashi Ueda
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa 259-1193, Japan.,Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Hodaka Hayabuchi
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Yukiko Tokifuji
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Masashi Kanayama
- Department of Biodefense Research, Medical Research Institute, Tokyo Medical and Dental University, Tokyo 113-8510, Japan
| | - Tadashi Okamura
- Department of Laboratory Animal Medicine, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan.,Department of Infectious Diseases, Research Institute, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Hisashi Arase
- Department of Immunochemistry, Research Institute for Microbial Disease, Osaka University, Osaka 565-0871, Japan; and.,Laboratory of Immunochemistry, World Premier International Research Center Initiative, Immunology Frontier Research Center, Osaka University, Osaka 565-0871, Japan
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo 160-8582, Japan
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Ohno A, Umezawa K, Asai S, Kryukov K, Nakagawa S, Miyachi H, Imanishi T. Rapid profiling of drug-resistant bacteria using DNA-binding dyes and a nanopore-based DNA sequencer. Sci Rep 2021; 11:3436. [PMID: 33564026 PMCID: PMC7873225 DOI: 10.1038/s41598-021-82903-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 08/24/2020] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
Spread of drug-resistant bacteria is a serious problem worldwide. We thus designed a new sequence-based protocol that can quickly identify bacterial compositions of clinical samples and their drug-resistance profiles simultaneously. Here we utilized propidium monoazide (PMA) that prohibits DNA amplifications from dead bacteria, and subjected the original and antibiotics-treated samples to 16S rRNA metagenome sequencing. We tested our protocol on bacterial mixtures, and observed that sequencing reads derived from drug-resistant bacteria were significantly increased compared with those from drug-sensitive bacteria when samples were treated by antibiotics. Our protocol is scalable and will be useful for quickly profiling drug-resistant bacteria.
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Affiliation(s)
- Ayumu Ohno
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Kazuo Umezawa
- Department of Emergency and Critical Care Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Satomi Asai
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.,Infection Control Division, Tokai University Hospital, Isehara, Kanagawa, 259-1193, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.,Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan
| | - Hayato Miyachi
- Department of Laboratory Medicine, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.,Infection Control Division, Tokai University Hospital, Isehara, Kanagawa, 259-1193, Japan
| | - Tadashi Imanishi
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa, 259-1193, Japan.
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Matsuo Y, Komiya S, Yasumizu Y, Yasuoka Y, Mizushima K, Takagi T, Kryukov K, Fukuda A, Morimoto Y, Naito Y, Okada H, Bono H, Nakagawa S, Hirota K. Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution. BMC Microbiol 2021; 21:35. [PMID: 33499799 PMCID: PMC7836573 DOI: 10.1186/s12866-021-02094-5] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [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: 05/19/2020] [Accepted: 01/18/2021] [Indexed: 12/13/2022] Open
Abstract
Background Species-level genetic characterization of complex bacterial communities has important clinical applications in both diagnosis and treatment. Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene has proven to be a powerful strategy for the taxonomic classification of bacteria. This study aims to improve the method for full-length 16S rRNA gene analysis using the nanopore long-read sequencer MinION™. We compared it to the conventional short-read sequencing method in both a mock bacterial community and human fecal samples. Results We modified our existing protocol for full-length 16S rRNA gene amplicon sequencing by MinION™. A new strategy for library construction with an optimized primer set overcame PCR-associated bias and enabled taxonomic classification across a broad range of bacterial species. We compared the performance of full-length and short-read 16S rRNA gene amplicon sequencing for the characterization of human gut microbiota with a complex bacterial composition. The relative abundance of dominant bacterial genera was highly similar between full-length and short-read sequencing. At the species level, MinION™ long-read sequencing had better resolution for discriminating between members of particular taxa such as Bifidobacterium, allowing an accurate representation of the sample bacterial composition. Conclusions Our present microbiome study, comparing the discriminatory power of full-length and short-read sequencing, clearly illustrated the analytical advantage of sequencing the full-length 16S rRNA gene. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02094-5.
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Affiliation(s)
- Yoshiyuki Matsuo
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan.
| | - Shinnosuke Komiya
- HORAC Grand Front Osaka Clinic, Osaka, Japan.,Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Hirakata, Japan
| | - Yoshiaki Yasumizu
- Department of Experimental Immunology, Immunology Frontier Research Center, Osaka University, Osaka, Japan.,Faculty of Medicine, Osaka University, Osaka, Japan
| | - Yuki Yasuoka
- Faculty of Medicine, Osaka University, Osaka, Japan
| | - Katsura Mizushima
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tomohisa Takagi
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan.,Department of Genomics and Evolutionary Biology, National Institute of Genetics, Mishima, Japan
| | | | | | - Yuji Naito
- Molecular Gastroenterology and Hepatology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hidetaka Okada
- Obstetrics and Gynecology, Kansai Medical University Graduate School of Medicine, Hirakata, Japan
| | - Hidemasa Bono
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems, Mishima, Japan.,Program of Biomedical Science, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Japan
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Japan
| | - Kiichi Hirota
- Department of Human Stress Response Science, Institute of Biomedical Science, Kansai Medical University, 2-5-1 Shin-machi, Hirakata, Osaka, 573-1010, Japan
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Orba Y, Matsuno K, Nakao R, Kryukov K, Saito Y, Kawamori F, Loza Vega A, Watanabe T, Maemura T, Sasaki M, Hall WW, Hall RA, Pereira JA, Nakagawa S, Sawa H. Diverse mosquito-specific flaviviruses in the Bolivian Amazon basin. J Gen Virol 2021; 102. [PMID: 33416463 DOI: 10.1099/jgv.0.001518] [Citation(s) in RCA: 3] [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] [Indexed: 01/13/2023] Open
Abstract
The genus Flavivirus includes a range of mosquito-specific viruses in addition to well-known medically important arboviruses. Isolation and comprehensive genomic analyses of viruses in mosquitoes collected in Bolivia resulted in the identification of three novel flavivirus species. Psorophora flavivirus (PSFV) was isolated from Psorophora albigenu. The coding sequence of the PSFV polyprotein shares 60 % identity with that of the Aedes-associated lineage II insect-specific flavivirus (ISF), Marisma virus. Isolated PSFV replicates in both Aedes albopictus- and Aedes aegypti-derived cells, but not in mammalian Vero or BHK-21 cell lines. Two other flaviviruses, Ochlerotatus scapularis flavivirus (OSFV) and Mansonia flavivirus (MAFV), which were identified from Ochlerotatus scapularis and Mansonia titillans, respectively, group with the classical lineage I ISFs. The protein coding sequences of these viruses share only 60 and 40 % identity with the most closely related of known lineage I ISFs, including Xishuangbanna aedes flavivirus and Sabethes flavivirus, respectively. Phylogenetic analysis suggests that MAFV is clearly distinct from the groups of the current known Culicinae-associated lineage I ISFs. Interestingly, the predicted amino acid sequence of the MAFV capsid protein is approximately two times longer than that of any of the other known flaviviruses. Our results indicate that flaviviruses with distinct features can be found at the edge of the Bolivian Amazon basin at sites that are also home to dense populations of human-biting mosquitoes.
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Affiliation(s)
- Yasuko Orba
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Keita Matsuno
- Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - Kirill Kryukov
- Department of Genomics and Evolutionary Biology, National Institute of Genetics, Shizuoka, Japan
| | - Yumi Saito
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Fumihiko Kawamori
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - Ariel Loza Vega
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tadashi Maemura
- Department of Pathobiological Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - William W Hall
- Global Virus Network, Baltimore, Maryland, USA.,Centre for Research in Infectious Diseases, University College Dublin, Dublin, Ireland.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Roy A Hall
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland, Australia
| | - Juan Antonio Pereira
- Faculty of Veterinary Sciences, Gabriel Rene Moreno Autonomous University, Santa Cruz, Bolivia
| | - So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Kanagawa, Japan
| | - Hirofumi Sawa
- Global Virus Network, Baltimore, Maryland, USA.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
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Fukaya Y, Goto M, Nakagawa S, Nakajima K, Takahashi K, Sakon A, Sano T, Hashimoto K. REACTOR PHYSICS EXPERIMENT IN A GRAPHITE-MODERATION SYSTEM FOR HTGR. EPJ Web Conf 2021. [DOI: 10.1051/epjconf/202124709017] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Japan Atomic Energy Agency (JAEA) started the Research and Development (R&D) to improve nuclear prediction techniques for High Temperature Gas-cooled Reactors (HTGRs). The objectives are to introduce a generalized bias factor method to avoid full mock-up experiment for the first commercial HTGR and to introduce reactor noise analysis to High Temperature Engineering Test Reactor (HTTR) experiment to observe sub-criticality. To achieve the objectives, the reactor core of graphite-moderation system named B7/4”G2/8”p8EUNU+3/8”p38EU(1) was newly composed in the B-rack of Kyoto University Critical Assembly (KUCA). The core is composed of the fuel assembly, driver fuel assembly, graphite reflector, and polyethylene reflector. The fuel assembly is composed of enriched uranium plate, natural uranium plate and graphite plates to realize the average fuel enrichment of HTTR and it’s spectrum. However, driver fuel assembly is necessary to achieve the criticality with the small-sized core. The core plays a role of the reference core of the bias factor method, and the reactor noise was measured to develop the noise analysis scheme. In this study, the overview of the criticality experiments is reported. The reactor configuration with graphite moderation system is rare case in the KUCA experiments, and this experiment is expected to contribute not only for an HTGR development but also for other types of a reactor in the graphite moderation system such as a molten salt reactor development.
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Affiliation(s)
- So Nakagawa
- Molecular Life Science, School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan. .,Institute of Medical Sciences, Tokai University, Kanagawa, Japan. .,Micro/Nano Technology Center, Tokai University, Hiratsuka, Japan.
| | - Takayuki Miyazawa
- Laboratory of Virus-Host Coevolution, Institute for Frontier Life and Medical Sciences, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan. .,Resilience Research Unit, Kyoto University, Kyoto, Japan.
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Nakagawa S, Kawashima M, Miyatake Y, Kudo K, Kotaki R, Ando K, Kotani A. Expression of ERV3-1 in leukocytes of acute myelogenous leukemia patients. Gene 2020; 773:145363. [PMID: 33338509 DOI: 10.1016/j.gene.2020.145363] [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: 09/18/2020] [Revised: 11/28/2020] [Accepted: 12/08/2020] [Indexed: 12/17/2022]
Abstract
Acute myelogenous leukemia (AML) is one of the major hematological malignancies. In the human genome, several have been found to originate from retroviruses, and some of which are involved in the progression of various cancers. Hence, to investigate whether retroviral-like genes are associated with AML development, we conducted a transcriptome sequencing analysis of 12 retroviral-like genes of 150 AML patients and 32 healthy donor samples, of which RNA sequencing data were obtained from public databases. We found high expression of ERV3-1, an envelope gene of endogenous retrovirus group 3 member 1, in all AML patients examined in this study. In particular, blood and bone marrow cells of the myeloid lineage in AML patients, exhibited higher expression of ERV3-1 than those of the monocytic AML lineage. We also examined the protein expression of ERV3-1 by immunohistochemical analysis and found expression of the ERV3-1 protein in all 12 myeloid-phenotype patients and 7 out of 12 monocytic-phenotype patients, with a particular concentration observed at the membrane of some leukemic cells. Transcriptome analysis further suggested that upregulated ERV3-1 expression may be associated with chromosome 8 trisomy as anomaly was found to be more common among the high expression group than the low expression group. However, this finding was not corroborated by the immunohistochemical data. This discrepancy may have been caused, in part, by the small number of samples analyzed in this study. Although the precise associated molecular mechanisms remain unclear, our results suggest that ERV3-1 may be involved in AML development.
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Affiliation(s)
- So Nakagawa
- Department of Molecular Life Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan; Division of Genome Sciences, Institute of Medical Sciences, Tokai University, Isehara, Kanagawa 259-1193, Japan.
| | - Masaharu Kawashima
- Division of Clinical Oncology and Hematology, The Jikei University School of Medicine, Minato-ku, Tokyo 105-8471, Japan; Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan
| | - Yuji Miyatake
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Kai Kudo
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Ryutaro Kotaki
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan
| | - Kiyoshi Ando
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Hematology and Oncology, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan
| | - Ai Kotani
- Department of Hematological Malignancy, Institute of Medical Science, Tokai University, Isehara, Kanagawa 259-1193, Japan; Department of Advanced Medical Science, Tokai University School of Medicine, Isehara, Kanagawa 259-1193, Japan.
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