Institute of MicrobiologyInstitute of Microbiology

Publications

2024

  1. Adachi T, Nakamura S, Michishita A, Kawahara D, Yamamoto M, Hamada M, Nakamura Y. RaptGen-assisted generation of an RNA/DNA hybrid aptamer against SARS-CoV-2 spike psrotein. Biochemistry. doi: 10.1021/acs.biochem.3c00596. Epub ahead of print. PMID: 38457656. (MAR 2024)

2023

  1. Hassan AHE, El-Sayed SM, Yamamoto M, Gohda J, Matsumoto T, Shirouzu M, Inoue J-i, Kawaguchi Y, Mansour RMA, Anvari A, Farahat AA. In Silico and In vitro evaluation of some amidine derivatives as hit compounds towards development of inhibitors against coronavirus diseases. Viruses 15(5): 1171, 2023. doi: 10.3390/v15051171. (MAY 2023)
  2. Hayashi Y, Nakayama J, Yamamoto M, Maekawa M, Watanabe S, Higashiyama S, Inoue JI, Yamamoto Y, Semba K. Aberrant accumulation of NIK promotes tumor growth by dysregulating translation and post-translational modifications in breast cancer. Cancer Cell Int 23(1): 57, 2023. doi: 10.1186/s12935-023-02904-y. (APR 2023)
  3. Hayashi Y, Huang X, Tanikawa T, Tanigawa K, Yamamoto M, Gohda J, Inoue JI, Fukase K, Kabayama K. Reactive oxygen species are associated with the inhibitory effect of N-(4-hydroxyphenyl)-retinamide on the entry of the severe acute respiratory syndrome-coronavirus 2. J Biochem: mvad020. doi: 10.1093/jb/mvad020. Epub ahead of print. PMID: 36888972. (MAR 2023)

2022

  1. Ogura H, Gohda J, Lu X, Yamamoto M, Takesue Y, Son A, Doi S, Matsushita K, Isobe F, Fukuda Y, Huang TP, Ueno T, Mambo N, Murakami H, Kawaguchi Y, Inoue JI, Shirai K, Yamasaki S, Hirata JI, Ishido S. Dysfunctional Sars-CoV-2-M protein-specific cytotoxic T lymphocytes in patients recovering from severe COVID-19. Nat Commun 13(1): 7063. (DEC 2022)
  2. Yamamoto M, Gohda J, Kobayashi A, Tomita K, Hirayama Y, Koshikawa N, Seiki M, Semba K, Akiyama T, Kawaguchi Y, Inoue JI. Metalloproteinase-dependent and TMPRSS2-independnt cell surface entry pathway of SARS-CoV-2 requires the furin-cleavage site and the S2 domain of spike protein. mBio e0051922, 2022. doi: 10.1128/mbio.00519-22. (JUN 2022)
  3. Yamamoto M, Tomita K, Hirayama Y, Inoue JI, Kawaguchi Y, Gohda J. SARS-CoV-2 Omicron spike H655Y mutation is responsible for enhancement of the endosomal entry pathway and reduction of cell surface entry pathways. BioRxiv, 2022. doi: https://doi.org/10.1101/2022.03.21.485084 (MAR 2022)

2021

  1. Kawashima K, Hirota-Tsukimachi M, Toma T, Koga R, Iwamaru K, Yanae M, Ahagon A, Nakamura Y, Anraku K, Tateishi H, Gohda J, Inoue JI, Otsuka M, Fujita M. Development of chimeric receptor activator of nuclear factor-kappa B with glutathione S-transferase in the extracellular domain: Artificial switch in a membrane receptor. Chem Biol Drug Des 99(4): 573-584, 2021. (DEC 2021)
  2. Yamamoto M, Gohda J, Cell-based membrane fusion assays with viral fusion proteins for identification of entry inhibitors. Translational and Regulatory Sciences 3(3): 72-76. (DEC 2021)
  3. Takeuchi Y, Kimura N, Murayama T, Machida Y, Iejima D, Nishimura T, Terashima M, Wang Y, Li M, Sakamoto R, Yamamoto M, Itano N, Inoue Y, Ito M, Yoshida N, Inoue JI, Akashi K, Saya H, Fujita K, Kuroda M, Kitabayashi I, Voon D, Suzuki T, Tojo A, Gotoh N. The membrane-linked adaptor FRS2β fashions a cytokine-rich inflammatory microenvironment that promotes breast cancer carcinogenesis. Proc Natl Acad Sci USA 118(43): e2103658118. doi: 10.1073/pnas.2103658118. (OCT 2021)
  4. Deletsu SD, Kitamura H, Ishida T, Gohda J, Yamaoka S, Takeuchi H. Identification and characterization of Stathmin 1 as a host factor involved in HIV-1 latency. Biochem Biophys Res Commun 567: 106-111, 2021 (AUG 2021)
  5. Hayashi Y, Tsuchiya K, Yamamoto M, Nemoto-Sasaki Y, Tanigawa K, Hama K, Ueda Y, Tanikawa T, Gohda J, Maeda K, Inoue J, Yamashit A. N-(4-Hydroxyphenyl) retinamide suppresses SARS-CoV-2 spike protein-mediated cell-cell fusion by a dihydroceramide Δ4-desaturase 1-independent mechanism. Journal of Virology 10;95(17), 2021 (AUG 2021)
  6. Kandeel M, Yamamoto M, Park BK, Al-Taher A, Watanabe A, Gohda J, Kawaguchi Y, Oh-hashi K, Kwon HJ, Inoue JI. Discovery of new potent anti-MERS CoV fusion inhibitors. Frontiers in Pharmacology 12: 685161, 2021. (JUN 2021)
  7. Kandeel M, Yamamoto M, Tani H, Kobayashi A, Gohda J, Kawaguchi Y, Park BK, Kwon HJ, Inoue JI, Alkattan A. Discovery of new fusion inhibitor peptides against SARS-CoV-2 by targeting the spike S2 subunit. Biomolecules & Therapeutics 29(3): 282-289. (MAY 2021)
  8. Yamamoto M, Gohda J, Akiyama T, Inoue JI. TNF receptor-associated factor 6 (TRAF6) plays crucial roles in multiple biological systems through polyubiquitination-mediated NF-κB activation. Proc Jpn Acad Ser B Phys Biol Sci 97(4): 145-160. (APR 2021)

2020

  1. Yamamoto M, Ichinohe T, Watanabe A, Kobayashi A, Zhang R, Song J, Kawaguchi Y, Matsuda Z, Inoue JI. The Antimalarial compound atovaquone inhibits Zika and Dengue virus infection by blocking E protein-mediated membrane fusion. Viruses 12 (12), 1475, 2020. (DEC 2020)
  2. Yamamoto M, Kiso M, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Imai M, Takeda M, Kinoshita N, Ohmagari N, Gohda J, Semba K, Matsuda Z, Kawaguchi Y, Kawaoka Y, Inoue JI. The anticoagulant nafamostat potently inhibits SARS-CoV-2 S protein-mediated fusion in a cell fusion assay system and viral infection in vitro in a cell-type-dependent manner. Viruses 12(6): 629, 2020. (JUN 2020)
  3. Yamamoto M, Kiso M, Sakai-Tagawa Y, Iwatsuki-Horimoto K, Imai M, Takeda M, Kinoshita N, Ohmagari N, Gohda J, Semba K, Matsuda Z, Kawaguchi Y, Kawaoka Y, Inoue JI. The anticoagulant nafamostat potently inhibits SARS-CoV-2 infection in vitro: an existing drug with multiple possible therapeutic effects. BioRxiv doi: https://doi.org/10.1101/2020.04.22.054981, 2020. (APR 2020)
    https://www.biorxiv.org/content/10.1101/2020.04.22.054981v1
  4. Nakamura T, Hashikawa C, Okabe K, Yokote Y, Chirifu M, Toma-Fukai S, Nakamura N, Matsuo M, Kamikariya M, Okamoto Y, Gohda J, Akiyama T, Semba K, Ikemizu S, Ostuka M, Inoue JI, Yamagata Y. Structural analysis of TIFA: Insight into TIFA-dependent signal transduction in innate Immunity. Sci Rep 10(1): 5152, 2020. (MAR 2020)
  5. Kandeel M, Yamamoto M, Al-Taher A, Watanabe A, Oh-Hashi K, Park BK, Kwon HJ, Inoue JI, Al-Nazawi M. Small molecule inhibitors of middle east respiratory syndrome coronavirus fusion by targeting cavities on heptad repeat trimers. Biomol Ther (Seoul) doi:10.4062/biomolther.2019.202., 2020. (MAR 2020)

2018

  1. Gohda J, Suzuki K, Liu K, Xie X, Takeuchi H, Inoue J, Kawaguchi Y, Ishida T. BI-2536 and BI-6727, dual Polo-like kinase/bromodomain inhibitors, effectively reactivate latentHIV-1. Scientific Reports 8 (1): 3521. doi: 10.1038/s41598-018-21942-5, 2018. (FEB 2018)

2015

  1. Liu C, Zhao Y, He W, Wang W, Chen Y, Zhang S, Ma Y, Gohda J, Ishida T, Walter TS, Owens RJ, Stuart DI, Ren J, Gao B. A RANKL mutant used as an inter-species vaccine for efficient immunotherapy of osteoporosis. Sci Rep 5:14150, 2015. (SEP 28, 2015）
  2. Gu L, Han Y, Li Y, Zhu T, Song X, Huang H, Yang F, Guan S, Xie J, Gohda J, Hosoya N, Kawana-Tachikawa A, Liu W, Gao GF, Iwamoto A, Li T, Ishida T. Emergence of Lamivudine-Resistant HBV during Antiretroviral Therapy Including Lamivudine for Patients Coinfected with HIV and HBV in China. PLoS ONE 10(8):e0134539, 2015. (AUG 2015)
  3. Li Y, Gu L, Han Y, Xie J, Wang H, Lv W, Song X, Li Y, Iwamoto A, Ishida T, Li T. HIV-1 subtype B/B' and baseline drug resistance mutation are associated with virologic failure: a multicenter cohort study in China. J Acquir Immune Defic Syndr 68(3):289-97, 2015. (MAR 2015)
  4. Gohda J, Ma Y, Huang Y, Zhang Y, Gu L, Han Y, Li T, Gao B, Gao GF, Inoue J-i, Iwamoto A, Ishida T. HIV-1 replicates in human osteoclasts and enhances their differentiation in vitro. Retrovirology 12:12, 2015. (FEB 7, 2015)
  5. Matsuda Y, Kobayashi-Ishihara M, Fujikawa D, Ishida T, Watanabe T, Yamagishi M. Epigenetic heterogeneity in HIV-1 latency establishment. Sci Rep 5:7701, 2015.（JAN 9, 2015）
  6. Nakayama-Hosoya K, Ishida T, Youngblood B, Nakamura H, Hosoya N, Koga M, Koibuchi T, Iwamoto A, Kawana-Tachikawa A. Epigenetic repression of interleukin 2 expression in senescent CD4+ T cells during chronic HIV type 1 infection. J Infect Dis 211:28-39, 2015. (JAN 1, 2015)

2014

  1. Gu L, Kawana-Tachikawa A, Shiino T, Nakamura H, Koga M, Kikuchi T, Adach E, Koibuchi T, Ishida T, Gao GF, Matsushita M, Sugiura W, Iwamoto A, Hosoya N. Development and Customization of a Color-Coded Microbeads-Based Assay for Drug Resistance in HIV-1 Reverse Transcriptase. PLos ONE 9: e09823, OCT 2014.
  2. Li Y, Han Y, Xie J, Gu L, Li W, Wang H, Li W, Song X, Li Y, Routy JP, Ishida T, Iwamoto A and Li T. CRF01_AE subtype is associated with X4 tropism and fast HIV progression in Chinese patients infected through sexual transmission. AIDS, 28, 521-530, FEB 20 2014

2013

  1. Suzuki K, Hattori S, Marks K, Ahlenstiel C, Maeda Y, Ishida T, Millington M, Boyd M, Symonds G, Cooper DA, Okada S, Kelleher AD. Promoter targeting shRNA suppresses HIV-1 infection in vivo through transcriptional gene silencing. Mol Ther Nucleic Acids. 2013 Dec 3;2:e137.
  2. Ohsugi T, Ishida T, Shimasaki T, Okada S, Umezawa K. p53 dysfunction precedes the activation of nuclear factor-κB during disease progression in mice expressing Tax, a human T-cell leukemia virus type 1 oncoprotein. Carcinogenesis, 34(9), 2129-36, 2013 Sep
  3. Nakano K, Ando T, Yamagishi M, Yokoyama K, Ishida T, Ohsugi T, Tanaka Y, Brighty DW, Watanabe T. Viral interference with host mRNA surveillance, the nonsense-mediated mRNA decay (NMD) pathway, through a new function of HTLV-1 Rex: implications for retroviral replication. Microbes Infect, 15, 491-505, JUN 2013.

2012

  1. Saito M, Kato Y, Ito E, Fujimoto J, Ishikawa K, Doi A, Kumazawa K, Matsui A, Takebe S, Ishida T, Azuma S, Mochizuki H, Kawamura Y, Yanagisawa Y, Honma R, Imai J, Ohbayashi H, Goshima N, Semba K, Watanabe S. Expression screening of 17q12-21 amplicon reveals GRB7 as an ERBB2-dependent oncogene. FEBS Lett. 12;586(12):1708-14, 2012.
  2. Kobayashi-Ishihara M, Yamagishi M, Hara T, Matsuda Y, Takahashi R, Miyake A, Nakano K, Yamochi T, Ishida T, Watanabe T. HIV-1-encoded antisense RNA suppresses viral replication for a prolonged period. Retrovirology.9:38, 2012. （doi:10.1186/1742-4690-9-38.）
  3. Taguchi, Y., Kiga, Y., Gohda, J.Inoue, J-I. Identification and characterization of anti-osteoclastogenic peptides derived from the cytoplasmic tail of RANK. J. Bone Miner. Metab. in press, 2012.（DOI: 10.1007/s00774-012-0353-5）
  4. Ahlenstiel C, Lim H, Cooper DA, Ishida T, Kelleher, AD, Suzuki, K. Direct evidence of nuclear Argonaute distribution during transcriptional silencing links the actin cytoskeleton to nuclear RNAi machinery in human cells. Nucleic Acids Research. 40:1579-1595, 2012.

2011

  1. Suzuki K, Ishida T, Yamagishi M, Ahlenstiel C, Swaminathan S, Marks K, Murray D, McCartney EM, Beard MR, Alexander M, Purcell DF, Cooper DA, Watanabe T, Kelleher AD. Transcriptional gene silencing of HIV-1 through promoter targeted RNA is highly specific. RNA Biology. 8:1035-46, 2011.
  2. Tsai HJ, Kobayashi S, Izawa K, Ishida T, Watanabe T, Umezawa K, Lin SF, Tojo A. Bioimaging analysis of nuclear factor-κB activity in Philadelphia chromosome-positive acute lymphoblastic leukemia cells reveals its synergistic upregulation by tumor necrosis factor-α-stimulated changes to the microenvironment. Cancer Sci. 102(11):2014-21, 2011.
  3. Shi G, Yagyu F, Shimizu Y, Shimizu K, Oshima M, Iwamoto A, Gao B, Liu W, Gao GF, Kitamura Y. Flow cytometric assay using two fluorescent proteins for the function of the internal ribosome entry site of hepatitis C virus. Cytometry: Part A. 79A: 653-660,2011.

2010

  1. Sun Y, Liu J, Yang M, Gao F, Zhou J, Kitamura Y, Gao B, Tien P, Shu Y, Iwamoto A, Chen Z, Gao GF. Identification and structural definition of H5-specific CTL epitopes restricted by HLA-A*0201 derived from the H5N1 subtype of influenza A viruses. J Gen Virol. 91:919-30, 2010.
  2. Song XH, Xiao H, Huang Y, Fu G, Jiang B, Kitamura Y, Liu W, Liu D, Gao GF. Serological surveillance of influenza A virus infection in swine populations in Fujian province, China: no evidence of naturally occurring H5N1 infection in pigs. Zoonoses Public Health. 57:291-8, 2010.
  3. Yu M, Liu X, Sun L, Chen C, Ma G, Kitamura Y, Gao GF, Liu W. Subcellular localization and topology of porcine reproductive and respiratory syndrome virus E protein. Virus Res. 152:104-14, 2010.
  4. Yu L, Aoki C, Shimizu Y, Shimizu K, Hou W, Yagyu F, Wen X, Oshima M, Iwamoto A, Gao B, Liu W, Gao GF, Kitamura Y. Development of a simple system for screening anti-hepatitis C virus drugs utilizing mutants capable of vigorous replication. J Virol Methods. 169:380-4, 2010.

2009

  1. Liu X, Sun L, Yu M, Wang Z, Xu C, Xue Q, Zhang K, Ye X, Kitamura Y, Liu W. Cyclophilin A interacts with influenza A virus M1 protein and impairs the early stage of the viral replication. Cellular Microbiology. 11:730-741, 2009.
  2. Sun L, Zhang G, Shu Y, Chen X, Zhu Y, Yang L, Ma G, Kitamura Y, Liu W. Genetic correlation between H3N2 human and swine influenza viruses. J Clin Virol. 44:141-144, 2009.

2008

  1. Hou W, Aoki C, Yu L, Wen X, Xue Y, Gao B, Liu W, Gao GF, Iwamoto A, Kitamura Y. A recombinant replication-competent hepatitis C virus expressing Azami-Green, a bright green-emitting fluorescent protein, suitable for visualization of infected cells. Biochem. Biophys. Res. Commun. 377:7-11, 2008.
  2. Hosoya N, Miura T, Kawana-Tachikawa A, Koibuchi T, Shioda T, Odawara T, Nakamura T, Kitamura Y, Kano M, Kato A, Hasegawa M, Nagai Y, Iwamoto A. Comparison between Sendai virus and adenovirus vectors to transduce HIV-1 genes into human dendritic cells. J Med. Virol. 80:373-82, 2008.
  3. Qin Z, Sun L, Ma B, Cui Z, Zhu Y, Kitamura Y, Liu W. F gene recombination between genotype II and VII Newcastle disease virus. Virus Res.131:299-303,2008.

2007

  1. Tian K, Yu X, Zhao T, Feng Y, Cao Z, Wang C, Hu Y, Chen X, Hu D, Tian X, Liu D, Zhang S, Deng X, Ding Y, Yang L, Zhang Y, Xiao H, Qiao M, Wang B, Hou L, Wang X, Yang X, Kang L, Sun M, Jin P, Wang S, Kitamura Y, Yan J, Gao GF. Emergence of fatal PRRSV variants: unparalleled outbreaks of atypical PRRS in China and molecular dissection of the unique hallmark. PLoS ONE. 13;2(6):e526, 2007.
  2. Wichukchinda N, Kitamura Y, Rojanawiwat A, Nakayama EE, Song H, Pathipvanich P, Auwanit W, Sawanpanyalert P, Iwamoto A, Shioda T, Ariyoshi K. The polymorphisms in DC-SIGNR affect susceptibility to HIV type 1 infection. AIDS Res Hum Retroviruses. 23:686-92, 2007.
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