Publications

2022

Saito A#, Irie T#, Suzuki Rigel#, Maemura T#, Nasser H#, Uriu K#, Kosugi Y# (#equal contribution), 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 Y, 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, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Tanaka S, Nakagawa S, Ikeda T, Fukuhara T, Kawaoka Y, Sato K (*equal correspondence). Enhanced fusogenicity and pathogenicity of SARS-CoV-2 Delta P681R mutation. Nature. 602, 300-306, 2022. [Link]

Okada S, Fukai Y, Tanoue Y, Nasser H, Fukuda T, Ikeda T, Saitoh H. Basic structure and cytocompatibility of giant membrane vesicles derived from paraformaldehyde-exposed human cells. J Biochem. 171, 339-347, 2022.

Suzuki R, Yamasoba D, Kimura I, Wang L, Kishimoto M, Ito J, Morioka Y, Nao N, Nasser H, Uriu K, Kosugi Y, Tsuda M, Orba Y, Sasaki M, Shimizu R, Kawabata R, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa H, Ikeda T, Irie T, Matsuno K, Tanaka S, Fukuhara T, Sato K. Attenuated fusogenicity and pathogenicity of SARS-CoV-2 Omicron variant. Nature. 603, 700-705, 2022.

Meng B, Abdullahi A, Ferreira IATM, Goonawardane N, Saito A, Kimura I, Yamasoba D, Gerber PP, Fatihi S, Rathore S, Zepeda SK, Papa G, Kemp SA, Ikeda T, Toyoda M, Seng TT, Kuramochi J, Mitsunaga S, UenoT, Shirakawa K, Takaori-Kondo A, Brevini T, Mallery DL, Charles OJ, CITIID-NIHR BioResource COVID-19 Collaboration, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Bowen JE, Joshi A, Walls AC, Jackson L, Martin D, Smith KGC, Bradley J, Briggs JAG, Choi J, Madissoon E, Meyer K, Mlcochova P, Ceron-Gutierrez L, Doffinger R, Teichmann SA, Fisher AJ, Pizzuto MS, de Marco A, Corti D, Hosmillo M, Lee JH, James LC, Thukral L, Veesler D, Sigal A, Sampaziotis F, Goodfellow IG, Matheson NJ, Sato K, Gupta RK. Altered TMPRSS2 usage by SARS-CoV-2 Omicron impacts tropism and fusogenicity. Nature. 603, 706-714, 2022.

Rajib SA, Ogi Y, Hossain MB, Ikeda T, Tanaka E, Kawaguchi, Satou Y. A SARS-CoV-2 Delta variant containing mutation in the probe binding region used for RT-qPCR test in Japan exhibited atypical PCR amplification and might induce false negative result. J Infect Chemother. 28, 669-667, 2022.

Yamasoba D#, Kimura I#, Nasser H#, Morioka Y#, Nao N#, Ito J#, Uriu K#, Tsuda M#, Zahradnik J# (#equal contribution), Shirakawa K, Suzuki R, Kishimoto M, Kosugi Y, Kobiyama K, Hara T, Toyoda M, Tanaka YL, Butlertanaka EP, Shimizu R, Ito H, Wang L, Oda Y, Orba Y, Sasaki M, Nagata K, Yoshimatsu K, Asakura H, Nagashima M, Sadamasu K, Yoshimura K, Kuramochi J, Seki M, Fujiki R, Kaneda A, Shimada T, Nakada T, Sakao S, Suzuki T, Ueno T, Takaori-Kondo A, Ishii KJ, Schreiber G, The Genotype to Phenotype Japan (G2P-Japan) Consortium, Sawa H, Saito A, Irie T, Tanaka T, Matsuno K, Fukuhara T, Ikeda T, Sato K* (*equal correspondence). Virological characteristics of the SARS-CoV-2 Omicron BA.2 spike. Cell. 2022. In press.

2021

Abe T, Ikeda T, Tokuda Y, Ito J, Suzuki Y, Narahara C, Iriyama H, Sato K. A patient infected with SARS-CoV-2 over 100 days. QJM: An International Journal of Medicine, 114, 47-49. 2021.

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, The Genotype to Phenotype Japan (G2P-Japan) consortium, Ikeda T, Nakagawa S, Ueno T, and Sato K (*equal correspondence). SARS-CoV-2 spike L452R variant evades cellular immunity and increases infectivity. Cell Host Microbe. 29, 1124-1136.e11, 2021. [Link]

Kaku Y, Kuwata T, Zahid HM, Hashiguchi T, Noda T, Kuramoto N, Biswas S, Matsumoto K, Shimizu M, Kawanami Y, Shimura K, Onishi C, Muramoto Y, Suzuki T, Sasaki J, Nagasaki Y, Minami R, Motozono C, Toyoda M, Takahashi H, Kishi H, Fujii K, Tatsuke T, Ikeda T, Maeda Y, Ueno T, Koyanagi Y, Iwagoe H, Matsushita S. Resistance of SARS-CoV-2 variants to neutralization by antibodies induced in convalescent patients with COVID-19. Cell Rep. 36, 109385, 2021.

Fukuda M, Islam MS, Shimizu R, Nasser H, Rabin NN, Takahashi Y, Sekine Y, Lindoy LF, Fukuda T, Ikeda T, Hayami S* (*equal correspondence). Lethal interactions of SARS-CoV-2 with graphene oxide: Implications for COVID-19 treatment. ACS Appl Nano Mater. 4, 11881-11887, 2021. [Link].

2020

Nakano Y, Yamamoto K, Takahashi Ueda M, Soper A, Konno Y, Kimura I, Uriu K, Kumata R, Aso H, Misawa N, Nagaoka S, Shimizu S, Mitsumune K, Kosugi Y, Juarez-Fernandez G, Ito J, Nakagawa S, Ikeda T, Koyanagi Y, Harris RS and Sato K. A role for gorilla APOBEC3G in shaping lentivirus evolution including transmission to humans. PLoS Pathog, 16, e1008812. 2020.

2019

Ikeda T, Walker SN, Tennyson RL, Harris RS, and McNaughton BR (equal contribution). Evolved Proteins Inhibit Entry of Enfuvirtide-Resistant HIV-1. ACS Infect Dis. 5, 634-640. 2019. [Link]

Brief description: The HIV-1 entry inhibitor, Enfuvirtide is poor solubility and bioavailability. In this paper, we improved more soluble and bioavailable.

Ikeda T, Molan AM, Jarvis MC, Carpenter MA, Salamango DJ, Brown WL, and Harris RS (*equal contribution). HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1. J Gen Virol. 100, 1140-1152. 2019. [Link]

Brief description: We demonstrated that endogenous APOBEC3G contributes to HIV-1 restriction in the human acute myelocytic leukemia cell line, THP-1.

Salamango DJ, Ikeda T, Moghadasi SA, Wang J, McCann JL, Serebrenik A, Ebrahimi D, Jarvis MC, Shaban NM, Brown WL, and Harris RS. HIV-1 Vif triggers cell cycle arrest by degrading cellular PPP2R5 phospho-regulators. Cell Rep. 29, 1057-1065.e4. 2019.

2018

Ikeda T, Symeonides M, Albin JS, Li M, Thali M, and Harris RS. HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G. PLoS Pathog. 14, e1007010. 2018. [Link]

Brief description: We demonstrated a Vif-independent mechanism that HIV-1 can escape the restriction activity by APOBEC3G。

Tennyson RL, Walker SN, Ikeda T, Harris RS, and McNaughton BR. Evaluation of sequence variability in HIV-1 gp41 C-peptide helix-grafted proteins. Bioorg Med Chem. 26, 1220-1224. 2018.

Ebrahimi D, Richards CM, Carpenter MA, Wang J, Ikeda T, Becker JT, Cheng, AZ, McCann JL, Shaban NM, Salamango DJ, Starrett GJ, Lingappa JR, Yong J, Brown WL, and Harris RS. Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease. Nat Commun. 9, 4137. 2018.

Anderson BD, Ikeda T, Moghadasi SA, St. Martin A, Brown WL and Harris RS (equal contribution). Natural APOBEC3C variants can elicit differential HIV-1 restriction activity. Retrovirology. 15, 78. 2018. [Link]

Brief description: We demonstrated that a naturally occuring APOBEC3C variant influences its anti-HIV-1 activity using a T cell model system.

2017

Ikeda T, Shimoda M, Ebrahimi D, VandeBerg JL, Harris RS, Koito A, and Maeda K (*equally correspondence).Opossum APOBEC1 is a DNA mutator with retrovirus and retroelement restriction activity. Sci Rep. 7, 46719. 2017. [Link]

Brief description: We demonstrated that opossum APOBEC1 proteins have restriction activity against retroviruses and retroelements

2016

Ikeda T, Ong EB, Watanabe N, Sakaguchi N, Maeda K, and Koito A (*equal correspondence). Creation of chimeric human/rabbit APOBEC1 with HIV-1 restriction and DNA mutation activities. Sci Rep. 6, 19035. 2016. [Link]

Brief description: We demonstrated the region of rabbit APOBEC1 proteins required for anti-HIV-1 activity.

Yoshikawa R, Izumi T, Yamada E, Nakano Y, Misawa N, Ren F, Carpenter MA, Ikeda T, Münk C, Harris RS, Miyazawa T, Koyanagi Y, and Sato K. A naturally occurring domestic cat APOBEC3 variant confers resistance to FIV infection. J Virol. 90, 474-85. 2016.

Tennyson RL, Walker SN, Ikeda T, Harris RS, Kennan AJ and McNaughton BR. Helix-grafted Pleckstrin homology domains suppress HIV-1 infection of CD4-positive cells. Chembiochem. 17, 1945-1950. 2016.

2014

Refsland EW, Hultquist JF, Luengas EM, Ikeda T, Shaban NM, Law EK, Brown WL, Reilly C, Emerman M, and Harris RS. Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity. PLoS Genet. 10, e1004761. 2014.

Maeda K, Almofty SA, Singh SK, Eid MM, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, and Sakaguchi N. GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity. J Immunol. 15, 6030-9. 2013.

2013

Rathore A, Carpenter MA, Demir O, Ikeda T, Li M, Shaban N, Law EK, Anokhin D, Brown WL, Amaro RE, and Harris RS. The local dinucleotide preference of APOBEC3G can be altered from 5’-CC to 5’-TC by a single amino acid substitution. J Mol Biol. 425, 4442-54. 2013.

2012

Watanabe N, Ikeda T, Mizuki F, and Tani T. Characterization of the ptr5+ gene involved in nuclear mRNA export in fission Yeast. Biochem Biophys Res Commun. 418, 62-6. 2012.

2011

Ikeda T, Abd El Galil KH, Tokunaga K, Maeda K, Sata T, Sakaguchi N, Heidmann T, and Koito A. Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons. Nucleic Acids Res. 39, 5538-54. 2011. [Link]

Brief description: We demonstrated that APOBEC1s play dual roles in the inhibition of retrotransposon mobility with a deamination-dependent restriction of LTR retrotransposons and a deamination-independent restriction of non-LTR.

2008

Ikeda T, Ohsugi T, Kimura T, Matsushita S, Maeda Y, Harada S, and Koito A. The anti-retroviral potency of APOBEC1 deaminase from small animal species. Nucleic Acids Res. 36, 6859-6871. 2008. [Link]

Brief description: We demonstrated that APOBEC1s from rodents (mouse, rat and hamster) and rabbits can inhibit the replication of several retroviruses (e.g., HIV-1), via deamination of viral cDNA and genomic RNA.

2007

Ikeda T, Shibata J, Yoshimura K, Koito A, and Matsushita S. Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy. J Infect Dis. 195, 716-25. 2007. [Link]

Brief description: We demonstrated two novel results; first, strong integration clusters in the BACH2 gene were observed in two patients. Second, through longitudinal analysis for 3 patients, multiple identical integration sites were detectable in HIV-1-infected cells, suggesting that these cells persist for long periods and clonal expansion may occur.

TOP

Publications: ニュース

Publications

Okada S, Fukai Y, Tanoue Y, Nasser H, Fukuda T, Ikeda T, Saitoh H. Basic structure and cytocompatibility of giant membrane vesicles derived from paraformaldehyde-exposed human cells. J Biochem. 171, 339-347, 2022.

​

​

​

Rajib SA, Ogi Y, Hossain MB, Ikeda T, Tanaka E, Kawaguchi, Satou Y. A SARS-CoV-2 Delta variant containing mutation in the probe binding region used for RT-qPCR test in Japan exhibited atypical PCR amplification and might induce false negative result. J Infect Chemother. 28, 669-667, 2022.

​

Abe T, Ikeda T, Tokuda Y, Ito J, Suzuki Y, Narahara C, Iriyama H, Sato K. A patient infected with SARS-CoV-2 over 100 days. QJM: An International Journal of Medicine, 114, 47-49. 2021.

​

Fukuda M, Islam MS, Shimizu R, Nasser H, Rabin NN, Takahashi Y, Sekine Y, Lindoy LF, Fukuda T*, Ikeda T*, Hayami S* (*equal correspondence). Lethal interactions of SARS-CoV-2 with graphene oxide: Implications for COVID-19 treatment. ACS Appl Nano Mater. 4, 11881-11887, 2021. [Link].

Ikeda T*, Walker SN*, Tennyson RL*, Harris RS, and McNaughton BR (*equal contribution). Evolved Proteins Inhibit Entry of Enfuvirtide-Resistant HIV-1. ACS Infect Dis. 5, 634-640. 2019. [Link]

​

Brief description: The HIV-1 entry inhibitor, Enfuvirtide is poor solubility and bioavailability. In this paper, we improved more soluble and bioavailable.

​

Ikeda T*, Molan AM*, Jarvis MC, Carpenter MA, Salamango DJ, Brown WL, and Harris RS (*equal contribution). HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1. J Gen Virol. 100, 1140-1152. 2019. [Link]

​

Brief description: We demonstrated that endogenous APOBEC3G contributes to HIV-1 restriction in the human acute myelocytic leukemia cell line, THP-1.

​

Salamango DJ, Ikeda T, Moghadasi SA, Wang J, McCann JL, Serebrenik A, Ebrahimi D, Jarvis MC, Shaban NM, Brown WL, and Harris RS. HIV-1 Vif triggers cell cycle arrest by degrading cellular PPP2R5 phospho-regulators. Cell Rep. 29, 1057-1065.e4. 2019.

Ikeda T, Symeonides M, Albin JS, Li M, Thali M, and Harris RS. HIV-1 adaptation studies reveal a novel Env-mediated homeostasis mechanism for evading lethal hypermutation by APOBEC3G. PLoS Pathog. 14, e1007010. 2018. [Link]

​

Brief description: We demonstrated a Vif-independent mechanism that HIV-1 can escape the restriction activity by APOBEC3G。

Tennyson RL, Walker SN, Ikeda T, Harris RS, and McNaughton BR. Evaluation of sequence variability in HIV-1 gp41 C-peptide helix-grafted proteins. Bioorg Med Chem. 26, 1220-1224. 2018.

​

​

Anderson BD*, Ikeda T*, Moghadasi SA*, St. Martin A, Brown WL and Harris RS (*equal contribution). Natural APOBEC3C variants can elicit differential HIV-1 restriction activity. Retrovirology. 15, 78. 2018. [Link]

​

Brief description: We demonstrated that a naturally occuring APOBEC3C variant influences its anti-HIV-1 activity using a T cell model system.

Ikeda T*, Shimoda M, Ebrahimi D, VandeBerg JL, Harris RS, Koito A, and Maeda K* (*equally correspondence).Opossum APOBEC1 is a DNA mutator with retrovirus and retroelement restriction activity. Sci Rep. 7, 46719. 2017. [Link]

Brief description: We demonstrated that opossum APOBEC1 proteins have restriction activity against retroviruses and retroelements

Ikeda T*, Ong EB, Watanabe N, Sakaguchi N, Maeda K*, and Koito A (*equal correspondence). Creation of chimeric human/rabbit APOBEC1 with HIV-1 restriction and DNA mutation activities. Sci Rep. 6, 19035. 2016. [Link]

Brief description: We demonstrated the region of rabbit APOBEC1 proteins required for anti-HIV-1 activity.

​

Yoshikawa R, Izumi T, Yamada E, Nakano Y, Misawa N, Ren F, Carpenter MA, Ikeda T, Münk C, Harris RS, Miyazawa T, Koyanagi Y, and Sato K. A naturally occurring domestic cat APOBEC3 variant confers resistance to FIV infection. J Virol. 90, 474-85. 2016.

​

Tennyson RL, Walker SN, Ikeda T, Harris RS, Kennan AJ and McNaughton BR. Helix-grafted Pleckstrin homology domains suppress HIV-1 infection of CD4-positive cells. Chembiochem. 17, 1945-1950. 2016.

Refsland EW, Hultquist JF, Luengas EM, Ikeda T, Shaban NM, Law EK, Brown WL, Reilly C, Emerman M, and Harris RS. Natural polymorphisms in human APOBEC3H and HIV-1 Vif combine in primary T lymphocytes to affect viral G-to-A mutation levels and infectivity. PLoS Genet. 10, e1004761. 2014.

​

Maeda K, Almofty SA, Singh SK, Eid MM, Shimoda M, Ikeda T, Koito A, Pham P, Goodman MF, and Sakaguchi N. GANP interacts with APOBEC3G and facilitates its encapsidation into the virions to reduce HIV-1 infectivity. J Immunol. 15, 6030-9. 2013.

​

Rathore A, Carpenter MA, Demir O, Ikeda T, Li M, Shaban N, Law EK, Anokhin D, Brown WL, Amaro RE, and Harris RS. The local dinucleotide preference of APOBEC3G can be altered from 5’-CC to 5’-TC by a single amino acid substitution. J Mol Biol. 425, 4442-54. 2013.

Watanabe N, Ikeda T, Mizuki F, and Tani T. Characterization of the ptr5+ gene involved in nuclear mRNA export in fission Yeast. Biochem Biophys Res Commun. 418, 62-6. 2012.

Ikeda T, Abd El Galil KH, Tokunaga K, Maeda K, Sata T, Sakaguchi N, Heidmann T, and Koito A. Intrinsic restriction activity by apolipoprotein B mRNA editing enzyme APOBEC1 against the mobility of autonomous retrotransposons. Nucleic Acids Res. 39, 5538-54. 2011. [Link]

Brief description: We demonstrated that APOBEC1s play dual roles in the inhibition of retrotransposon mobility with a deamination-dependent restriction of LTR retrotransposons and a deamination-independent restriction of non-LTR.

Ikeda T, Ohsugi T, Kimura T, Matsushita S, Maeda Y, Harada S, and Koito A. The anti-retroviral potency of APOBEC1 deaminase from small animal species. Nucleic Acids Res. 36, 6859-6871. 2008. [Link]

Brief description: We demonstrated that APOBEC1s from rodents (mouse, rat and hamster) and rabbits can inhibit the replication of several retroviruses (e.g., HIV-1), via deamination of viral cDNA and genomic RNA.

Ikeda T, Shibata J, Yoshimura K, Koito A, and Matsushita S. Recurrent HIV-1 integration at the BACH2 locus in resting CD4+ T cell populations during effective highly active antiretroviral therapy. J Infect Dis. 195, 716-25. 2007. [Link]

Fukuda M, Islam MS, Shimizu R, Nasser H, Rabin NN, Takahashi Y, Sekine Y, Lindoy LF, Fukuda T, Ikeda T, Hayami S* (*equal correspondence). Lethal interactions of SARS-CoV-2 with graphene oxide: Implications for COVID-19 treatment. ACS Appl Nano Mater. 4, 11881-11887, 2021. [Link].

Ikeda T, Walker SN, Tennyson RL, Harris RS, and McNaughton BR (equal contribution). Evolved Proteins Inhibit Entry of Enfuvirtide-Resistant HIV-1. ACS Infect Dis. 5, 634-640. 2019. [Link]

Ikeda T, Molan AM, Jarvis MC, Carpenter MA, Salamango DJ, Brown WL, and Harris RS (*equal contribution). HIV-1 restriction by endogenous APOBEC3G in the myeloid cell line THP-1. J Gen Virol. 100, 1140-1152. 2019. [Link]

Anderson BD, Ikeda T, Moghadasi SA, St. Martin A, Brown WL and Harris RS (equal contribution). Natural APOBEC3C variants can elicit differential HIV-1 restriction activity. Retrovirology. 15, 78. 2018. [Link]

Ikeda T, Shimoda M, Ebrahimi D, VandeBerg JL, Harris RS, Koito A, and Maeda K (*equally correspondence).Opossum APOBEC1 is a DNA mutator with retrovirus and retroelement restriction activity. Sci Rep. 7, 46719. 2017. [Link]

Ikeda T, Ong EB, Watanabe N, Sakaguchi N, Maeda K, and Koito A (*equal correspondence). Creation of chimeric human/rabbit APOBEC1 with HIV-1 restriction and DNA mutation activities. Sci Rep. 6, 19035. 2016. [Link]