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HIV-1 transcriptome analysis

Research Project

Project/Area Number 17K09016
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Laboratory medicine
Research InstitutionKumamoto University

Principal Investigator

SATO YORIFUMI  熊本大学, ヒトレトロウイルス学共同研究センター, 教授 (70402807)

Project Period (FY) 2017-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2019: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2018: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
KeywordsHIV-1 / HIV-1感染症 / 慢性ウイルス感染症 / ウイルス / 感染症 / 微生物 / 発現制御 / 遺伝子
Outline of Final Research Achievements

First, we have established DNA-probe based viral sequence enrichment protocol for HIV-1 transcriptomic analysis by using cell lines. The efficiency was very high. We could enrich viral transcripts with more than 1,000 times.
Then, we applied the new protocol for clinical sample. We analyzed PBMCs from HIV-1-infected individuals. We analyzed them before and after cART. We found that even before cART, we could not detect enough number of HIV-1 transcripts even after enrichment.
We concluded that even our current is not good enough to detect HIV-1 RNA from clinical samples, especially PBMCs. We need to increase sensitivity or analyze different samples such as lymph nodes. We are going to continue this research h to make further progress.

Academic Significance and Societal Importance of the Research Achievements

HIV-1感染者において、抗ウイルス療法下で残存するウイルスリザーバの研究のために高感度ウイルス遺伝子発現検出系の開発を行った。従来の方法に比べ検出感度を数千倍高める事に成功した。
しかしながら、臨床検体でウイルスRNAを検出するには、それでも感度が不十分であったため、今後も研究を継続して、解析系の更なる改良を行う。

Report

(4 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • Research Products

    (34 results)

All 2020 2019 2018 2017 Other

All Int'l Joint Research (2 results) Journal Article (7 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 7 results,  Open Access: 6 results) Presentation (24 results) (of which Int'l Joint Research: 4 results,  Invited: 2 results) Remarks (1 results)

  • [Int'l Joint Research] インペリアル大学(英国)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] インペリアルカレッジロンドン(英国)

    • Related Report
      2017 Research-status Report
  • [Journal Article] HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus2019

    • Author(s)
      Iwase Saori C.、Miyazato Paola、Katsuya Hiroo、Islam Saiful、Yang Benjy Tan Jek、Ito Jumpei、Matsuo Misaki、Takeuchi Hiroaki、Ishida Takaomi、Matsuda Kouki、Maeda Kenji、Satou Yorifumi
    • Journal Title

      Scientific Reports

      Volume: 9 Issue: 1 Pages: 12326-12326

    • DOI

      10.1038/s41598-019-48681-5

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Nature of the HTLV-1 Provirus in Naturally Infected Individuals Analyzed by the Viral DNA-Capture-Seq Approach2019

    • Author(s)
      Katsuya H, Islam S, Tan, Ito J, Miyazato P, Matsuo, Inada Y, Iwase, Uchiyama Yoshikazu、Hata Hiroyuki、Sato T, Yagishita N, Araya N, Ueno T, Nosaka K, Tokunaga M, Yamagishi M, Watanabe T, Uchimaru K, Fujisawa J-i, Utsunomiya A, Yamano Y, Satou Y
    • Journal Title

      Cell Reports

      Volume: 29 Issue: 3 Pages: 724-735

    • DOI

      10.1016/j.celrep.2019.09.016

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP2019

    • Author(s)
      Miyazato Paola、Matsuo Misaki、Tan Benjy J. Y.、Tokunaga Michiyo、Katsuya Hiroo、Islam Saiful、Ito Jumpei、Murakawa Yasuhiro、Satou Yorifumi
    • Journal Title

      Retrovirology

      Volume: 16 Issue: 1 Pages: 38-38

    • DOI

      10.1186/s12977-019-0500-3

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] TFE3 Xp11.2 translocation renal cell carcinoma mouse model reveals novel therapeutic targets and identifies GPNMB as a diagnostic marker for human disease.2019

    • Author(s)
      Baba M, Furuya M, Motoshima T, Lang M, Funasaki S, Ma W, Sun HW, Hasumi H, Huang Y, Kato I, Kadomatsu T, Satou Y, Morris N, Karim BO, Ileva L, Kalen JD, Wilan Krisna LA, Hasumi Y, Sugiyama A, Kurahashi R, Nishimoto K, Oyama M, Nagashima Y, Kuroda N, Araki K, Eto M, Yao M, Kamba T, Suda T, Oike Y, Schmidt LS, Linehan WM
    • Journal Title

      Molecular Cancer Research

      Volume: 印刷中 Issue: 8 Pages: 1613-1626

    • DOI

      10.1158/1541-7786.mcr-18-1235

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 「HIV-1ウイルスリザーバの成立・維持の仕組み」2019

    • Author(s)
      佐藤賢文
    • Journal Title

      日本エイズ学会誌

      Volume: 21 Pages: 167-172

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Total HIV-1 DNA dynamics and influencing factors in long-term ART-treated Japanese adults: a retrospective longitudinal analysis.2018

    • Author(s)
      Stanoeva KR, König A, Fukuda A, Kawanami Y, Kuwata T, Satou Y, Matsushita S.
    • Journal Title

      J Acquir Immune Defic Syndr

      Volume: - Issue: 2 Pages: 239-247

    • DOI

      10.1097/qai.0000000000001662

    • Related Report
      2018 Research-status Report 2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Dynamics and mechanisms of clonal expansion of HIV-1-infected cells in a humanized mouse model2017

    • Author(s)
      Satou Yorifumi、Katsuya Hiroo、Fukuda Asami、Misawa Naoko、Ito Jumpei、Uchiyama Yoshikazu、Miyazato Paola、Islam Saiful、Fassati Ariberto、Melamed Anat、Bangham Charles R. M.、Koyanagi Yoshio、Sato Kei
    • Journal Title

      Scientific Reports

      Volume: 7(1) Issue: 1 Pages: 6913-6913

    • DOI

      10.1038/s41598-017-07307-4

    • NAID

      120006364095

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 30.HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 proviruses2020

    • Author(s)
      佐藤賢文
    • Organizer
      United States - Japan Cooperative Medical Sciences Program22nd International Conference on Emerging Infectious Diseases in the Pacific Rim
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 28.Genome-wide RNAi screen identifies MAPK-RPK required for HIV-1 proviral silencing in non-T cell reservoir cell-line model2019

    • Author(s)
      Takaomi Ishida, Yorifumi Satou, Jin Gohda, Haruki Kitamura, Shiyu Gan, Kazuho Takahashi, and Hiroaki Takeuchi
    • Organizer
      9th HIV persistence during therapy
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 27.Underlying mechanisms of experimental HIV-1 cure observed in the newly developed in vitro model named WIPE assay.2019

    • Author(s)
      Yorifumi Satou, Islam Mohammad Saiful, Kouki Matsuda, Hiroo Katsuya, Paola Miyazato, Kiyoto Tsuchiya, Kazuhisa Yoshimura, Shuzo Matsushita and Kenji Maeda
    • Organizer
      Cold Spring Harbor Laboratory - Meetings & Courses 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 26.A novel in vitro model of HIV-1-provirus elimination by latency-reversing agents (LRA) and other antiretroviral drugs2019

    • Author(s)
      Kenji Maeda, Kouki Matsuda, Islam Mohammad Saiful, Kiyoto Tsuchiya, Kazuhisa Yoshimura, and Yorifumi Satou
    • Organizer
      Cold Spring Harbor Laboratory - Meetings & Courses 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 6.HIV-1 DNA-capture-seq is a useful tool for the comprehensive characterization of HIV-1 provirus,2019

    • Author(s)
      佐藤賢文
    • Organizer
      レトロウイルス夏期セミナー2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] 治癒を目指したHIV研究2019

    • Author(s)
      佐藤賢文
    • Organizer
      第227回HIVカンファランス
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] Identification of an intragenic regulatory region within HIV-1 provirus and its transcriptional regulatory mechanism-HIV-1 プロウイルスのintragenic転写調節領域の探索および機能的解析2018

    • Author(s)
      Saori C. Iwase, Misaki Matsuo, Benjy Tan Jek Yang, Paola Miyazato, Eriko Kudo, Kouki Matsuda, Islam Saiful, Kenji Maeda, Seiji Okada, Yorifumi Satou
    • Organizer
      日本レトロウイルス研究会夏季セミナ―
    • Related Report
      2018 Research-status Report
  • [Presentation] Clonal selection of HIV-1-infected cells during ART in an in vitro model of persistent infection2018

    • Author(s)
      Saiful Islam, Kouki Matsuda, Benjy Tan Jek Yang, Hiroo Katsuya, Paola Miyazato, Kenji Maeda, Yorifumi Sato
    • Organizer
      第66回日本ウイルス学会学術集会
    • Related Report
      2018 Research-status Report
  • [Presentation] Identification of an intragenic regulatory region within HIV-1 provirus and its transcriptional regulatory mechanism2018

    • Author(s)
      Saori C. Iwase, Misaki Matsuo, Benjy Tan Jek Yang, Paola Miyazato, Eriko Kudo, Kouki Matsuda, Islam Saiful, Kenji Maeda, Seiji Okada, Yorifumi Satou
    • Organizer
      第66回日本ウイルス学会学術集会
    • Related Report
      2018 Research-status Report
  • [Presentation] Selection of HIV-1 proviruses under combined treatment with LRA and anti-retroviral drug in vitro2018

    • Author(s)
      Yorifumi Satou, Kouki Matsuda, Saiful Islam, Kenji Maeda
    • Organizer
      第19回熊本エイズセミナ―
    • Related Report
      2018 Research-status Report
  • [Presentation] Clonal selection of HIV-1-infected cells during ART in an in vitro model of persistent infection2018

    • Author(s)
      Saiful Islam, Kouki Matsuda, Benjy Tan Jek Yang, Hiroo Katsuya, Paola Miyazato, Kenji Maeda, Yorifumi Satou
    • Organizer
      第19回熊本エイズセミナ―
    • Related Report
      2018 Research-status Report
  • [Presentation] Identification of an intragenic regulatory region within HIV-1 provirus and its transcriptional regulatory mechanism2018

    • Author(s)
      Saori C. Iwase, Misaki Matsuo, Benjy Tan Jek Yang, Paola Miyazato, Eriko Kudo, Kouki Matsuda, Islam Saiful, Kenji Maeda, Seiji Okada, Yorifumi Satou
    • Organizer
      第19回熊本エイズセミナ―
    • Related Report
      2018 Research-status Report
  • [Presentation] Clonal selection of HIV-1-infected cells during ART in an in vitro model of persistent infection2018

    • Author(s)
      Saiful Islam, Kouki Matsuda, Benjy Tan Jek Yang, Hiroo Katsuya, Paola Miyazato, Kenji Maeda, Yorifumi Satou
    • Organizer
      第32回日本エイズ学会学術集会・総会
    • Related Report
      2018 Research-status Report
  • [Presentation] An Investigation on the Potential Role of HIV-Host Chimeric Transcripts in Maintaining the Latent Reservoir2018

    • Author(s)
      Benjy Tan Jek Yang, Iwase Saori, Katsuya Hiroo, Miyazato Paola, Islam Mohammad Saiful, Maeda Kenji, Matsushita Shuzo, Satou Yorifumi
    • Organizer
      第32回日本エイズ学会学術集会・総会
    • Related Report
      2018 Research-status Report
  • [Presentation] Identification of an intragenic regulatory region within HIV-1 provirus and its transcriptional regulatory mechanism2018

    • Author(s)
      Saori C. Iwase, Misaki Matsuo, Benjy Tan Jek Yang, Paola Miyazato, Eriko Kudo, Kouki Matsuda, Islam Saiful, Kenji Maeda, Seiji Okada, Yorifumi Satou
    • Organizer
      第32回日本エイズ学会学術集会・総会
    • Related Report
      2018 Research-status Report
  • [Presentation] Evaluation of HIV-1 Proviral DNA by Newly Established Approaches2018

    • Author(s)
      Islam Mohammad Saiful, Paola Miyazato, Kouki Matsuda, Benjy Tan Jek Yan, Saori Iwase, Yohei Seki, Kazuhisa Yoshimura, Hirofumi Akari, Kenji Maeda, Yorifumi Satou
    • Organizer
      JSPS_NUS Symposium
    • Related Report
      2017 Research-status Report
  • [Presentation] 次世代シークエンスによるヒト化マウスHIV-1感染モデルにおけるウイルス感染細胞クローン動態解析2017

    • Author(s)
      佐藤賢文、勝屋弘雄、福田麻美、三沢尚子、伊東潤平、内山良一、宮里パオラ、Mohammad S Islam、Ariberto Fassati、Charles RM Bangham、小柳義夫、佐藤圭
    • Organizer
      第27回抗ウイルス療法学会学術集会
    • Related Report
      2017 Research-status Report
  • [Presentation] Improving the Resolution of HIV-1 Transcriptome Analysis Through Targeted Enrichment2017

    • Author(s)
      Benjy Tan Jek Yang, Miyazato Paola, Islam Mohammad Saiful, Iwase Saori, Kudo Eriko, Okada Seiji, Satou Yorifumi
    • Organizer
      第20回日本レトロウイルス研究会 夏期セミナー
    • Related Report
      2017 Research-status Report
  • [Presentation] Absolute Quantitation of Integrated HIV-1 DNA In Vivo by using Droplet Digital PC2017

    • Author(s)
      Islam Mohammad Saiful, Yohei Seki, Paola Miyazato, Benjy Tan Jek Yang, Hirofumi Akari and Yorifumi Satou
    • Organizer
      第65回日本ウイルス学会学術集会
    • Related Report
      2017 Research-status Report
  • [Presentation] Improving the Resolution of HIV-1 Provirus RNA Sequencing through Targeted Enrichment2017

    • Author(s)
      Benjy Tan Jek Yang, Miyazato Paola, Islam Mohammad Saiful, Iwase Saori, Kudo Eriko, Okada Seiji, Satou Yorifumi
    • Organizer
      第65回日本ウイルス学会学術集会
    • Related Report
      2017 Research-status Report
  • [Presentation] Quantitative and Qualitative Evaluation of HIV-1 Proviral DNA by Droplet Digital PCR and High-throughput Sequencing2017

    • Author(s)
      Saiful Islam, Paola Miyazato, Yohei Seki, Benjy Tan Jek Yan, Saori Iwase, Hirofumi Akri, Yorifumi Satou
    • Organizer
      第18回熊本エイズ学セミナー
    • Related Report
      2017 Research-status Report
  • [Presentation] High Resolution HIV-1 Provirus Transcriptome Analysis with DNA Probe Enrichment2017

    • Author(s)
      Benjy Tan Jek Yang, Miyazato Paola, Islam Mohammad Saiful, Iwase Saori, Kudo Eriko, Okada Seiji, Satou Yorifumi
    • Organizer
      第18回熊本エイズ学セミナー
    • Related Report
      2017 Research-status Report
  • [Presentation] Quantitative and qualitative evaluation of HIV-1 proviral DNA by digital droplet PCR and high-throughput sequencing2017

    • Author(s)
      Islam Mohammad Saiful, Paola Miyazato, Yohei Seki, Benjy Tan Jek Yang, Saori Iwase, Hirofumi Akari, Yorifumi Satou
    • Organizer
      第31回日本エイズ学会学術集会・総会
    • Related Report
      2017 Research-status Report
  • [Presentation] High Resolution HIV-1 Provirus Transcriptome Analysis with DNA Probe Enrichment2017

    • Author(s)
      Benjy Tan Jek Yang, Miyazato Paola, Islam Mohammad Saiful, Iwase Saori, Kudo Eriko, Okada Seiji, Satou Yorifumi
    • Organizer
      第31回日本エイズ学会学術集会・総会
    • Related Report
      2017 Research-status Report
  • [Remarks] 熊本大学国際先端医学研究機構 エイズ学研究センター佐藤研究室_「RESEARCH」

    • URL

      http://www.caids.kumamoto-u.ac.jp/satou/research.html

    • Related Report
      2018 Research-status Report

URL: 

Published: 2017-04-28   Modified: 2022-02-22  

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