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Trans-omic analysis of metabolic adaptation

Administrative Group

Project AreaTransomic Analysis of Metabolic Adaptation
Project/Area Number 17H06299
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

Kueoda Shinya  東京大学, 大学院理学系研究科(理学部), 教授 (50273850)

Co-Investigator(Kenkyū-buntansha) 角田 達彦  東京大学, 大学院理学系研究科(理学部), 教授 (10273468)
岡田 眞里子  大阪大学, 蛋白質研究所, 教授 (10342833)
馬場 健史  九州大学, 生体防御医学研究所, 教授 (10432444)
鈴木 穣  東京大学, 大学院新領域創成科学研究科, 教授 (40323646)
松田 史生  大阪大学, 大学院情報科学研究科, 教授 (50462734)
伊藤 隆司  九州大学, 医学研究院, 教授 (90201326)
中山 敬一  九州大学, 生体防御医学研究所, 主幹教授 (80291508)
Project Period (FY) 2017-06-30 – 2022-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥156,520,000 (Direct Cost: ¥120,400,000、Indirect Cost: ¥36,120,000)
Fiscal Year 2021: ¥34,970,000 (Direct Cost: ¥26,900,000、Indirect Cost: ¥8,070,000)
Fiscal Year 2020: ¥34,970,000 (Direct Cost: ¥26,900,000、Indirect Cost: ¥8,070,000)
Fiscal Year 2019: ¥34,970,000 (Direct Cost: ¥26,900,000、Indirect Cost: ¥8,070,000)
Fiscal Year 2018: ¥31,980,000 (Direct Cost: ¥24,600,000、Indirect Cost: ¥7,380,000)
Fiscal Year 2017: ¥19,630,000 (Direct Cost: ¥15,100,000、Indirect Cost: ¥4,530,000)
Keywordsトランスオミクス / 代謝アダプテーション / 代謝 / オミクス計測
Outline of Final Research Achievements

Under the Integrated Metabolic Omics Research Group, various omics measurement centers and omics data analysis centers (mathematical modeling and statistical analysis) have been established to ensure a research system that can perform trans-omics analysis seamlessly. To support the development of young researchers, inter-laboratory exchanges are conducted mainly among young researchers to provide them with opportunities to acquire basic knowledge and skills in measurement and data analysis. In addition, open tutorials are held in conjunction with the group meetings, and are open to the public. At the group meetings, not only the progress of research, but also the needs of metabolic adaptation and the seeds of trans-omics technology were matched.

Academic Significance and Societal Importance of the Research Achievements

ヒト全身トランスオミクスおよびGWASを多階層オミクス今後さまざまなヒト疾患の実データ解析に基づくTrans-OWASにより、肝がん・肝疾患、糖尿病、心疾患を解析することで、がん転移などの環境適応や、動的な薬剤の選択などの precision medicineの基盤となることが期待される。また、代謝アダプテーションのトランスオミクス解析を微生物や植物へ適応することにより、バイオプロダクション発展の基盤となる合成生物学・代謝工学などの幅広い分野におけるブレイクスルーのキーテクノロジーとして期待される。

Report

(6 results)
  • 2022 Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • Research Products

    (32 results)

All 2023 2022 2021 2020 2019 2018 2017

All Journal Article (23 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 23 results,  Open Access: 22 results) Presentation (6 results) (of which Int'l Joint Research: 3 results,  Invited: 3 results) Funded Workshop (3 results)

  • [Journal Article] Optogenetic decoding of Akt2-regulated metabolic signaling pathways in skeletal muscle cells using transomics analysis2023

    • Author(s)
      Kawamura Genki、Kokaji Toshiya、Kawata Kentaro、Sekine Yuka、Suzuki Yutaka、Soga Tomoyoshi、Ueda Yoshibumi、Endo Mizuki、Kuroda Shinya、Ozawa Takeaki
    • Journal Title

      Science Signaling

      Volume: 16 Issue: 773 Pages: 773-773

    • DOI

      10.1126/scisignal.abn0782

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Features extracted using tensor decomposition reflect the biological features of the temporal patterns of human blood multimodal metabolome2023

    • Author(s)
      Fujita Suguru、Karasawa Yasuaki、Hironaka Ken-ichi、Taguchi Y.-h.、Kuroda Shinya
    • Journal Title

      PLOS ONE

      Volume: 18 Issue: 2 Pages: e0281594-e0281594

    • DOI

      10.1371/journal.pone.0281594

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states.2022

    • Author(s)
      Kokaji T, Eto M, Hatano A, Yugi K, Morita K, Ohno S, Fujii M, Hironaka KI, Ito Y, Egami R, Uematsu S, Terakawa A, Pan Y, Maehara H, Li D, Bai Y, Tsuchiya T, Ozaki H, Inoue H, Kubota H, Suzuki Y, Hirayama A, Soga T, Kuroda S.
    • Journal Title

      Sci Rep

      Volume: 12 Issue: 1 Pages: 13719-13719

    • DOI

      10.1038/s41598-022-17964-9

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trans-omics analysis of insulin action reveals a cell growth subnetwork which co-regulates anabolic processes2022

    • Author(s)
      Terakawa Akira、Hu Yanhui、Kokaji Toshiya、Yugi Katsuyuki、Morita Keigo、Ohno Satoshi、Pan Yifei、Bai Yunfan、Parkhitko Andrey A.、Ni Xiaochun、Asara John M.、Bulyk Martha L.、Perrimon Norbert、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 25 Issue: 5 Pages: 104231-104231

    • DOI

      10.1016/j.isci.2022.104231

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantitative metabolic fluxes regulated by trans-omic networks2022

    • Author(s)
      Ohno Satoshi、Uematsu Saori、Kuroda Shinya
    • Journal Title

      Biochemical Journal

      Volume: 479 Issue: 6 Pages: 787-804

    • DOI

      10.1042/bcj20210596

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Enhanced transcriptional heterogeneity mediated by NF-κB super-enhancers2022

    • Author(s)
      Wibisana Johannes N.、Inaba Takehiko、Shinohara Hisaaki、Yumoto Noriko、Hayashi Tetsutaro、Umeda Mana、Ebisawa Masashi、Nikaido Itoshi、Sako Yasushi、Okada Mariko
    • Journal Title

      PLOS Genetics

      Volume: 18 Issue: 6 Pages: 1010235-1010235

    • DOI

      10.1371/journal.pgen.1010235

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantitative metabolomics for dynamic metabolic engineering using stable isotope labeled internal standards mixture (SILIS).2022

    • Author(s)
      Soma Y#, Takahashi M#, Fujiwara Y, Tomiyasu N, Goto M, Hanai T, Izumi Y, Bamba T*.
    • Journal Title

      J. Biosci. Bioeng.

      Volume: 133(1) Issue: 1 Pages: 46-55

    • DOI

      10.1016/j.jbiosc.2021.09.009

    • NAID

      40022801277

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Four features of temporal patterns characterize similarity among individuals and molecules by glucose ingestion in humans2022

    • Author(s)
      Fujita Suguru、Karasawa Yasuaki、Fujii Masashi、Hironaka Ken-ichi、Uda Shinsuke、Kubota Hiroyuki、Inoue Hiroshi、Sumitomo Yohei、Hirayama Akiyoshi、Soga Tomoyoshi、Kuroda Shinya
    • Journal Title

      npj Systems Biology and Applications

      Volume: 8 Issue: 1 Pages: 6-6

    • DOI

      10.1038/s41540-022-00213-0

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism2022

    • Author(s)
      Uematsu Saori、Ohno Satoshi、Tanaka Kaori Y.、Hatano Atsushi、Kokaji Toshiya、Ito Yuki、Kubota Hiroyuki、Hironaka Ken-ichi、Suzuki Yutaka、Matsumoto Masaki、Nakayama Keiichi I.、Hirayama Akiyoshi、Soga Tomoyoshi、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 25 Issue: 2 Pages: 103787-103787

    • DOI

      10.1016/j.isci.2022.103787

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer.2021

    • Author(s)
      Oka M, Xu L, Suzuki T, Yoshikawa T, Sakamoto H, Uemura H, Yoshizawa AC, Suzuki Y, Nakatsura T, Ishihama Y, Suzuki A, Seki M
    • Journal Title

      Genome Biol.

      Volume: 22(1):9 Issue: 1 Pages: 1-9

    • DOI

      10.1186/s13059-020-02240-8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Calibration-curve-locking database for semi-quantitative metabolomics by gas chromatography/mass spectrometry.2021

    • Author(s)
      Hata K#, Soma Y#, Yamashita T, Takahashi M, Sugitate K, Serino T, Miyagawa H, Suzuki K, Yamada K, Kawamukai T, Shiota T, Izumi Y*, Bamba T*.
    • Journal Title

      Metabolites

      Volume: 11(4) Issue: 4 Pages: 207-207

    • DOI

      10.3390/metabo11040207

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fat Induces Glucose Metabolism in Nontransformed Liver Cells and Promotes Liver Tumorigenesis2021

    • Author(s)
      L. A. Broadfield, J. A. G. Duarte, R. Schmieder, D. Broekaert, K. Veys, M. Planque, K. Vriens, Y. Karasawa, F. Napolitano, S. Fujita, M. Fujii, M. Eto, B. Holvoet, R. Vangoitsenhoven, J. Fernandez-Garcia, J. van Elsen, J. Dehairs, J. Zeng, J. Dooley, R. Alba Rubio, J. van Pelt et al.
    • Journal Title

      Cancer Research

      Volume: 81 Issue: 8 Pages: 1988-2001

    • DOI

      10.1158/0008-5472.can-20-1954

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver2021

    • Author(s)
      Matsuzaki Fumiko、Uda Shinsuke、Yamauchi Yukiyo、Matsumoto Masaki、Soga Tomoyoshi、Maehara Kazumitsu、Ohkawa Yasuyuki、Nakayama Keiichi I.、Kuroda Shinya、Kubota Hiroyuki
    • Journal Title

      Cell Reports

      Volume: 36 Issue: 8 Pages: 109569-109569

    • DOI

      10.1016/j.celrep.2021.109569

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trans-omic analysis reveals obesity-associated dysregulation of inter-organ metabolic cycles between the liver and skeletal muscle2021

    • Author(s)
      Egami Riku、Kokaji Toshiya、Hatano Atsushi、et al.
    • Journal Title

      iScience

      Volume: 24 Issue: 3 Pages: 102217-102217

    • DOI

      10.1016/j.isci.2021.102217

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics2020

    • Author(s)
      N. Matsuda, K. Hironaka, M. Fujii, T. Wada, K. Kunida, H. Inoue, M. Eto, D. Hoshino, Y. Furuichi, Y. Manabe, N. L. Fujii, H. Noji, H. Imamura, S. Kuroda
    • Journal Title

      Quantitative Biology

      Volume: 8 Issue: 3 Pages: 228-237

    • DOI

      10.1007/s40484-020-0211-8

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise2020

    • Author(s)
      Wada Takumi、Hironaka Ken-ichi、Wataya Mitsutaka、Fujii Masashi、Eto Miki、Uda Shinsuke、Hoshino Daisuke、Kunida Katsuyuki、Inoue Haruki、Kubota Hiroyuki、Takizawa Tsuguto、Karasawa Yasuaki、Nakatomi Hirofumi、Saito Nobuhito、Hamaguchi Hiroki、Furuichi Yasuro、Manabe Yasuko、Fujii Nobuharu L.、Kuroda Shinya
    • Journal Title

      Cell Reports

      Volume: 32 Issue: 9 Pages: 108051-108051

    • DOI

      10.1016/j.celrep.2020.108051

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Kinetic Trans-omic Analysis Reveals Key Regulatory Mechanisms for Insulin-Regulated Glucose Metabolism in Adipocytes2020

    • Author(s)
      Ohno Satoshi、Quek Lake-Ee、Krycer James R.、Yugi Katsuyuki、Hirayama Akiyoshi、Ikeda Satsuki、Shoji Futaba、Suzuki Kumi、Soga Tomoyoshi、James David E.、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 23 Issue: 9 Pages: 101479-101479

    • DOI

      10.1016/j.isci.2020.101479

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Trans-omic Analysis Reveals ROS-Dependent Pentose Phosphate Pathway Activation after High-Frequency Electrical Stimulation in C2C12 Myotubes2020

    • Author(s)
      Hoshino Daisuke、Kawata Kentaro、Kunida Katsuyuki、Hatano Atsushi、Yugi Katsuyuki、Wada Takumi、Fujii Masashi、Sano Takanori、Ito Yuki、Furuichi Yasuro、Manabe Yasuko、Suzuki Yutaka、Fujii Nobuharu L.、Soga Tomoyoshi、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 23 Issue: 10 Pages: 101558-101558

    • DOI

      10.1016/j.isci.2020.101558

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity2020

    • Author(s)
      Kokaji Toshiya、Hatano Atsushi、Ito Yuki、et al.
    • Journal Title

      Science Signaling

      Volume: 13 Issue: 660 Pages: 1236-1236

    • DOI

      10.1126/scisignal.aaz1236

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Logical design of oral glucose ingestion pattern minimizing blood glucose in humans.2019

    • Author(s)
      Fujii M, Murakami Y, Karasawa Y, Sumitomo Y, Fujita S, Koyama M, Uda S, Kubota H, Inoue H, Konishi K, Oba S, Ishii S, Kuroda S.
    • Journal Title

      NPJ Syst Biol Appl.

      Volume: 5 Issue: 1 Pages: 31-31

    • DOI

      10.1038/s41540-019-0108-1

    • NAID

      120006939199

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data2018

    • Author(s)
      Kawata Kentaro、Yugi Katsuyuki、Hatano Atsushi、Kokaji Toshiya、Tomizawa Yoko、Fujii Masashi、Uda Shinsuke、Kubota Hiroyuki、Matsumoto Masaki、Nakayama Keiichi I.、Kuroda Shinya
    • Journal Title

      Genes to Cells

      Volume: 24 Issue: 1 Pages: 82-93

    • DOI

      10.1111/gtc.12655

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Trans-omic Analysis Reveals Selective Responses to Induced and Basal Insulin across Signaling, Transcriptional, and Metabolic Networks2018

    • Author(s)
      Kawata Kentaro、Hatano Atsushi、Yugi Katsuyuki、Kubota Hiroyuki、Sano Takanori、Fujii Masashi、Tomizawa Yoko、Kokaji Toshiya、Tanaka Kaori Y.、Uda Shinsuke、Suzuki Yutaka、Matsumoto Masaki、Nakayama Keiichi I.、Saitoh Kaori、Kato Keiko、Ueno Ayano、Ohishi Maki、Hirayama Akiyoshi、Soga Tomoyoshi、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 7 Pages: 212-229

    • DOI

      10.1016/j.isci.2018.07.022

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] In?Vivo Decoding Mechanisms of the Temporal Patterns of Blood Insulin by the Insulin-AKT Pathway in the Liver2018

    • Author(s)
      Kubota Hiroyuki、Uda Shinsuke、Matsuzaki Fumiko、Yamauchi Yukiyo、Kuroda Shinya
    • Journal Title

      Cell Systems

      Volume: 7 Issue: 1 Pages: 1-11

    • DOI

      10.1016/j.cels.2018.05.013

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Presentation] Trans-omic Analysis of Insulin Action2019

    • Author(s)
      Shinya Kuroda
    • Organizer
      The 20th International Conference on Systems Biology (ICSB) 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トラ ンスオミクスによる肝臓での糖応答システムの解析2019

    • Author(s)
      黒田 真也
    • Organizer
      第62回日本糖尿病学会年次学術集会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Trans-omic analysis of the liver of lean and obese mice during an oral glucose challenge2019

    • Author(s)
      黒田 真也
    • Organizer
      第92回日本生化学会大会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Systems biology of insulin action2017

    • Author(s)
      Shinya Kuroda
    • Organizer
      Hunter meeting
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-Omics analysis of the liver of lean and obese mice during an oral glucose administration2017

    • Author(s)
      Shinya Kuroda
    • Organizer
      The 1st International Symposium for Trans-Omics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 血中ホルモンによる血糖ホメオスタシスの数理モデルを用いた血糖摂取のロジカルデザイン2017

    • Author(s)
      黒田真也
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Funded Workshop] ICSB2019 satellite workshop Trans-Omics workshop The 3rd International Symposium for Trans-Omics2019

    • Related Report
      2019 Annual Research Report
  • [Funded Workshop] 2nd international symposium for trans-omics2018

    • Related Report
      2018 Annual Research Report
  • [Funded Workshop] The 1st International Symposium for Trans-Omics2017

    • Related Report
      2017 Annual Research Report

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Published: 2017-07-04   Modified: 2024-01-30  

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