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Temporal coding of single cell signal transduction

Research Project

Project/Area Number 18H03979
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionThe University of Tokyo

Principal Investigator

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

Co-Investigator(Kenkyū-buntansha) 眞鍋 康子  東京都立大学, 人間健康科学研究科, 准教授 (60467412)
Project Period (FY) 2018-04-01 – 2021-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥44,070,000 (Direct Cost: ¥33,900,000、Indirect Cost: ¥10,170,000)
Fiscal Year 2020: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2019: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Fiscal Year 2018: ¥12,350,000 (Direct Cost: ¥9,500,000、Indirect Cost: ¥2,850,000)
Keywordsシグナル伝達 / 1細胞 / 情報理論 / 細胞間変動 / 細胞内変動 / 時間情報コード / システム生物学 / ゾネーション / トランスオミクス / 1細胞計測 / 相互情報量 / 自動認識 / 確率的ゆらぎ
Outline of Final Research Achievements

In this study, information-theoretic analysis of the response to stimuli on a per-cell basis revealed that the existence of cell-by-cell response variability enables more precise control of the response of tissues, which are collections of cells. The present study reveals that the existence of cell-by-cell variability in response characteristics leads to an increase in the range in which stimuli can be distinguished as a tissue, and thus enables accurate response control.

Academic Significance and Societal Importance of the Research Achievements

この研究では骨格筋の実験系を用いて細胞間変動の影響を明らかにしましたが、得られた知見は組織としての応答が各細胞の応答の合計であると考えられる系であれば当てはまると考えられ、例えばホルモン分泌制御などにも適用可能であると考えられる。細胞ごとの応答のばらつきによる正確な応答制御機構が明らかになったことで、臓器レベルの応答制御がより明らかになっていくものと考えられ、疾病などによる臓器の応答制御異常のメカニズム解明にも役立っていくものと期待される。

Report

(4 results)
  • 2022 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • Research Products

    (22 results)

All 2023 2022 2021 2020 2019 2018

All Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 16 results,  Open Access: 15 results) Presentation (6 results) (of which Int'l Joint Research: 3 results,  Invited: 4 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
      2020 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
      2020 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
      2020 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
      2020 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
      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] 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] 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] 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
      2020 Annual Research Report 2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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] 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] 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] 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] Robustness against additional noise in cellular information transmission2019

    • Author(s)
      Tottori Takehiro、Fujii Masashi、Kuroda Shinya
    • Journal Title

      Physical Review E

      Volume: 100 Issue: 4 Pages: 042403-042403

    • DOI

      10.1103/physreve.100.042403

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] NMDAR-mediated Ca2+ increase shows robust information transfer in dendritic spines2019

    • Author(s)
      Tottori Takehiro、Fujii Masashi、Kuroda Shinya
    • Journal Title

      Biophysical Journal

      Volume: 印刷中 Issue: 9 Pages: 1748-1758

    • DOI

      10.1016/j.bpj.2019.03.030

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Automatic Quantitative Segmentation of Myotubes Reveals Single-cell Dynamics of S6 Kinase Activation2018

    • Author(s)
      Inoue Haruki、Kunida Katsuyuki、Matsuda Naoki、Hoshino Daisuke、Wada Takumi、Imamura Hiromi、Noji Hiroyuki、Kuroda Shinya
    • Journal Title

      Cell Structure and Function

      Volume: 43 Issue: 2 Pages: 153-169

    • DOI

      10.1247/csf.18012

    • NAID

      130007472951

    • ISSN
      0386-7196, 1347-3700
    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Transomic network analysis of glucose metabolism and its dysfunction associated with obesity2022

    • Author(s)
      Shinya Kuroda
    • Organizer
      The 21th International Conference on Systems Biology (ICSB) 2022
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] The roles of inter- and intra-cellular variations in cellular information transfer2022

    • Author(s)
      Shinya Kuroda
    • Organizer
      Workshop on Non-equilibrium Phenomena in Physics and Biology (NE-PB2022)
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Systems Biology of Insulin Action2022

    • Author(s)
      Shinya Kuroda
    • Organizer
      Biomedical Mathematics Online Colloquium
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 骨格筋のシステムバイオロジー:代謝トランスオミクスと情報誌論解析2022

    • Author(s)
      黒田 真也
    • Organizer
      第9回骨格筋生物学研究会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] インスリン作用のトランスオミクスネットワーク2021

    • Author(s)
      黒田 真也
    • Organizer
      第64回日本糖尿病学会年次学術集会The 64th Annual Meeting of the Japan Diabetes Society
    • Related Report
      2020 Annual Research Report
  • [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2021

    • Author(s)
      黒田 真也
    • Organizer
      第94回日本内分泌学会学術集会The 94th Annual Congress of the Japan Endocrine Society
    • Related Report
      2020 Annual Research Report

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Published: 2018-04-23   Modified: 2024-01-30  

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