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Mathematical analysis of biological signaling networks across multiple layers

Planned Research

Project AreaIntegrative understanding of biological signaling networks based on mathematical science
Project/Area Number 16H06577
Research Category

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

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionKyushu University

Principal Investigator

Kubota Hiroyuki  九州大学, 生体防御医学研究所, 教授 (40376603)

Project Period (FY) 2016-06-30 – 2021-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥94,380,000 (Direct Cost: ¥72,600,000、Indirect Cost: ¥21,780,000)
Fiscal Year 2020: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2019: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2018: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2017: ¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2016: ¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Keywords数理解析 / トランスオミクス解析 / インスリン / 肥満 / システム生物学 / ネットワーク / システムバイオロジー / 数理モデル / 多階層ネットワーク / インスリンシグナル伝達 / シミュレーション / シグナル伝達 / 糖尿病 / 多階層データ / インスリン作用 / 動的特性
Outline of Final Research Achievements

We focused on the insulin signaling pathway and conducted mathematical analysis and multi-omics analysis at the individual level. In the mathematical analysis, we developed the first mathematical model of hormone action in vivo and revealed that the insulin signaling pathway in the liver processes information encoded into the blood insulin patterns and its mechanism. Using the model, we also predicted the insulin signaling pathway responses in type 2 diabetes mellitus conditions, and the model deepened our understanding on T2DM mechanisms. In the multi-omics analysis, we obtained time-series data across four omics layers, such as metabolome, phospho-proteome, expression proteome, and transcriptome. Also, we found that insulin action is coordinately regulated at different timing by reconstructing the trans-omic network across multi-omic layers.

Academic Significance and Societal Importance of the Research Achievements

これまでの分子メカニズムに注目したシステム生物学の研究は、培養された細胞などを用いた解析が中心であった。我々は個体における肝臓のインスリン作用に注目し研究を行った。その結果、数理モデルでは世界で初めて生体内におけるホルモン作用の数理モデルを作成した。また、代謝・タンパク質リン酸化・タンパク質発現・遺伝子発現の4階層のオミクスデータから多階層に跨るネットワークを再構築し、協調的な制御機構を明らかにした。これらの個体を用いた研究は、今後のヒトに対する治療や創薬研究を推し進めると期待される。

Report

(6 results)
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (49 results)

All 2022 2021 2020 2019 2018 2017 2016 Other

All Journal Article (16 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 16 results,  Open Access: 11 results) Presentation (23 results) (of which Int'l Joint Research: 11 results,  Invited: 17 results) Book (7 results) Remarks (3 results)

  • [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] 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] Selective Regulation of the Insulin-Akt Pathway by Simultaneous Processing of Blood Insulin Pattern in the Liver.2021

    • Author(s)
      Kubota H.
    • Journal Title

      Methods of Mathematical Oncology,

      Volume: 1 Pages: 203-213

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [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
    • 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
      2020 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
      2020 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
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Trans-omics impact of thymoproteasome in cortical thymic epithelial cells.2019

    • Author(s)
      Ohigashi I, Tanaka Y, Kondo K, Fujimori S, Kondo H, Palin A, Hoffmann V, Kozai M, Matsushita Y, Uda S, Motosugi R, Hamazaki J, Kubota H, Murata S, Tanaka K, Katagiri T, Kosako H, Takahama Y
    • Journal Title

      Cell Reports

      Volume: 29 Issue: 9 Pages: 2901-2916

    • DOI

      10.1016/j.celrep.2019.10.079

    • NAID

      120006894616

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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
      2019 Annual Research Report 2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects2018

    • Author(s)
      Ohashi Kaoru、Fujii Masashi、Uda Shinsuke、Kubota Hiroyuki、Komada Hisako、Sakaguchi Kazuhiko、Ogawa Wataru、Kuroda Shinya
    • Journal Title

      npj Systems Biology and Applications

      Volume: 4 Issue: 1 Pages: 14-14

    • DOI

      10.1038/s41540-018-0051-6

    • NAID

      120006599090

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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
      2018 Annual Research Report
    • Peer Reviewed
  • [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
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Increase in hepatic and decrease in peripheral insulin clearance characterize abnormal temporal patterns of serum insulin in diabetic subjects.2018

    • Author(s)
      Ohashi K., Fujii M., Uda S., Kubota H., Komada H., Sakaguchi K., Ogawa W., and Kuroda S.
    • Journal Title

      NPJ Syst Biol Appl.

      Volume: 14

    • NAID

      120006599090

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sparse Gaussian graphical model with missing values2017

    • Author(s)
      Uda Shinsuke、Kubota Hiroyuki
    • Journal Title

      Proceedings of the 21st Conference of Open Innovations Association

      Volume: - Pages: 336-343

    • DOI

      10.23919/fruct.2017.8250201

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] System identification of signaling dependent gene expression with different time-scale data.2017

    • Author(s)
      Tsuchiya T., Fujii M., Matsuda N., Kunida K., Uda S., Kubota H., Konishi K., and Kuroda S.
    • Journal Title

      PLoS Comput. Biol.

      Volume: 13

    • NAID

      120006555357

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Presentation] Trans-omic analysis of insulin response in the liver.2022

    • Author(s)
      Matsuzaki F., Uda S., Yamauchi Y., Kubota H.
    • Organizer
      International Symposium on Evolutionary Genomics and Bioinformatics 2022 (ISEGB2022),
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トランスオミクス解析を用いたマウス肝臓におけるインスリン作用の全体像の理解2021

    • Author(s)
      久保田 浩行
    • Organizer
      第3回日本メディカルAI学会学術集会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] トランスオミクス解析を用いた疾患の理解2021

    • Author(s)
      久保田浩行
    • Organizer
      第46回日本脳卒中学会学術集会
    • Related Report
      2020 Annual Research Report
    • Invited
  • [Presentation] Selective regulation of the Insulin-AKT pathway by simultaneous processing of blood insulin pattern in the liver.2020

    • Author(s)
      Hiroyuki Kubota.
    • Organizer
      Fusion of Mathematics and Biology, Online Meeting.
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Comparison of hepatic responses to glucose perturbation between normal and obese mice using edge ontology.2020

    • Author(s)
      Yuki Ito, Shinsuke Uda, Toshiya Kokaji, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Shinya Kuroda and Hiroyuki Kubota.
    • Organizer
      Fusion of Mathematics and Biology, Online Meeting.
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Selective regulation of the Insulin-AKT pathway by simultaneous processing of blood insulin pattern in the liver2020

    • Author(s)
      Hiroyuki Kubota.
    • Organizer
      Establishing International Research Network of Mathematical Oncology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Integrated analysis through multiple molecular layers: transomic network dynamics. The 29th Hot Spring Harbor International Symposium, Cutting Edge of Technical Innovations in Trans-Omics.2020

    • Author(s)
      Matsuzaki F., Uda S., Yamauchi Y., Matsumoto M., Soga T., Maehara K., Ohkawa Y., Nakayama K. I., Kuroda S., Kubota H.
    • Organizer
      The 20th International Conference on Systems Biology.
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 時系列トランスオミクス解析2019

    • Author(s)
      松崎芙美子、宇田新介、山内幸代、松本雅記、曽我朋義、前原一満、大川恭行、中山敬一、黒田真也、久保田浩行
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] 血中インスリンパターンによる生体応答の制御2019

    • Author(s)
      久保田浩行
    • Organizer
      生物物理リズム若手研究会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 肝臓と筋肉におけるAkt経路の定量的な比較2019

    • Author(s)
      加藤寛彬、宇田新介、松崎芙美子、久保田浩行
    • Organizer
      第42回日本分子生物学会年会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Regulation of insulin action by temporal patterns of insulin.2019

    • Author(s)
      Hiroyuki Kubota
    • Organizer
      iTHEMSセミナー
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Regulation of insulin action by temporal patterns of insulin.2019

    • Author(s)
      Hiroyuki Kubota.
    • Organizer
      JSMB2019 Conference
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] In vivo decoding mechanisms of the temporal patterns of blood insulin by the insulin-AKT pathway in the liver.2019

    • Author(s)
      Hiroyuki Kubota
    • Organizer
      1st international symposium on interdisciplinary approaches to integrative understanding of biological signaling networks,
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トランスオミクス解析を用いた生体応答のシステム的理解2018

    • Author(s)
      久保田 浩行
    • Organizer
      科学技術未来戦略ワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 単純なネットワーク構造と入力刺激パターンが生み出す生命応答の制御2018

    • Author(s)
      久保田 浩行
    • Organizer
      数理シグナル第3回若手ワークショップ
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] トランスオミクス解析を用いたインスリン作用の理解2018

    • Author(s)
      久保田 浩行
    • Organizer
      第22回日本心血管内分泌代謝学会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Trans-Omic analysis of the acute insulin action in the liver =Toward in vivo trans-omic analysis-2017

    • Author(s)
      Kubota H., Uda S., Matsuzaki F. and Kuroda S.
    • Organizer
      The 1st International Symposium for Trans-Omics
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] インスリンパターンによる生体内シグナル分子の選択的制御2017

    • Author(s)
      久保田 浩行、宇田 新介、松崎 芙美子、山内 幸代、黒田 真也
    • Organizer
      2017年度 生命科学系学会合同年次大会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] An estimation method of sparse partial correlation matrix for omics data analysis.2017

    • Author(s)
      Uda, S. and Kubota, H.
    • Organizer
      11th International Symposium of The Institute Network “Frontiers in Biomedical Sciences"
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Sparse Gaussian Graphical Model with Missing values.2017

    • Author(s)
      Uda, S. and Kubota H.
    • Organizer
      The 21st Conference of Open Innovations Association FRUCT.
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Toward in vivo Trans-omic analysis2016

    • Author(s)
      Kubota H., Fumiko M., Shinsuke, U. and Kuroda S.
    • Organizer
      14th JHUPO Conference
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omic analysis of insulin action - toward in vivo trans-omic analysis-2016

    • Author(s)
      Kubota H.
    • Organizer
      The 26th Hot Spring Harbor International Symposium
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] マウス肝臓におけるインスリン作用のトランスオミクス解析2016

    • Author(s)
      松崎芙美子、久保田浩行
    • Organizer
      第1回代謝モデリング勉強会
    • Related Report
      2016 Annual Research Report
  • [Book] 疾患原因遺伝子・タンパク質の解析技術と創薬/診断技術への応用2022

    • Author(s)
      松﨑芙美子、久保田浩行
    • Total Pages
      530
    • Publisher
      技術情報協会
    • Related Report
      2020 Annual Research Report
  • [Book] 遺伝学の百科事典2021

    • Author(s)
      久保田浩行
    • Total Pages
      690
    • Publisher
      丸善出版
    • Related Report
      2020 Annual Research Report
  • [Book] レディオミクス入門2021

    • Author(s)
      久保田浩行
    • Total Pages
      338
    • Publisher
      オーム社
    • Related Report
      2020 Annual Research Report
  • [Book] 生物をシステムとして理解する‐細胞とラジオは同じ!?‐2018

    • Author(s)
      久保田 浩行
    • Total Pages
      149
    • Publisher
      共立スマートセレクション
    • Related Report
      2018 Annual Research Report
  • [Book] 血中インスリン濃度パターンによる肝臓シグナル分子の選択的制御2018

    • Author(s)
      久保田浩行,黒田真也
    • Total Pages
      4
    • Publisher
      羊土社
    • Related Report
      2018 Annual Research Report
  • [Book] 1.はじめての数理モデルとシミュレーション2017

    • Author(s)
      鈴木 貴,久保田 浩行 編集
    • Total Pages
      238
    • Publisher
      羊土社
    • Related Report
      2017 Annual Research Report
  • [Book] 医学のあゆみ2016

    • Author(s)
      久保田浩行、黒田真也
    • Total Pages
      6
    • Publisher
      医歯薬出版株式会社
    • Related Report
      2016 Annual Research Report
  • [Remarks]

    • URL

      https://www.bioreg.kyushu-u.ac.jp/labo/omics/

    • Related Report
      2020 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所 統合オミクス分野 HP

    • URL

      http://www.bioreg.kyushu-u.ac.jp/labo/omics/index.html

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report
  • [Remarks] 九州大学生体防御医学研究所 年報

    • URL

      http://www.bioreg.kyushu-u.ac.jp/mib/about_reports_j.html

    • Related Report
      2018 Annual Research Report 2017 Annual Research Report

URL: 

Published: 2016-07-04   Modified: 2023-01-30  

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