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Identification and control of disease-specific network by trans-omic analysis

Research Project

Project/Area Number 15H05582
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field System genome science
Research InstitutionInstitute of Physical and Chemical Research (2016-2019)
The University of Tokyo (2015)

Principal Investigator

Yugi Katsuyuki  国立研究開発法人理化学研究所, 生命医科学研究センター, 上級研究員 (70433745)

Project Period (FY) 2015-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥23,660,000 (Direct Cost: ¥18,200,000、Indirect Cost: ¥5,460,000)
Fiscal Year 2018: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
Fiscal Year 2017: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2016: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2015: ¥11,700,000 (Direct Cost: ¥9,000,000、Indirect Cost: ¥2,700,000)
Keywords代謝 / システム生物学 / トランスオミクス / 数理モデル / メタボローム / プロテオーム / トランスクリプトーム / シグナル伝達 / 代謝ネットワーク / シグナル伝達ネットワーク
Outline of Final Research Achievements

As originally planned, we have established a methodology of trans-omics that includes omics layers for gene expression and metabolic flux. This methodology was applied to characterization of metabolic regulation in the mouse liver. We successfully reconstructed a multi-layered metabolic regulatory network in the livers of wild type and obese mice subjected to oral glucose tolerance tests. This is the first full-scale trans-omics analysis using in vivo data in our attempts. In addition, we published several review articles systematically defining the concept and methodology of trans-omics, and its future direction. These review articles, particularly the one on the cover of the April 2016 issue of Trends in Biotechnology, provided further recognition of the methodology.

Academic Significance and Societal Importance of the Research Achievements

我々が本研究を通して確立したトランスオミクスの方法論は、これまで主に哺乳類の糖代謝調節機構の全体像解明に関して成果を上げている。代謝調節機構の解明は、栄養や関連生理機能についてのより正確な理解につながり、さらに2型糖尿病など代謝疾患のメカニズム解明やその予防へとつながる。また近年、微生物によって有用物質を生産する代謝工学・発酵工学に関しても欧州を中心にトランスオミクスの応用が始まっており、代謝を調節するメカニズムに関して細胞や臓器のみならず種を超えて応用可能な方法論であることが示されつつある。したがって、トランスオミクスは広く代謝に関連する科学全般の発展に資する方法論である。

Report

(5 results)
  • 2019 Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (41 results)

All 2020 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (3 results) Journal Article (12 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 8 results,  Open Access: 5 results,  Acknowledgement Compliant: 1 results) Presentation (24 results) (of which Int'l Joint Research: 11 results,  Invited: 15 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results)

  • [Int'l Joint Research] シドニー大学(オーストラリア)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] University of Sydney(オーストラリア)

    • Related Report
      2017 Annual Research Report
  • [Int'l Joint Research] University of Sydney/University of Queensland/University of New South Wales(Australia)

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Dynamic 13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response to Insulin2020

    • Author(s)
      Quek Lake-Ee、Krycer James R.、Ohno Satoshi、Yugi Katsuyuki、Fazakerley Daniel J.、Scalzo Richard、Elkington Sarah D.、Dai Ziwei、Hirayama Akiyoshi、Ikeda Satsuki、Shoji Futaba、Suzuki Kumi、Locasale Jason W.、Soga Tomoyoshi、James David E.、Kuroda Shinya
    • Journal Title

      iScience

      Volume: 23 Issue: 2 Pages: 100855-100855

    • DOI

      10.1016/j.isci.2020.100855

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Rate-oriented trans-omics: integration of multiple omic data on the basis of reaction kinetics2019

    • Author(s)
      Yugi Katsuyuki、Ohno Satoshi、Krycer James R.、James David E.、Kuroda Shinya
    • Journal Title

      Current Opinion in Systems Biology

      Volume: 15 Pages: 109-120

    • DOI

      10.1016/j.coisb.2019.04.005

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] トランスオミクスの考え方と実験デザイン2019

    • Author(s)
      柚木克之
    • Journal Title

      細胞

      Volume: 51 Pages: 701-705

    • Related Report
      2018 Annual Research Report
  • [Journal Article] トランスオミクス・統合オミクス研究による免疫代謝・腸内細菌代謝研究2019

    • Author(s)
      出野泉花, 柚木克之
    • Journal Title

      臨床免疫・アレルギー科

      Volume: 72 Pages: 342-350

    • Related Report
      2018 Annual Research Report
  • [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
      2018 Annual Research 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] Metabolism as a signal generator across trans-omic networks at distinct time scales2018

    • Author(s)
      Yugi Katsuyuki、Kuroda Shinya
    • Journal Title

      Current Opinion in Systems Biology

      Volume: 8 Pages: 59-66

    • DOI

      10.1016/j.coisb.2017.12.002

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] GWASをトランスオミクスで読み解く2018

    • Author(s)
      柚木克之, 角田達彦, 黒田真也
    • Journal Title

      遺伝子医学Mook

      Volume: 33 Pages: 127-136

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Dynamic Metabolomics Reveals that Insulin Primes the Adipocyte for Glucose Metabolism2017

    • Author(s)
      James R. Krycer, Satoshi Ohnoら全21名
    • Journal Title

      Cell Reports

      Volume: 21 Issue: 12 Pages: 3536-3547

    • DOI

      10.1016/j.celrep.2017.11.085

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Metabolism-Centric Trans-Omics2017

    • Author(s)
      Yugi Katsuyuki、Kuroda Shinya
    • Journal Title

      Cell Systems

      Volume: 4 Issue: 1 Pages: 19-20

    • DOI

      10.1016/j.cels.2017.01.007

    • Related Report
      2016 Annual Research Report
  • [Journal Article] Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin2016

    • Author(s)
      Takanori Sano,* Kentaro Kawata, * Satoshi Ohno,* Katsuyuki Yugi, Hiroaki Kakuda, Hiroyuki Kubota, Shinsuke Uda, Masashi Fujii, Katsuyuki Kunida, Daisuke Hoshino, Atsushi Hatano, Yuki Ito,1 Miharu Sato, Yutaka Suzuki, Shinya Kuroda†
    • Journal Title

      Science Signaling

      Volume: 9 Issue: 455

    • DOI

      10.1126/scisignal.aaf3739

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers2016

    • Author(s)
      Yugi, K., Kubota, H., Hatano, A., and Kuroda, S.
    • Journal Title

      Trends in Biotechnology

      Volume: 34 Issue: 4 Pages: 276-290

    • DOI

      10.1016/j.tibtech.2015.12.013

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Presentation] Trans-omics: integration of multiple omic data on the basis of reaction kinetics2020

    • Author(s)
      Yugi, K.
    • Organizer
      Karolinska Institutet _ RIKEN Joint International Doctoral Course 2020
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トランスオミクス解析によるインスリン代謝制御ネットワークの再構築2019

    • Author(s)
      柚木克之
    • Organizer
      第92回日本内分泌学会学術総会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Integration of phosphoproteome and 13C-metabolome data reveals ‘metabolic priming’ in the adipocyte2019

    • Author(s)
      Yugi, K.
    • Organizer
      3rd RIKEN IMS-Stanford ISCBRM Joint Symposium
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トランスオミクス研究の現在地および免疫代謝研究への展望2019

    • Author(s)
      柚木克之
    • Organizer
      第7回がんと代謝研究会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 多階層オミクスデータ解析の自動化に向けて2019

    • Author(s)
      柚木克之
    • Organizer
      第44回日本医用マススペクトル学会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 3 つのオミクス階層を縦断するインスリン濃度選択的制御軸の発見2019

    • Author(s)
      柚木克之
    • Organizer
      第13回メタボロームシンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] Dose-selective metabolic regulation by insulin across multiple omic layers2019

    • Author(s)
      Yugi, K.
    • Organizer
      The 3rd International Symposium for TransOmics
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omics: integration of multiple omic data on the basis of reaction kinetic2019

    • Author(s)
      Yugi, K.
    • Organizer
      The 6th RIKEN-KI-SciLifeLab Symposium: Biomedical Data for Artificial Intelligence
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omics: integration of multiple omic data on the basis of reaction kinetics2019

    • Author(s)
      Yugi, K.
    • Organizer
      The 4th Symposium of Inter-University Research Network for Trans-Omics Medicine
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dose-selective metabolic regulation by insulin across multiple omic layers2019

    • Author(s)
      Yugi, K.
    • Organizer
      RIKEN-KU Leuven Joint Symposium 2019
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] トランスオミクス:細胞の反応速度論的描像に基づく統合オミクス解析2019

    • Author(s)
      柚木克之
    • Organizer
      第412回CBI学会講演会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Dynamic metabolomics and phosphoproteomics reveals that insulin primes the adipocyte for glucose metabolism2018

    • Author(s)
      Katsuyuki Yugi, James R. Krycer, Shinya Kuroda, David E. James
    • Organizer
      19th International Conference on Systems Biology, Lyon, France
    • Related Report
      2017 Annual Research Report
  • [Presentation] 統合オミクス解析の現状と未来2018

    • Author(s)
      柚木克之
    • Organizer
      味の素株式会社 イノベーション研究所
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Trans-omic analysis reveals fed and fasting insulin signal across phosphoproteome, transcriptome, and metabolome2017

    • Author(s)
      Katsuyuki Yugi
    • Organizer
      The 1st International Symposium for Trans-Omics, Tokyo
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] A trans-omic reconstruction of insulin-dependent regulatory networks for metabolism2017

    • Author(s)
      Katsuyuki Yugi
    • Organizer
      The 4th International Symposium of Gunma University Initiative for Advanced Research
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Reconstruction of insulin-dependent metabolic regulatory networks from phosphoproteome and metabolome data2017

    • Author(s)
      Katsuyuki Yugi
    • Organizer
      RIKEN IMS - Japan Society for Immunology International Symposium on Immunology 2017
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Dynamic metabolomics reveals that insulin primes the 16 adipocyte for glucose metabolism2017

    • Author(s)
      Katsuyuki Yugi
    • Organizer
      From Single- to Multiomics: Applications and Challenges in Data Integration
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 動的13C-メタボロミクスおよびリン酸化プロテオミクスの統合解析により明らかとなった脂肪細胞の代謝プライミング機構2017

    • Author(s)
      柚木克之
    • Organizer
      第42回日本医用マススペクトル学会年会
    • Related Report
      2016 Annual Research Report
  • [Presentation] Reconstruction of a ‘trans-omic’ network of insulin signal from phosphoproteome and metabolome data2015

    • Author(s)
      Katsuyuki Yugi
    • Organizer
      16th International Conference on Systems Biology
    • Place of Presentation
      Singapore (Singapore)
    • Year and Date
      2015-11-23
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] トランスオミクス解析によるインスリン代謝制御ネットワークの再構築2015

    • Author(s)
      柚木克之
    • Organizer
      第 40 回日本医用マススペクトル学会年会
    • Place of Presentation
      アクトシティ浜松(静岡県浜松市)
    • Year and Date
      2015-09-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] トランスオミクス解析によるインスリン代謝制御ネットワークの再構 築2015

    • Author(s)
      柚木克之
    • Organizer
      日本プロテオーム学会 2015 年会
    • Place of Presentation
      くまもと森都心プラザ(熊本県熊本市)
    • Year and Date
      2015-07-23
    • Related Report
      2015 Annual Research Report
  • [Presentation] トランスオミクス解析によるインスリン代謝制御ネットワークの再構築2015

    • Author(s)
      柚木克之
    • Organizer
      第42回BMSコンファレンス
    • Place of Presentation
      岐阜グランドホテル(岐阜県岐阜市)
    • Year and Date
      2015-07-06
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] トランスオミクス解析によるインスリン代謝制御ネットワークの再構築2015

    • Author(s)
      柚木克之
    • Organizer
      第 63 回 質量分析総合討論会
    • Place of Presentation
      つくば国際会議場 エポカルつくば(茨城県つくば市)
    • Year and Date
      2015-06-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] トランスオミクス解析による多階層代謝制御ネットワークおよび薬剤応答ネットワークの再構築2015

    • Author(s)
      柚木克之
    • Organizer
      東北大学東北メディカル・メガバンク機構・臨床メ タボロミクスセミナー
    • Place of Presentation
      東北大学東北メディカルメガバンク機構(宮城県仙台市)
    • Year and Date
      2015-05-28
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Remarks] Australian Biochemist 4月号

    • URL

      https://www.asbmb.org.au/magazine/

    • Related Report
      2016 Annual Research Report
  • [Patent(Industrial Property Rights)] 多階層網羅的データに基づく細胞内分子間ネットワーク自動推定法2015

    • Inventor(s)
      柚木克之、久保田浩行、黒田真也
    • Industrial Property Rights Holder
      柚木克之、久保田浩行、黒田真也
    • Industrial Property Rights Type
      特許
    • Filing Date
      2015
    • Acquisition Date
      2017
    • Related Report
      2016 Annual Research Report

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Published: 2015-04-16   Modified: 2022-11-04  

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