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Understanding of fatty liver progression using time-series Trans-omics analysis

Research Project

Project/Area Number 20H03237
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43050:Genome biology-related
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) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,940,000 (Direct Cost: ¥13,800,000、Indirect Cost: ¥4,140,000)
Fiscal Year 2022: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2021: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2020: ¥9,100,000 (Direct Cost: ¥7,000,000、Indirect Cost: ¥2,100,000)
Keywordsシステム生物学 / 脂肪肝 / トランスオミクス解析 / マルチオミクス解析 / 肥満 / 肝臓 / システムバイオロジー / トランスオミクス
Outline of Research at the Start

脂肪肝はインスリン抵抗性や非アルコール性脂肪肝炎・肝ガンの原因である。これまでに食餌性肥満誘導マウス(DIOマウス)を用いて複数のオーム階層の網羅的な解析が行われてきた。しかし、これらの研究の殆どが単一階層の解析であり、対象サンプルとの2点間比較である。そこで本研究ではエピゲノム・トランスクリプトーム・プロテオーム・メタボロームのデータを取得し、多階層に跨るネットワークを同定する。同定したネットワークを基に数理モデルを作成し、肥満を制御することを目指す。

Outline of Final Research Achievements

Trans-omics network was constructed using seven omics data on five layers derived from the livers of diet-induced obesity and control mice through mathematical methods, statistical methods, and databases. We found that many of the molecules in all layers changed at two different timings. Also, from the results of the mathematical analysis, we found that other regulations between the layers contributed at the two same timing. These results indicated that fatty liver progression was divided into two stages. Furthermore, based on the trans-omics network, we extracted the characteristics of the metabolic pathways and found that each pathway showed different characteristics. Moreover, we also revealed the coordinated regulation among the layers: a meta-level regulation. These results will provide new insights into fatty liver progression.

Academic Significance and Societal Importance of the Research Achievements

生命現象は全て多階層に跨るネットワークに制御されているため、生命現象の全体像を明らかにするには、この多階層ネットワークを明らかにする必要がある。本研究で開発したトランスオミクス解析の手法は階層を繋げるのみならず、階層間の制御に関与する他の制御の寄与とタイミングも明らかにすることができた。本手法により、今後のオミクス研究に新たな方法と視点を与えられると期待される。また、肥満に伴う脂肪肝の進行が、2段階によって変容するという知見は、肥満の状態に応じた対応(治療)が必要であることを意味しており、治療への応用も期待できる。本研究の手法と結果は、他の疾患の理解にも貢献すると期待される。

Report

(4 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Annual Research Report
  • 2020 Annual Research Report
  • Research Products

    (19 results)

All 2023 2022 2021 2020

All Journal Article (9 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 9 results,  Open Access: 8 results) Presentation (6 results) (of which Int'l Joint Research: 4 results,  Invited: 4 results) Book (4 results)

  • [Journal Article] Comparison of hepatic responses to glucose perturbation between healthy and obese mice based on the edge type of network structures2023

    • Author(s)
      Ito Yuki、Uda Shinsuke、Kokaji Toshiya、Hirayama Akiyoshi、Soga Tomoyoshi、Suzuki Yutaka、Kuroda Shinya、Kubota Hiroyuki
    • Journal Title

      Scientific Reports

      Volume: 13 Issue: 1 Pages: 4758-4758

    • DOI

      10.1038/s41598-023-31547-2

    • Related Report
      2022 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
      2022 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
      2022 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
      2022 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
      2021 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
      2021 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 Liver2021

    • Author(s)
      Hiroyuki Kubota
    • Journal Title

      Methods of Mathematical Oncology

      Volume: 1 Pages: 203-213

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [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] 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
  • [Presentation] Trans-omic analysis of obesity revealed time-dependent regulation across multiple omic layer.2022

    • Author(s)
      Kubota H.
    • Organizer
      Hot Spring Harbor International Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Trans-omic analysis of inulin response in the liver.2022

    • Author(s)
      2.Matsuzaki F., Uda S., Yamauchi Y., Matumoto M., Soga T., Maehara K., Ohkawa Y., Nakayama K. I., Kuroda S., Kubota H.
    • Organizer
      Hot Spring Harbor International Symposium
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] トランスオミクス解析による生命現象の理解2022

    • Author(s)
      久保田浩行
    • Organizer
      最先端バイオインフォマティクス研究ミニシンポジウム
    • Related Report
      2022 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
      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
    • 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
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Book] 遺伝学の百科事典2022

    • Author(s)
      久保田浩行
    • Total Pages
      690
    • Publisher
      丸善出版
    • Related Report
      2022 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
      2022 Annual Research Report
  • [Book] レディオミクス入門2021

    • Author(s)
      2.久保田浩行
    • Total Pages
      338
    • Publisher
      オーム社
    • Related Report
      2021 Annual Research Report
  • [Book] 医薬品開発におけるオミクス解析技術2020

    • Author(s)
      久保田浩行
    • Total Pages
      181
    • Publisher
      情報機構
    • Related Report
      2020 Annual Research Report

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Published: 2020-04-28   Modified: 2024-01-30  

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