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Multi-omics analysis of ovarian cancer using a stepwise tumorigenesis model

Research Project

Project/Area Number 21K15519
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 50010:Tumor biology-related
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

Machino Hidenori  国立研究開発法人理化学研究所, 革新知能統合研究センター, 研究員 (60833762)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2023: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2022: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2021: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Keywords高異型度卵巣漿液性がん / マルチオミックス解析 / 上皮間葉転換 / 転写因子 / AP-1 family / GATA family
Outline of Research at the Start

高異型度卵巣漿液性がんの予後不良なサブタイプHomologous recombination (HR)-proficient typeの発がん機序を解明するために、正常由来細胞である卵管分泌上皮細胞にがん遺伝子を導入し、段階的な発がんモデルサンプルを作成する。ATAC-seq・ChIP-seq・RNA-seqによるマルチオミックス解析を実施し、発がん過程でクロマチン構造が変化するゲノム領域を抽出する。正常卵管・上皮内がん・浸潤がんの臨床検体標本に免疫組織化学染色を実施し、マルチオミックス解析結果を検証する。この過程で高異型度卵巣漿液性がんの新規治療標的・バイオマーカーを同定する。

Outline of Final Research Achievements

We established a stepwise tumorigenesis model of high-grade serous ovarian carcinoma (HGSOC) and conducted integrated epigenetic analysis using RNA-seq, ATAC-seq, and ChIP-seq. Our analysis revealed activation of AP-1 family transcription factors (TFs) and inactivation of GATA family TFs during the transition from cell-of-origin to cancerous cells in the process of ovarian cancer development. Dysfunction of these TFs was implicated in promoting invasion and metastasis of ovarian cancer through epithelial-mesenchymal transition in the early stages of tumorigenesis. Treatment with a MEK inhibitor was found to partially reverse these epigenetic abnormalities. These findings hold promise for contributing to the early detection and treatment of HGSOCs.

Academic Significance and Societal Importance of the Research Achievements

高異型度漿液性卵巣がんは最も頻度が高く死亡者数が多い婦人科系悪性腫瘍である。網羅的ゲノム解析が世界規模で完了した現在においても、相同組換え修復経路に異常が認められないサブタイプには有効な治療法が確立しておらず予後不良である。そこで本研究では、高異型度漿液性卵巣がんの正常由来細胞から予後不良なサブタイプの段階的発がんモデル細胞を樹立し、網羅的エピゲノム解析を実施した。この結果、発がん初期にエピゲノム異常を介して転写因子の結合異常が生じ、卵巣がん細胞の浸潤・播種が促進されることが明らかになった。この成果は、高異型度漿液性卵巣がんの新規バイオマーカー・新規治療法の開発に寄与することが期待される。

Report

(4 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (18 results)

All 2023 2022 2021 Other

All Int'l Joint Research (3 results) Journal Article (9 results) (of which Int'l Joint Research: 7 results,  Peer Reviewed: 9 results,  Open Access: 9 results) Presentation (4 results) Remarks (2 results)

  • [Int'l Joint Research] National Cancer Institute(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] Memorial Sloan-Kettering Cancer Center(米国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] National Cancer Institute(米国)

    • Related Report
      2022 Research-status Report
  • [Journal Article] Analysis of super-enhancer using machine learning and its application to medical biology2023

    • Author(s)
      Hamamoto Ryuji、Takasawa Ken、Shinkai Norio、Machino Hidenori、Kouno Nobuji、Asada Ken、Komatsu Masaaki、Kaneko Syuzo
    • Journal Title

      Briefings in Bioinformatics

      Volume: - Issue: 3

    • DOI

      10.1093/bib/bbad107

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrative analysis reveals early epigenetic alterations in high-grade serous ovarian carcinomas2023

    • Author(s)
      Machino Hidenori、Dozen Ai、Konaka Mariko、Komatsu Masaaki、Nakamura Kohei、Ikawa Noriko、Shozu Kanto、Asada Ken、Kaneko Syuzo、Yoshida Hiroshi、Kato Tomoyasu、Nakayama Kentaro、Saloura Vassiliki、Kyo Satoru、Hamamoto Ryuji
    • Journal Title

      Experimental & Molecular Medicine

      Volume: 55 Issue: 10 Pages: 2205-2219

    • DOI

      10.1038/s12276-023-01090-1

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Advances in cancer DNA methylation analysis with methPLIER: use of non-negative matrix factorization and knowledge-based constraints to enhance biological interpretability2023

    • Author(s)
      Takasawa K, Asada K, Kaneko S, Shiraishi K, Machino H, Takahashi S, Shinkai N, Kouno N, Kobayashi K, Komatsu M, Mizuno T, Okubo Y, Mukai M, Yoshida T, Yoshida Y, Horinouchi H, Watanabe S, Ohe Y, Yatabe Y, Kohno T, Hamamoto R
    • Journal Title

      Experimental and Molecular Medicine

      Volume: 56 Issue: 3 Pages: 646-655

    • DOI

      10.1038/s12276-024-01173-7

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Medical Professional Enhancement Using Explainable Artificial Intelligence in Fetal Cardiac Ultrasound Screening2022

    • Author(s)
      Sakai Akira、Komatsu Masaaki、Komatsu Reina、Matsuoka Ryu、Yasutomi Suguru、Dozen Ai、Shozu Kanto、Arakaki Tatsuya、Machino Hidenori、Asada Ken、Kaneko Syuzo、Sekizawa Akihiko、Hamamoto Ryuji
    • Journal Title

      Biomedicines

      Volume: 10 Issue: 3 Pages: 551-551

    • DOI

      10.3390/biomedicines10030551

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Appkication of non-negative matrix fractorization in oncology: one approach for establishing precision medicine2022

    • Author(s)
      Hamamoto R, Takasawa K, Machino H, Kobayashi K, Takahashi S, Bolatkan A, Shinkai N, Sakai A, Aoyama R, Yamada M, Asada K, Komatsu M, Okamoto K, Kameoka H, Kaneko S
    • Journal Title

      Briefings in Bioinformatics

      Volume: 23 Issue: 4

    • DOI

      10.1093/bib/bbac246

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Introducing AI to the molecular tumor board: one direction toward the establishment of precision medicine using large-scale cancer clinical and biological information2022

    • Author(s)
      Hamamoto R, Koyama T, Kouno N, Yasuda T, Yui S, Sudo K, Hirata M, Sunami K, Kubo T, Takasawa K, Takahashi S, Machino H, Kobayashi K, Asada K, Komatsu M, Kaneko S, Yatabe Y, Yamamoto N
    • Journal Title

      Experimental Biology and Oncology

      Volume: 11 Issue: 1 Pages: 8-8

    • DOI

      10.1186/s40164-022-00333-7

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Repression of the PRELP gene is relieved by histone deacetylase inhibitors through acetylation of histone H2B lysine 5 in bladder cancer2022

    • Author(s)
      Shozu Kanto、Kaneko Syuzo、Shinkai Norio、Dozen Ai、Kosuge Hirofumi、Nakakido Makoto、Machino Hidenori、Takasawa Ken、Asada Ken、Komatsu Masaaki、Tsumoto Kouhei、Ohnuma Shin-Ichi、Hamamoto Ryuji
    • Journal Title

      Clinical Epigenetics

      Volume: 14 Issue: 1 Pages: 1-13

    • DOI

      10.1186/s13148-022-01370-z

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Tumor Suppressive Role of the PRELP Gene in Ovarian Clear Cell Carcinoma2022

    • Author(s)
      Dozen Ai、Shozu Kanto、Shinkai Norio、Ikawa Noriko、Aoyama Rina、Machino Hidenori、Asada Ken、Yoshida Hiroshi、Kato Tomoyasu、Hamamoto Ryuji、Kaneko Syuzo、Komatsu Masaaki
    • Journal Title

      Journal of Personalized Medicine

      Volume: 12 Issue: 12 Pages: 1999-1999

    • DOI

      10.3390/jpm12121999

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma2022

    • Author(s)
      Hidenori Machino, Syuzo Kaneko, Masaaki Komatsu, Noriko Ikawa, Ken Asada, Ryuichiro Nakato, Kanto Shozu, Ai Dozen, Kenbun Sone, Hiroshi Yoshida, Tomoyasu Kato, Katsutoshi Oda, Yutaka Osuga, Tomoyuki Fujii, Gottfried von Keudell, Vassiliki Saloura, Ryuji Hamamoto
    • Journal Title

      Communications Biology

      Volume: 5 Issue: 1 Pages: 39-39

    • DOI

      10.1038/s42003-021-02992-4

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Comprehensive transcription factor motif analysis focusing on mutational signatures in multiple cancer types2023

    • Author(s)
      Hidenori Machino
    • Organizer
      日本癌学会
    • Related Report
      2023 Annual Research Report
  • [Presentation] 複数がん種のmutational signatureに着目した包括的転写因子モチーフ解析2023

    • Author(s)
      Hidenori Machino
    • Organizer
      日本メディカルAI学会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Epigenetic dysregulation of AP-1 and GATA family genes induces epithelial-mesenchymal transition in ovarian carcinomas2022

    • Author(s)
      Hidenori Machino
    • Organizer
      日本癌学会
    • Related Report
      2022 Research-status Report
  • [Presentation] Integrative analysis revealed early epigenetic changes in high-grade serous ovarian carcinogenesis2021

    • Author(s)
      Hidenori Machino
    • Organizer
      日本癌学会
    • Related Report
      2021 Research-status Report
  • [Remarks] 卵巣がんの発がんメカニズムを解明 -がんエピゲノムを標的としたマルチオミックス解析による成果-

    • URL

      https://www.riken.jp/press/2023/20231004_2/index.html

    • Related Report
      2023 Annual Research Report
  • [Remarks] 卵巣がんの新しい治療標的を同定 -がん研究に医療ビッグデータとコンピュータ科学を活用-

    • URL

      https://www.riken.jp/press/2022/20220207_1/

    • Related Report
      2023 Annual Research Report

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Published: 2021-04-28   Modified: 2025-01-30  

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