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Multimodal analysis of chromatin 3D structure using deep learning in gynecological malignancies

Research Project

Project/Area Number 20H03820
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 56040:Obstetrics and gynecology-related
Research InstitutionThe University of Tokyo

Principal Investigator

Sone Kenbun  東京大学, 医学部附属病院, 講師 (90598872)

Co-Investigator(Kenkyū-buntansha) 田口 歩  東京大学, 医学部附属病院, 届出研究員 (60756782)
Project Period (FY) 2020-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
Fiscal Year 2022: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2021: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2020: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000)
Keywordsエピゲノム / ヒストン修飾 / 子宮体癌 / 卵巣癌 / SUV39H2 / PARP阻害剤 / 子宮肉腫 / ChIP-seq / ATAC-seq / 卵巣類内膜癌 / 深層学習 / 薬剤耐性 / クロマチン立体構造 / Hi-C解析 / ChIP-seq法
Outline of Research at the Start

我々は婦人科悪性腫瘍を対象とし、多層的なヒストン修飾が及ぼすクロマチンの3次元構造の変化を解析する事により、がん化、がんの進展メカニズムを解明する。また多種類のヒストン修飾、クロマチンの立体構造の変化、DNAメチル化、ゲノム変異、臨床情報についてマルチモーダル解析を行い、がんの全体像を解明する。最終的にクロマチンの3次元構造の解析から抗がん剤の治療効果を予測するエピゲノムバイオマーカーの同定や新規エピゲノム治療薬の開発を行う。以上の事を明らかにするためにChIP-seq法、実験ロボット、Hi-C解析、人工知能による深層学習といった最先端の技術を駆使して解析する。

Outline of Final Research Achievements

We conducted the following studies on gynecological malignancies, mainly by analyzing the effects of multilayered histone modifications on chromatin changes. We analyzed the following studies: (1) Potential therapeutic targets of the histone methyltransferase SETD8 in gynecological cancers: SETD8 was upregulated in endometrial and ovarian serous carcinomas, and suppression of SETD8 induced apoptosis by upregulating specific tumor suppressor genes via H4K20 methylation. (2) Novel therapy targeting PRMT6-ERV network in uterine carcinoma: High expression of PRMT6 was observed in endometrial carcinoma, and its suppression induced apoptosis by upregulating endogenous retroviruses through histone modification.

Academic Significance and Societal Importance of the Research Achievements

ヒトゲノム計画が終了し、がん研究においてもゲノムの網羅的解析が進んでいるにも関わらず、がんの解明、根治には至っていない。その大きな理由としてエピゲノム、特にヒストン修飾の解析が進んでいない事が挙げられる。本研究によりヒストン修飾が癌化、その進展に関わることがChIP-sea法等のエピゲノム解析により示唆された。また婦人科癌においてヒストン修飾が新たな治療標的となり得ることがわかり、ゲノムを超えた新規治療標的薬開発の一旦を担う研究であると考える。

Report

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

    (20 results)

All 2022 2021 2020

All Journal Article (20 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 17 results,  Open Access: 14 results)

  • [Journal Article] Histone arginine methyltransferase CARM1 selective inhibitor TP-064 induces apoptosis in endometrial cancer2022

    • Author(s)
      Inoue Futaba、Sone Kenbun、Toyohara Yusuke、Tanimoto Saki、Takahashi Yu、Kusakabe Misako、Kukita Asako、Honjoh Harunori、Nishijima Akira、Taguchi Ayumi、Miyamoto Yuichiro、Tanikawa Michihiro、Iriyama Takayuki、Uchino Mayuyo-mori、Tsuruga Tetsushi、Wada-Hiraike Osamu、Oda Katsutoshi、Osuga Yutaka
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 601 Pages: 123-128

    • DOI

      10.1016/j.bbrc.2022.02.086

    • Related Report
      2022 Annual Research Report 2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] MED1, a novel binding partner of BRCA1, regulates homologous recombination and R-loop processing2022

    • Author(s)
      Honjoh Harunori、Tanikawa Michihiro、Wada-Hiraike Osamu、Oda Katsutoshi、Inaba Hirofumi、Kukita Asako、Kawata Yoshiko、Kusakabe Misako、Tsuchimochi Saki、Taguchi Ayumi、Miyamoto Yuichiro、Sone Kenbun、Tsuruga Tetsushi、Mori-Uchino Mayuyo、Matsumoto Yoko、Osuga Yutaka
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 17140-17140

    • DOI

      10.1038/s41598-022-21495-8

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of a deep learning method for improving diagnostic accuracy for uterine sarcoma cases2022

    • Author(s)
      Toyohara Yusuke、Sone Kenbun、Noda Katsuhiko、Yoshida Kaname、Kurokawa Ryo、Tanishima Tomoya、Kato Shimpei、Inui Shohei、Nakai Yudai、Ishida Masanori、Gonoi Wataru、Tanimoto Saki、Takahashi Yu、Inoue Futaba、Kukita Asako、Kawata Yoshiko、Taguchi Ayumi、Furusawa Akiko、Miyamoto Yuichiro et al
    • Journal Title

      Scientific Reports

      Volume: 12 Issue: 1 Pages: 19612-19612

    • DOI

      10.1038/s41598-022-23064-5

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Suspicious Positive Peritoneal Cytology (Class III) in Endometrial Cancer Does Not Affect Prognosis2022

    • Author(s)
      Sone Kenbun、Suzuki Eri、Taguchi Ayumi、Honjoh Harunori、Nishijima Akira、Eguchi Satoko、Miyamoto Yuichiro、Iriyama Takayuki、Mori Mayuyo、Osuga Yutaka
    • Journal Title

      Journal of Clinical Medicine

      Volume: 11 Issue: 21 Pages: 6527-6527

    • DOI

      10.3390/jcm11216527

    • Related Report
      2022 Annual Research Report
  • [Journal Article] Recurrent malignant melanoma of the uterine cervix treated with anti-PD-1 antibodies and anti-CTLA-4 antibodies: A case report2022

    • Author(s)
      Sone Kenbun、Kukita Asako、Masui Yuri、Yamada Daisuke、Shinozaki-Ushiku Aya、Kawata Akira、Taguchi Ayumi、Miyamoto Yuichiro、Tanikawa Michihiro、Iriyama Takayuki、Mori-Uchino Mayuyo、Tsuruga Tetsushi、Osuga Yutaka
    • Journal Title

      Molecular and Clinical Oncology

      Volume: 16 Issue: 3 Pages: 1-6

    • DOI

      10.3892/mco.2022.2496

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Histone Methyltransferase SETD8 Regulates the Expression of Tumor Suppressor Genes via H4K20 Methylation and the p53 Signaling Pathway in Endometrial Cancer Cells2022

    • Author(s)
      Kukita Asako、Sone Kenbun、Wada-Hiraike Osamu (21)、Oda Katsutoshi、Hamamoto Ryuji、Osuga Yutaka
    • Journal Title

      Cancers

      Volume: 14 Issue: 21 Pages: 5367-5367

    • DOI

      10.3390/cancers14215367

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Transiently elevated D‐dimer levels post‐concentrated ascites reinfusion therapy cannot be used to predict deep vein thrombosis‐pulmonary embolism2022

    • Author(s)
      Sone Kenbun、Taguchi Ayumi、Kawata Akira、Eguchi Satoko、Miyamoto Yuichiro、Tanikawa Michihiro、Uchino‐Mori Mayuyo、Iriyama Takayuki、Tsuruga Tetsushi、Osuga Yutaka
    • Journal Title

      Journal of Obstetrics and Gynaecology Research

      Volume: 48 Issue: 3 Pages: 817-823

    • DOI

      10.1111/jog.15162

    • Related Report
      2022 Annual Research Report
  • [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 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Application of artificial intelligence in gynecologic malignancies: A review2021

    • Author(s)
      Sone Kenbun、Toyohara Yusuke、Taguchi Ayumi、Miyamoto Yuichiro、Tanikawa Michihiro、Uchino‐Mori Mayuyo、Iriyama Takayuki、Tsuruga Tetsushi、Osuga Yutaka
    • Journal Title

      Journal of Obstetrics and Gynaecology Research

      Volume: 47 Issue: 8 Pages: 2577-2585

    • DOI

      10.1111/jog.14818

    • Related Report
      2021 Annual Research Report
  • [Journal Article] Genome-Wide Chromatin Analysis of FFPE Tissues Using a Dual-Arm Robot with Clinical Potential2021

    • Author(s)
      Kaneko S、Mitsuyama T、Shiraishi K、Ikawa N、Shozu K、Dozen A、Machino H、Asada K、Komatsu M、Kukita A、Sone K、Yoshida H、Motoi N、Hayami S、Yoneoka Y、Kato T、Kohno T、Natsume T、Keudell GV、Saloura V、Yamaue H、Hamamoto R
    • Journal Title

      Cancers

      Volume: 13 Issue: 9 Pages: 2126-2126

    • DOI

      10.3390/cancers13092126

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Enhanced antitumor activity of combined lipid bubble ultrasound and anticancer drugs in gynecological cervical cancers2021

    • Author(s)
      Yamaguchi Kohei、Matsumoto Yoko、Suzuki Ryo、Nishida Haruka、Omata Daiki、Inaba Hirofumi、Kukita Asako、Tanikawa Michihiro、Sone Kenbun、Oda Katsutoshi、Osuga Yutaka、Maruyama Kazuo、Fujii Tomoyuki
    • Journal Title

      Cancer Science

      Volume: 112 Issue: 6 Pages: 2493

    • DOI

      10.1111/cas.14907

    • URL

      https://pure.teikyo.jp/en/publications/7c6e869b-2f4f-4a5e-8353-50089b7443e8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A low preoperative albumin-to-globulin ratio is a negative prognostic factor in patients with surgically treated cervical cancer2021

    • Author(s)
      Kawata Akira、Taguchi Ayumi、Baba Satoshi、Miyamoto Yuichiro、Tanikawa Michihiro、Sone Kenbun、Tsuruga Tetsushi、Mori Mayuyo、Oda Katsutoshi、Kawana Kei、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      International Journal of Clinical Oncology

      Volume: 26 Issue: 5 Pages: 980-985

    • DOI

      10.1007/s10147-021-01861-8

    • Related Report
      2021 Annual Research Report 2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Intraperitoneal Administration of a Cisplatin-Loaded Nanogel through a Hybrid System Containing an Alginic Acid-Based Nanogel and an <i>In Situ</i> Cross-Linkable Hydrogel for Peritoneal Dissemination of Ovarian Cancer2021

    • Author(s)
      Yamaguchi Kohei、Hiraike Osamu、Iwaki Haruna、Matsumiya Kazuki、Nakamura Noriko、Sone Kenbun、Ohta Seiichi、Osuga Yutaka、Ito Taichi
    • Journal Title

      Molecular Pharmaceutics

      Volume: 18 Issue: 11 Pages: 4090-4098

    • DOI

      10.1021/acs.molpharmaceut.1c00514

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Elevated placental histone H3K4 methylation via upregulated histone methyltransferases SETD1A and SMYD3 in preeclampsia and its possible involvement in hypoxia-induced pathophysiological process.2021

    • Author(s)
      H. Matsui, T. Iriyama, S. Sayama, N. Inaoka, K. Suzuki, M. Yoshikawa, M. Ichinose, K. Sone, K. Kumasawa, T. Nagamatsu, T. Fujisawa, I. Naguro, H. Ichijo, T. Fujii, Y. Osuga
    • Journal Title

      Placenta

      Volume: 115 Pages: 60-69

    • DOI

      10.1016/j.placenta.2021.09.009

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] History of whole pelvis plus para-aortic radiation is a risk factor associated with febrile neutropenia during chemotherapy for recurrent cervical cancer2021

    • Author(s)
      Nara Katsuhiko、Taguchi Ayumi、Tojima Yuri、Miyamoto Yuichiro、Tanikawa Michihiro、Sone Kenbun、Mori Mayuyo、Tsuruga Tetsushi、Yamamoto Takehito、Takenaka Ryosuke、Takada Tappei、Osuga Yutaka、Suzuki Hiroshi
    • Journal Title

      International Journal of Clinical Oncology

      Volume: 26 Issue: 9 Pages: 1759-1766

    • DOI

      10.1007/s10147-021-01950-8

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Effect of murine double‐minute 2 inhibitors in preclinical models of advanced clear cell carcinomas originating from ovaries and kidneys2020

    • Author(s)
      Kawata Yoshiko、Nagasaka Kazunori、Oda Katsutoshi、Makii Chinami、Takeuchi Makoto、Oki Shinya、Honjo Harunori、Kojima Machiko、Miyagawa Yuko、Taguchi Ayumi、Tanikawa Michihiro、Sone Kenbun、Hiraike Haruko、Matsumoto Yoko、Wada‐Hiraike Osamu、Ayabe Takuya、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      Cancer Science

      Volume: 111 Issue: 10 Pages: 3824-3834

    • DOI

      10.1111/cas.14583

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Usefulness of biopsy by office hysteroscopy for endometrial cancer: A case report2020

    • Author(s)
      Sone Kenbun、Eguchi Satoko、Asada Kayo、Inoue Futaba、Miyamoto Yuichiro、Tanikawa Michihiro、Tsuruga Tetsushi、Mori?Uchino Mayuyo、Matsumoto Yoko、Hiraike?Wada Osamu、Oda Katsutoshi、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      Molecular and Clinical Oncology

      Volume: 13 Issue: 2 Pages: 141-145

    • DOI

      10.3892/mco.2020.2053

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Desensitization strategy for hypersensitivity reactions to carboplatin in five patients with gynecological cancer2020

    • Author(s)
      Toyohara Yusuke、Sone Kenbun、Nishida Haruka、Taguchi Ayumi、Miyamoto Yuichiro、Tanikawa Michihiro、Mori Mayuyo、Tsuruga Tetsushi、Matsumoto Yoko、Oda Katsutoshi、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      Journal of Obstetrics and Gynaecology Research

      Volume: 46 Issue: 11 Pages: 2298

    • DOI

      10.1111/jog.14443

    • URL

      https://pure.teikyo.jp/en/publications/010a9fd1-e401-4fcc-a844-2dc86b9e3418

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The histone methyltransferase SMYD2 is a novel therapeutic target for the induction of apoptosis in ovarian clear cell carcinoma cells2020

    • Author(s)
      Kojima Machiko、Sone Kenbun、Oda Katsutoshi、Hamamoto Ryuji、Kaneko Syuzo、Oki Shinya、Kukita Asako、Kawata Akira、Honjoh Harunori、Kawata Yoshiko、Kashiyama Tomoko、Sato Masakazu、Taguchi Ayumi、Miyamoto Yuichiro、Tanikawa Michihiro、Tsuruga Tetsushi、Nagasaka Kazunori、Wada?Hiraike Osamu、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      Oncology Letters

      Volume: 20 Issue: 5 Pages: 1-1

    • DOI

      10.3892/ol.2020.12014

    • URL

      https://pure.teikyo.jp/en/publications/ad17524e-a8ec-4070-af7c-2b302e2637bf

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Epigenetic Modifier SETD8 as a Therapeutic Target for High-Grade Serous Ovarian Cancer2020

    • Author(s)
      Wada Miku、Kukita Asako、Sone Kenbun、Hamamoto Ryuji、Kaneko Syuzo、Komatsu Masaaki、Takahashi Yu、Inoue Futaba、Kojima Machiko、Honjoh Harunori、Taguchi Ayumi、Kashiyama Tomoko、Miyamoto Yuichiro、Tanikawa Michihiro、Tsuruga Tetsushi、Mori-Uchino Mayuyo、Wada-Hiraike Osamu、Osuga Yutaka、Fujii Tomoyuki
    • Journal Title

      Biomolecules

      Volume: 10 Issue: 12 Pages: 1686-1686

    • DOI

      10.3390/biom10121686

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research

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

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