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Establishing the type I CRISPR platform for extra chromosome elimination through epigenetic modulation

Research Project

Project/Area Number 21K06835
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Review Section Basic Section 48040:Medical biochemistry-related
Research InstitutionMie University

Principal Investigator

Hashizume Ryotaro  三重大学, 医学系研究科, 講師 (50456662)

Co-Investigator(Kenkyū-buntansha) 河野 光雄  三重大学, 医学系研究科, 講師 (00234097)
脇田 幸子  三重大学, 医学系研究科, 技術員 (20782981)
倉橋 浩樹  藤田医科大学, 医科学研究センター, 教授 (30243215)
北畠 康司  大阪大学, 大学院医学系研究科, 教授 (80506494)
宮川 世志幸  日本医科大学, 医学部, 講師 (90415604)
Project Period (FY) 2021-04-01 – 2025-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2024: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2023: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2022: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Keywordsゲノム編集技術 / トリソミー21 / Down症候群 / CRISPR/Cas / 染色体消去 / 細胞生物学 / iPS細胞 / haplotype phasing / 遺伝子発現プロファイル / トリソミー / 染色体 / CRISPR
Outline of Research at the Start

本課題では、Down症候群などの異数性染色体異常に対する、染色体消去技術の新規開発を試みる。本研究では、ゲノム編集技術であるCRISPR/Casシステムを用いて、アレル特異的に、ゲノム改変リスクを最少化する目的でペリセントロメア領域に対する染色体分解や、標的染色体へのエピゲノム修飾によるゲノム改変フリーの染色体消去を試みる。これらを通じて、過剰染色体を後天的に細胞から消去する、革新的な細胞再生技術の開発を追求する。

Outline of Final Research Achievements

This study demonstrated that CRISPR/Cas9-mediated cleavage of a single allele of chromosome 21 in human trisomy 21 iPS cells can induce targeted chromosome elimination. The rate of chromosome removal positively correlated with the number of cleavage sites. Allele-specific recruitment of the cleavage enzyme was more effective in inducing chromosome loss compared to allele-non-specific methods, and this approach was effective even in non-dividing cells. Importantly, the elimination of the extra chromosome normalized the gene expression profile, antioxidant capacity, and cell proliferation rate in the iPS cells. These findings highlight the potential of allele-specific CRISPR/Cas9-mediated chromosome elimination as a precise and efficient approach to restore normal cellular function in chromosomal abnormalities. The results provide compelling evidence for the therapeutic potential of targeted chromosome elimination in disorders such as trisomy 21.

Academic Significance and Societal Importance of the Research Achievements

本成果は、体外における細胞レベルでの過剰染色体を消去する概念実証研究の成果であり、ゲノム編集技術とアレル特異的操作を基軸とした技術で、標的染色体を細胞から消去できる原理を学術的に提案するものである。これまでほとんどみられなかった過剰染色体を細胞から取り除くという発想と、その原理を提案したという意味において学術的意義があると考えられる。この学術領域の発展を通じて、将来的には、ダウン症候群に伴う様々な合併症の予防や低減に貢献することが期待される。

Report

(5 results)
  • 2024 Annual Research Report   Final Research Report ( PDF )
  • 2023 Research-status Report
  • 2022 Research-status Report
  • 2021 Research-status Report
  • Research Products

    (15 results)
  • Research Data

    (2 results)

All 2025 2024 2023 2022 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results,  Open Access: 4 results) Presentation (7 results) (of which Int'l Joint Research: 3 results,  Invited: 1 results) Remarks (2 results)

  • [Journal Article] Trisomic rescue via allele-specific multiple chromosome cleavage using CRISPR-Cas9 in trisomy 21 cells2025

    • Author(s)
      Hashizume Ryotaro、Wakita Sachiko、Sawada Hirofumi、Takebayashi Shin-ichiro、Kitabatake Yasuji、Miyagawa Yoshitaka、Hirokawa Yoshifumi S、Imai Hiroshi、Kurahashi Hiroki
    • Journal Title

      PNAS Nexus

      Volume: 4 Issue: 2

    • DOI

      10.1093/pnasnexus/pgaf022

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Extrachromosomal DNA Dynamics Contribute to Intratumoral Receptor Tyrosine Kinase Genetic Heterogeneity and Drug Resistance in Gastric Cancer2025

    • Author(s)
      Kanayama Kazuki、Imai Hiroshi、Hashizume Ryotaro、Matsuda Chise、Usugi Eri、Hirokawa Yoshifumi S.、Watanabe Masatoshi
    • Journal Title

      Molecular Cancer Research

      Volume: - Issue: 6 Pages: 503-514

    • DOI

      10.1158/1541-7786.mcr-24-0741

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Case report: Severe arrhythmogenic cardiomyopathy in a young girl with compound heterozygous DSG2 and MYBPC3 variants with a 6-year follow-up2025

    • Author(s)
      Hashizume Ryotaro、Imai Hiroshi、Ohashi Hiroyuki、Sawada Hirofumi、Yodoya Noriko、Okamoto Ryuji、Dohi Kaoru、Kasai Chika、Kitajima Takahito、Fujiwara Takumi、Mochiki Ikuyo、Nakatani Kaname、Wakita Sachiko、Ohno Seiko、Kato Koichi、Okugawa Yoshinaga、Mitani Yoshihide、Hirayama Masahiro
    • Journal Title

      Frontiers in Genetics

      Volume: 16 Pages: 1545561-1545561

    • DOI

      10.3389/fgene.2025.1545561

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cytomegalovirus DNA Loads in Organs of Congenitally Infected Fetus2024

    • Author(s)
      Toriyabe Kuniaki、Kitamura Asa、Ikejiri Makoto、Hashizume Ryotaro、Nakamura Maki、Teramoto Emi、Takeuchi Hiroki、Kondo Eiji、Ikeda Tomoaki
    • Journal Title

      Viruses

      Volume: 16 Issue: 6 Pages: 891-891

    • DOI

      10.3390/v16060891

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] A 3000-year-old founder variant in the DRC1 gene causes primary ciliary dyskinesia in Japan and Korea2024

    • Author(s)
      Hashizume Ryotaro、Xu Yifei、Ikejiri Makoto、Gotoh Shimpei、Takeuchi Kazuhiko
    • Journal Title

      Journal of Human Genetics

      Volume: 69 Issue: 12 Pages: 655-661

    • DOI

      10.1038/s10038-024-01289-8

    • Related Report
      2024 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Experimental method for haplotype phasing across the entire length of chromosome 21 in trisomy 21 cells using a chromosome elimination technique2022

    • Author(s)
      Sachiko Wakita, Mari Hara, Yasuji Kitabatake, Keiji Kawatani, Hiroki Kurahashi, Ryotaro Hashizume
    • Journal Title

      Journal of human genetics

      Volume: 67 Issue: 10 Pages: 565-572

    • DOI

      10.1038/s10038-022-01049-6

    • Related Report
      2022 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] Allele-specific chromosome cleavage using CRISPR-Cas9 can rescue cells with trisomy 212024

    • Author(s)
      Ryotaro Hashizume, Sachiko Wakita, Hirofumi Sawada, Shin-ichiro Takebayashi, Yasuji Kitabatake, Yoshitaka Miyagawa, Yoshifumi S Hirokawa, Hiroshi Imai, and Hiroki Kurahashi
    • Organizer
      5th International Conference of the Trisomy 21 Research Society
    • Related Report
      2024 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 細胞周期制御下におけるアレル特異的染色体切断によるダウン症候群由来細胞の核型修正2024

    • Author(s)
      脇田幸子、原万里、宮川世志幸、北畠康司、倉橋浩樹、橋詰令太郎
    • Organizer
      第3回 ダウン症基礎研究会
    • Related Report
      2024 Annual Research Report
  • [Presentation] ゲノム編集技術によるダウン症候群由来細胞の核型修正を通じた細胞再生2023

    • Author(s)
      脇田幸子、原万里、宮川世志幸、北畠康司、倉橋浩樹、橋詰令太郎
    • Organizer
      第2回 ダウン症基礎研究会
    • Related Report
      2023 Research-status Report
  • [Presentation] Gene signatures in genetically homogeneous trisomy 21 and euploid at the induced pluripotent stem cell level2023

    • Author(s)
      Ryotaro Hashizume, Sachiko Wakita, Mari Hara, Hirofumi Sawada, Shin-ichiro Takebayashi, Yasuji Kitabatake, Yoshitaka Miyagawa, Yoshifumi S Hirokawa, Hiroshi Imai, and Hiroki Kurahashi
    • Organizer
      Human Genetics Asia 2023
    • Related Report
      2023 Research-status Report
    • Int'l Joint Research
  • [Presentation] Special Interest Group; Genomic and Epigenomic Analysis for Prenatal and Perinatal Disorders: Trisomic rescue via allele-specific multiple chromosome cleavages using the CRISPR-Cas9 platform in trisomy 21 cells2023

    • Author(s)
      Ryotaro Hashizume
    • Organizer
      Human Genetics Asia 2023
    • Related Report
      2023 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] CRISPR/Cas9を用いた染色体切断による異数性細胞からの染色体除去は可能か?2022

    • Author(s)
      橋詰令太郎、脇田幸子、原万里、北畠康司、宮川世志幸、倉橋浩樹
    • Organizer
      第111回日本病理学会総会
    • Related Report
      2022 Research-status Report
  • [Presentation] CRISPR/Cas9システムの染色体削減と核型修正への応用 Extra chromosome 21 elimination using the CRISPR-Cas9 platform in the iPS cell model for Down syndrome2022

    • Author(s)
      橋詰 令太郎、脇田 幸子、原 万里、澤田 博文、竹林 慎一郎、北畠 康司、宮川 世志幸、倉橋 浩樹
    • Organizer
      日本人類遺伝学会第67回大会
    • Related Report
      2022 Research-status Report
  • [Remarks] 【プレスリリース】ダウン症候群の人の細胞から過剰な 21 番染色体を除去

    • URL

      https://www.mie-u.ac.jp/R-navi/release/44f4b93f35b702a7c038e3835e375871.pdf

    • Related Report
      2024 Annual Research Report
  • [Remarks] NEWS RELEASE 18-FEB-2025

    • URL

      https://www.eurekalert.org/news-releases/1073061

    • Related Report
      2024 Annual Research Report

All 2026

  • Allele-specific-SpCas9 Targets Extract2026

    • Funder
      • Funder Name
        Japan Society For The Promotion Of Science
      • e-Rad_funder
        1025
      • Identifier of Crossref Funder Registry

        https://doi.org/10.13039/501100001691

      • Japan Grant Number
        JP21K06835
      • Project Name
        I型CRISPRを利用した新規エピゲノム型トリソミックレスキュー誘導法の開発
    • Title
      Allele-specific-SpCas9 Targets Extract
    • Issued Date
      2026-04-06
    • Abstract
      UNIX pipeline
    • Research Field
      自然科学一般
    • Data Type
      dataset
    • Data Utilization and Provision Policy
      無償、制約なし、利用条件なし。
    • Access Rights Type
      open access
    • Repository Information
      GitHubリポジトリ
    • URI

      https://github.com/RayHashizume/Allele-specific-Cas9TargetExtract

    • Contributor
      • Contributor Type
        Data Manager
      • Contributor Name
        研究・地域連携部研究推進チーム
      • Contributor Type
        Hosting Institution
      • Contributor Name
        国立大学法人三重大学
      • Contributor Type
        Contact Of Data Manager
      • Contributor Name
        kakenhi*ab.mie-u.ac.jp (メールアドレスは「@」を「*」に置換しています。)
    • Data No.

      JP21K06835-2024-0001

    • Related Report
      2024 Annual Research Report
  • BioProject2026

    • Funder
      • Funder Name
        Japan Society For The Promotion Of Science
      • e-Rad_funder
        1025
      • Identifier of Crossref Funder Registry

        https://doi.org/10.13039/501100001691

      • Japan Grant Number
        JP21K06835
      • Project Name
        I型CRISPRを利用した新規エピゲノム型トリソミックレスキュー誘導法の開発
    • Title
      BioProject
    • Issued Date
      2026-04-06
    • Abstract
      Raw sequence reads
    • Research Field
      ライフサイエンス
    • Data Type
      experimental data
    • Data Utilization and Provision Policy
      クレジットを表示かつ、利用目的が非営利目的であること。
    • Access Rights Type
      open access
    • Repository Information
      SRAリポジトリ
    • URI

      https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA899979

    • Contributor
      • Contributor Type
        Data Manager
      • Contributor Name
        研究・地域連携部研究推進チーム
      • Contributor Type
        Hosting Institution
      • Contributor Name
        国立大学法人三重大学
      • Contributor Type
        Contact Of Data Manager
      • Contributor Name
        kakenhi*ab.mie-u.ac.jp (メールアドレスは「@」を「*」に置換しています。)
    • Data No.

      JP21K06835-2024-0002

    • Related Report
      2024 Annual Research Report

URL: 

Published: 2021-04-28   Modified: 2026-04-14  

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