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Research of Genetic Code Restoration Therapy-Restoration of Mutated RNAs by Artificial RNA Editing

Research Project

Project/Area Number 21H02067
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 37020:Chemistry and chemical methodology of biomolecules-related
Research InstitutionJapan Advanced Institute of Science and Technology

Principal Investigator

Tsukahara Toshifumi  北陸先端科学技術大学院大学, 先端科学技術研究科, 名誉教授 (60207339)

Co-Investigator(Kenkyū-buntansha) 竹中 瑞樹  京都大学, 理学研究科, 准教授 (10796163)
青木 吉嗣  国立研究開発法人国立精神・神経医療研究センター, 神経研究所 遺伝子疾患治療研究部, 部長 (80534172)
Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2023: ¥6,110,000 (Direct Cost: ¥4,700,000、Indirect Cost: ¥1,410,000)
Fiscal Year 2022: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2021: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
KeywordsRNA編集 / 遺伝コード修復 / デアミナーゼ / ツノゴケ / DYWドメイン / GRPドメイン / DRHドメイン / PPR56 / DYWドメイン相同体 / DYW相同体 / MS2システム / PPRタンパク質 / 脱アミノ化酵素 / アミノ転移酵素 / 疾患治療 / 脱アミノ化 / アミノ基転移 / 人為的RNA編集 / 脱アミン化 / ADAR1 / RNA editing / RNA修復
Outline of Research at the Start

本研究では、遺伝子の点変異を原因とする疾患に対する治療法として、人為的なRNA editingを利用して、発現している変異RNAの遺伝コードを部位特異的に修復して疾患を治療するという、遺伝コード修復による疾患治療法の確立を目指している。
具体的には、実用化を目指した遺伝子治療法の開発を行うとともに、人為的なU⇒C変換を実現するための人工酵素の創成を行う。
そのため、(a) C⇒U RNA editingを利用した治療法の確立、および(b) U⇒C RNA editingを触媒する人工酵素複合体の創成とそれを利用した遺伝子治療、を目指した研究を実施する。

Outline of Final Research Achievements

Artificial RNA editing tools were improved by optimizing guide RNAs and using APOBEC3A, 3G, and the DYW domain of a hornwort PPR protein as enzymes to achieve RNA editing efficiencies of more than 50%, and were also successfully applied to disease cases by C-to-U restoration of the mutated ATP7a mRNA in the cells from a macular mouse due to T>C mutations.
GRP and DRH domains are homologous to the DYW domain and were isolated from hornwort, which exhibits significant U⇒C RNA editing. Then, it was found to possess amino group donor-dependent U⇒C and G⇒A conversion activities, respectively. Furthermore, using PPR56 for RNA recognition showed that U⇒C and G⇒A base conversion are possible in HEK293 cells using GRP or DRH domains.

Academic Significance and Societal Importance of the Research Achievements

本研究で得られた様々な結果によって、RNA内の変異塩基の脱アミノ化あるいはアミノ転移によって遺伝コードを変換するRNA編集を人為的に再現することで、点変異したRNAを標的に、遺伝コードを細胞内で部位特異的に変換・修復による疾患治療が可能であることが示され、編集効率の高い人為的RNA編集ツールの開発で、A⇒I(G)およびC⇒U RNA編集では疾患治療に有効なレベルのツール開発に成功した。さらにツノゴケ由来のGRPあるいはDRHドメインによってHEK293細胞内でのU⇒C及びG⇒A変換にも成功した。GRP及びDRHドメインについては世界初の発見であり、学術的にも高い意義が認められる。

Report

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

    (38 results)

All 2023 2022 2021 Other

All Int'l Joint Research (3 results) Journal Article (25 results) (of which Int'l Joint Research: 15 results,  Peer Reviewed: 25 results,  Open Access: 21 results) Presentation (7 results) (of which Int'l Joint Research: 7 results,  Invited: 2 results) Patent(Industrial Property Rights) (3 results) (of which Overseas: 1 results)

  • [Int'l Joint Research] University of Southampton(英国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] 紹興文理学院(中国)

    • Related Report
      2023 Annual Research Report
  • [Int'l Joint Research] University of Rajshahi(バングラデシュ)

    • Related Report
      2023 Annual Research Report
  • [Journal Article] Improvement of C‐to‐U RNA editing using an artificial MS2‐APOBEC system2023

    • Author(s)
      Jiarui Li, Guangyao Fan, Matomo Sakari, Toshifumi Tsukahar
    • Journal Title

      Biotechnology Journal

      Volume: 19 Issue: 1 Pages: 230032-230032

    • DOI

      10.1002/biot.202300321

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Examination of factors affecting site-directed RNA editing by the MS2-ADAR1 deaminase system2023

    • Author(s)
      Md Thoufic Anam Azad, Umme Qulsum, and Toshifumi Tsukahara
    • Journal Title

      Genes

      Volume: 14 Issue: 8 Pages: 1584-1584

    • DOI

      10.3390/genes14081584

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] MEF2C/p300-mediated epigenetic remodeling promotes the maturation of?induced cardiomyocytes2023

    • Author(s)
      Kojima Hidenori、Sadahiro Taketaro、Muraoka Naoto、Yamakawa Hiroyuki、Hashimoto Hisayuki、Ishii Ryota、Gosho Masahiko、Abe Yuto、Yamada Yu、Nakano Koji、Honda Seiichiro、Fujita Ryo、Akiyama Tatsuya、Sunagawa Yoichi、Morimoto Tatsuya、Tsukahara Toshifumi、Hirai Hiroyuki、Fukuda Keiichi、Ieda Masaki
    • Journal Title

      Stem Cell Reports

      Volume: 18 Issue: 6 Pages: 1274-1283

    • DOI

      10.1016/j.stemcr.2023.05.001

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] 5.Increasing the Editing Efficiency of the MS2-ADAR System for Site-Directed RNA Editing2023

    • Author(s)
      Jiarui Li, Tomoko Oonishi, Guangyao Fan, Matomo Sakari and Toshifumi Tsukahar
    • Journal Title

      Applied Sciences

      Volume: 13 Issue: 4 Pages: 2383-2383

    • DOI

      10.3390/app13042383

    • Related Report
      2023 Annual Research Report 2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Identification of Zinc Finger (ZnF) Genes that Undergo Tissue-specific Alternative Splicing in Arabidopsis thaliana2023

    • Author(s)
      Umme Qulsum, Md Thoufic Anam Azad, Toshifumi Tsukahara
    • Journal Title

      Egyptian Journal of Botany

      Volume: 63 Issue: 0 Pages: 292-292

    • DOI

      10.21608/ejbo.2023.189961.2247

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Structural insight into the activation of an Arabidopsis organellar C-to-U RNA editing enzyme by active site complementation2023

    • Author(s)
      Toma-Fukai Sachiko、Sawada Yuto、Maeda Ayako、Shimizu Hikaru、Shikanai Toshiharu、Takenaka Mizuki、Shimizu Toshiyuki
    • Journal Title

      The Plant Cell

      Volume: 35 Issue: 6 Pages: 1888-1900

    • DOI

      10.1093/plcell/koac318

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] A Nonsequencing Approach for the Rapid Detection of RNA Editing2022

    • Author(s)
      Ruchika, Toshifumi Tshukahara, Manish Biyani
    • Journal Title

      Journal of Visualized Experiment

      Volume: -

    • DOI

      10.3791/63591-v

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Development of Therapeutic RNA Manipulation for Muscular Dystrophy2022

    • Author(s)
      Saifullah, Norio Motohashi, Toshifumi Tsukahara, Yoshitsugu Aoki
    • Journal Title

      Front Genome Ed

      Volume: 4 Pages: 863651-863651

    • DOI

      10.3389/fgeed.2022.863651

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated analysis of ALK higher expression in human cancer and downregulation in LUAD using RNA molecular scissors2022

    • Author(s)
      Saifullah, Tsukahara T.
    • Journal Title

      Clin Transl Oncol.

      Volume: 24 Issue: 9 Pages: 1785-1799

    • DOI

      10.1007/s12094-022-02835-6

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Integrated analysis of the clinical consequence and associated gene expression of ALK in ALK-positive human cancers.2022

    • Author(s)
      Saifullah, Tsukahara T.
    • Journal Title

      Heliyon

      Volume: 8 Issue: 7 Pages: e09878-e09878

    • DOI

      10.1016/j.heliyon.2022.e09878

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] C-to-U RNA Editing: A Site Directed RNA Editing Tool for Restoration of Genetic Code2022

    • Author(s)
      S Bhakta, T Tsukahara
    • Journal Title

      Genes

      Volume: 13 Issue: 9 Pages: 13091636-13091636

    • DOI

      10.3390/genes13091636

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Role of the Exonic lncRNA PRKDC-210 in Transcription Regulation by Junling Mo2022

    • Author(s)
      J Mo, G Fan, T Tsukahara, M Sakari
    • Journal Title

      Int. J. Mol. Sci

      Volume: 23 Issue: 22 Pages: 232213783-232213783

    • DOI

      10.3390/ijms232213783

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Investigating the role of dystrophin isoform deficiency in motor function in Duchenne muscular dystrophy2022

    • Author(s)
      Chesshyre Mary、Ridout Deborah、Hashimoto Yasumasa、Ookubo Yoko、Torelli Silvia、Maresh Kate、Ricotti Valeria、Abbott Lianne、Gupta Vandana Ayyar、Main Marion、Ferrari Giulia、Kowala Anna、Lin Yung‐Yao、Tedesco Francesco Saverio、Scoto Mariacristina、Baranello Giovanni、Manzur Adnan、Aoki Yoshitsugu、Muntoni Francesco
    • Journal Title

      Journal of Cachexia, Sarcopenia and Muscle

      Volume: 13 Issue: 2 Pages: 1360-1372

    • DOI

      10.1002/jcsm.12914

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Clinical development of novel therapies for Duchenne muscular dystrophy-Current and future2022

    • Author(s)
      Tsukasa Tominari, Yoshitsugu Aoki
    • Journal Title

      Neurology and Clinical Neuroscience

      Volume: - Issue: 3 Pages: 12691-12691

    • DOI

      10.1111/ncn3.12691

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] <scp>DYW</scp> deaminase domain has a distinct preference for neighboring nucleotides of the target <scp>RNA</scp> editing sites2022

    • Author(s)
      Maeda Ayako、Takenaka Sachi、Wang Tenghua、Frink Brody、Shikanai Toshiharu、Takenaka Mizuki
    • Journal Title

      The Plant Journal

      Volume: 111 Issue: 3 Pages: 756-767

    • DOI

      10.1111/tpj.15850

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Integrated analysis of ALK higher expression in human cancer and downregulation in LUAD using RNA molecular scissor2022

    • Author(s)
      Saifullah, Toshifumi Tsukahara
    • Journal Title

      Clinical and Translational Oncology

      Volume: in press

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A non-sequencing approach for the rapid detection of RNA editing2022

    • Author(s)
      Ruchika, Toshifumi Tsukahara, Manish Biyani
    • Journal Title

      Journal of Visualized Experiments

      Volume: in press

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] The U-to-C RNA editing affects the mRNA stability of nuclear genes in Arabidopsis thaliana2021

    • Author(s)
      Ruchika、Tsukahara Toshifumi
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 571 Pages: 110-117

    • DOI

      10.1016/j.bbrc.2021.06.098

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Double MS2 guided restoration of genetic code in amber (TAG), opal (TGA) and ochre (TAA) stop codon2021

    • Author(s)
      Bhakta Sonali、Tsukahara Toshifumi
    • Journal Title

      Enzyme and Microbial Technology

      Volume: 149 Pages: 109851-109851

    • DOI

      10.1016/j.enzmictec.2021.109851

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome-Wide Identification of U-To-C RNA Editing Events for Nuclear Genes in Arabidopsis thaliana2021

    • Author(s)
      Ruchika、Okudaira Chisato、Sakari Matomo、Tsukahara Toshifumi
    • Journal Title

      Cells

      Volume: 10 Issue: 3 Pages: 635-635

    • DOI

      10.3390/cells10030635

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Unfolding the apoptotic mechanism of antioxidant enriched-leaves of Tabebuia pallida (lindl.) miers in EAC cells and mouse model2021

    • Author(s)
      Rahman Md Mahbubur、Reza A.S.M. Ali、Khan Muhammad Ali、Sujon Khaled Mahmud、Sharmin Rokshana、Rashid Mamunur、Sadik Md Golam、Reza Md Abu、Tsukahara Toshifumi、Capasso Raffaele、Mosaddik Ashik、Gobe Glenda C.、Alam AHM Khurshid
    • Journal Title

      Journal of Ethnopharmacology

      Volume: 278 Pages: 114297-114297

    • DOI

      10.1016/j.jep.2021.114297

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] DYW domain structures imply an unusual regulation principle in plant organellar RNA editing catalysis2021

    • Author(s)
      Takenaka Mizuki、Takenaka Sachi、Barthel Tatjana、Frink Brody、Haag Sascha、Verbitskiy Daniil、Oldenkott Bastian、Schallenberg-Ru?dinger Mareike、Feiler Christian G.、Weiss Manfred S.、Palm Gottfried J.、Weber Gert
    • Journal Title

      Nature Catalysis

      Volume: 4 Issue: 6 Pages: 510-522

    • DOI

      10.1038/s41929-021-00633-x

    • NAID

      120007089252

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Quantification of Mitochondrial RNA Editing Efficiency Using Data2021

    • Author(s)
      Takenaka Mizuki
    • Journal Title

      Methods in Molecular Biology

      Volume: 2363 Pages: 263-278

    • DOI

      10.1007/978-1-0716-1653-6_18

    • ISBN
      9781071616529, 9781071616536
    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Immortalized Canine Dystrophic Myoblast Cell Lines for Development of Peptide-Conjugated Splice-Switching Oligonucleotides2021

    • Author(s)
      Tone Yuichiro、Mamchaoui Kamel、Tsoumpra Maria K.、Hashimoto Yasumasa、Terada Reiko、Maruyama Rika、Gait Michael J.、Arzumanov Andrey A.、McClorey Graham、Imamura Michihiro、Takeda Shin'ichi、Yokota Toshifumi、Wood Matthew J.A.、Mouly Vincent、Aoki Yoshitsugu
    • Journal Title

      Nucleic Acid Therapeutics

      Volume: 31 Issue: 2 Pages: 172-181

    • DOI

      10.1089/nat.2020.0907

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Pharmacological activation of SERCA ameliorates dystrophic phenotypes in dystrophin-deficient <i>mdx</i> mice2021

    • Author(s)
      Nogami Ken'ichiro、Maruyama Yusuke、Sakai-Takemura Fusako、Motohashi Norio、Elhussieny Ahmed、Imamura Michihiro、Miyashita Satoshi、Ogawa Megumu、Noguchi Satoru、Tamura Yuki、Kira Jun-ichi、Aoki Yoshitsugu、Takeda Shin'ichi、Miyagoe-Suzuki Yuko
    • Journal Title

      Human Molecular Genetics

      Volume: 30 Issue: 11 Pages: 1006-1019

    • DOI

      10.1093/hmg/ddab100

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Artificial RNA editing for genetic cord restoration2023

    • Author(s)
      Toshifumi Tsukahara
    • Organizer
      BIOLOGICS AND BIOSIMILARS; ADVANCES IN MEDICINAL CHEMISTRY & PHARMACOLOG
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Artificial RNA Editing toward Treatment for Diseases Caused by Point Mutation2023

    • Author(s)
      Toshifumi Tsukahara
    • Organizer
      Gene and Cell Technology Conference 2023
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Development of bioengineered MS2 system for restoration of genetic code2021

    • Author(s)
      Ruchika, Toshifumi Tsukahara
    • Organizer
      Nano today
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Genome-wide identification and analysis of U-to-C RNA editing events in Arabidopsis thaliana by transcriptome sequencing2021

    • Author(s)
      Ruchika, Chisato Okudaira, Matomo Sakari, Toshifumi Tsukahara
    • Organizer
      3rd Annual Plant Biology and Biotechnology
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Development of RNA editing system using hornwort specific DYW type PPR proteins,2021

    • Author(s)
      Ruchika, Toshifumi Tsukahara
    • Organizer
      Harnessing the plant Microbiome
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Effect of U-to-C RNA editing on the mRNA half-life of PPR protein2021

    • Author(s)
      Ruchika, Toshifumi Tsukahara
    • Organizer
      5th World Plant Genomics and Plant Science Congress
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RNA guided CRISPR-Cas protein downregulates the oncogenic driver ALK expression in human lung cancer cell2021

    • Author(s)
      Saifullah, Matomo Sakari, Takeshi Suzuki, Toshifumi Tsukahara
    • Organizer
      54th annual European Human Genetics Conferenc
    • Related Report
      2021 Annual Research Report
    • Int'l Joint Research
  • [Patent(Industrial Property Rights)] 酵素、酵素複合体、および、これらの利用2023

    • Inventor(s)
      塚原 俊文、范 光輝
    • Industrial Property Rights Holder
      株式会社GeCoRT
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2023-185814
    • Filing Date
      2023
    • Related Report
      2023 Annual Research Report
  • [Patent(Industrial Property Rights)] 酵素、複合体、組換えベクター、遺伝性疾患治療薬及びポリヌクレオチド2022

    • Inventor(s)
      塚原俊文、
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Filing Date
      2022
    • Related Report
      2022 Annual Research Report
    • Overseas
  • [Patent(Industrial Property Rights)] 酵素、複合体、組換えベクター、遺伝性疾患治療薬及びポリヌクレオチド2021

    • Inventor(s)
      塚原俊文、Ruchika
    • Industrial Property Rights Holder
      北陸先端科学技術大学院大学
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2021-210380
    • Filing Date
      2021
    • Related Report
      2021 Annual Research Report

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

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