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Development of an information/hypothesis-driven proteogenomics strategy

Research Project

Project/Area Number 20K21386
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 43:Biology at molecular to cellular levels, and related fields
Research InstitutionNiigata University

Principal Investigator

Matsumoto Masaki  新潟大学, 医歯学系, 教授 (60380531)

Project Period (FY) 2020-07-30 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2021: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Keywordsプロテオミクス / プロテオゲノミクス / 質量分析 / プロテオーム / タンパク質 / 定量プロテオミクス
Outline of Research at the Start

生命システムの本質である多様性を理解する上で、核酸オミクス情報とプロテオームの間の関数の解明が極めて重要な課題である。本研究は、申請者らが構築した大規模精密定量プロテオーム解析技術iMPAQT法を発展させ、核酸情報とプロテオーム情報の間に存在するブラックボックスの解明に挑むことを目的とする。任意のペプチド配列に対する同位体標識ペプチドを大規模に取得する技術とそれを支援するデータベースを構築することで、その実現を試みる。

Outline of Final Research Achievements

In this study, we developed a technology to link nucleic acid information and proteome information through "information/hypothesis-driven proteogenomics," a strategy that is opposite to existing proteogenomics research. We created an isotope-labeled internal standard production system using E. coli, and developed QuantiCode, an ultra-multiplex quantitative tag system for large-scale absolute quantification, and Quantimer, which functions as an internal standard. Furthermore, we developed the SLiM method, a new ultra-sensitive mass spectrometry technique that seamlessly links two mass spectrometry techniques called DIA and PRM, and conducted a proof-of-concept experiment for proteogenomics using this method.

Academic Significance and Societal Importance of the Research Achievements

本研究によって、任意のペプチド配列の存在を確定的に検証することが可能となり、プロテオームに存在する多数の未確認タンパク質を同定あるいは定量が可能となった。これらの新規タンパク質の発見や機能解析は、ゲノム機能の注釈やタンパク質のミスセンス変異やスプライシング異常などがタンパク質発現への影響を知る手段となるため、学術的な意義はとても大きい。また、真のプロテオームの把握は、基礎生物学的な意義だけでなく、疾患研究や創薬における基盤的情報となるため、将来的に人類の健康等に貢献できると期待される。

Report

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

    (28 results)

All 2023 2022 2021 2020

All Journal Article (17 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 17 results,  Open Access: 15 results) Presentation (11 results) (of which Int'l Joint Research: 1 results,  Invited: 9 results)

  • [Journal Article] Monitoring autophagic flux in vivo revealed its physiological response and significance of heterogeneity in pancreatic beta cells2023

    • Author(s)
      Aoyama Shuhei、Nishida Yuya、Uzawa Hirotsugu、Himuro Miwa、Kanai Akiko、Ueki Kyosei、Ito Minami、Iida Hitoshi、Tanida Isei、Miyatsuka Takeshi、Fujitani Yoshio、Matsumoto Masaki、Watada Hirotaka
    • Journal Title

      Cell Chemical Biology

      Volume: - Issue: 6 Pages: 658-671.e4

    • DOI

      10.1016/j.chembiol.2023.03.001

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] LIGHTHOUSE illuminates therapeutics for a variety of diseases including COVID-192022

    • Author(s)
      Shimizu Hideyuki、Kodama Manabu、Matsumoto Masaki、Orba Yasuko、Sasaki Michihito、Sato Akihiko、Sawa Hirofumi、Nakayama Keiichi I.
    • Journal Title

      iScience

      Volume: 25 Issue: 11 Pages: 105314-105314

    • DOI

      10.1016/j.isci.2022.105314

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] HSF1 phosphorylation establishes an active chromatin state via the TRRAP TIP60 complex and promotes tumorigenesis2022

    • Author(s)
      Fujimoto Mitsuaki、Takii Ryosuke、Matsumoto Masaki、Okada Mariko、Nakayama Keiich I.、Nakato Ryuichiro、Fujiki Katsunori、Shirahige Katsuhiko、Nakai Akira
    • Journal Title

      Nature Communications

      Volume: 13 Issue: 1 Pages: 4355-4355

    • DOI

      10.1038/s41467-022-32034-4

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Phosphorylation of PBX2, a novel downstream target of mTORC1, is determined by GSK3 and PP12022

    • Author(s)
      Wada Reona、Fujinuma Shun、Nakatsumi Hirokazu、Matsumoto Masaki、Nakayama Keiichi I
    • Journal Title

      The Journal of Biochemistry

      Volume: 173 Issue: 2 Pages: 129-138

    • DOI

      10.1093/jb/mvac094

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] in situ digestion of alcohol-fixed cells for quantitative proteomics2022

    • Author(s)
      Hatano Atsushi、Takami Tomoyo、Matsumoto Masaki
    • Journal Title

      The Journal of Biochemistry

      Volume: 173 Issue: 4 Pages: 243-254

    • DOI

      10.1093/jb/mvac101

    • 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
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Candesartan prevents arteriopathy progression in cerebral autosomal recessive arteriopathy with subcortical infarcts and leukoencephalopathy model2021

    • Author(s)
      Kato T, Manabe RI, Igarashi H, Kametani F, Hirokawa S, Sekine Y, Fujita N, Saito S, Kawashima Y, Hatano Y, Ando S, Nozaki H, Sugai A, Uemura M, Fukunaga M, Sato T, Koyama A, Saito R, Sugie A, Toyoshima Y, Kawata H, Murayama S, Matsumoto M, Kakita A, Hasegawa M, Ihara M, Kanazawa M, Nishizawa M, Tsuji S, Onodera O.
    • Journal Title

      Journal of Clinical Investigation

      Volume: 131 Issue: 22

    • DOI

      10.1172/jci140555

    • Related Report
      2021 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] The Bioactive Peptide SL-13R Expands Human Umbilical Cord Blood Hematopoietic Stem and Progenitor Cells In Vitro2021

    • Author(s)
      Nii Takenobu、Konno Katsuhiro、Matsumoto Masaki、Bhukhai Kanit、Borwornpinyo Suparerk、Sakai Kazuhiro、Hongeng Suradej、Sugiyama Daisuke
    • Journal Title

      Molecules

      Volume: 26 Issue: 7 Pages: 1995-1995

    • DOI

      10.3390/molecules26071995

    • Related Report
      2021 Research-status 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 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A ubiquitin-like protein encoded by the “noncoding” RNA TINCR promotes keratinocyte proliferation and wound healing2021

    • Author(s)
      Nita Akihiro、Matsumoto Akinobu、Tang Ronghao、Shiraishi Chisa、Ichihara Kazuya、Saito Daisuke、Suyama Mikita、Yasuda Tomoharu、Tsuji Gaku、Furue Masutaka、Katayama Bumpei、Ozawa Toshiyuki、Murata Teruasa、Dainichi Teruki、Kabashima Kenji、Hatano Atsushi、Matsumoto Masaki、Nakayama Keiichi I.
    • Journal Title

      PLOS Genetics

      Volume: 17 Issue: 8 Pages: 1009686-1009686

    • DOI

      10.1371/journal.pgen.1009686

    • Related Report
      2021 Research-status 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
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders2021

    • Author(s)
      Johmura Yoshikazu、Yamanaka Takehiro、Omori Satotaka、Wang Teh-Wei、Sugiura Yuki、Matsumoto Masaki、Suzuki Narumi、Kumamoto Soichiro、Yamaguchi Kiyoshi、Hatakeyama Seira、Takami Tomoyo、Yamaguchi Rui、Shimizu Eigo、Ikeda Kazutaka、Okahashi Nobuyuki、Mikawa Ryuta、Suematsu Makoto、Arita Makoto、Sugimoto Masataka et al
    • Journal Title

      Science

      Volume: 371 Issue: 6526 Pages: 265-270

    • DOI

      10.1126/science.abb5916

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [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 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis2020

    • Author(s)
      Tsukiyama Tadasuke、Zou Juqi、Kim Jihoon、Ogamino Shohei、Shino Yuki、Masuda Takamasa、Merenda Alessandra、Matsumoto Masaki、Fujioka Yoichiro、Hirose Tomonori、Terai Sayuri、Takahashi Hidehisa、Ishitani Tohru、Nakayama Keiichi I.、Ohba Yusuke、Koo Bon-Kyoung、Hatakeyama Shigetsugu
    • Journal Title

      Nature Communications

      Volume: 11 Issue: 1 Pages: 1-16

    • DOI

      10.1038/s41467-020-18257-3

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Chemical acetylation of mitochondrial transcription factor A occurs on specific lysine residues and affects its ability to change global DNA topology2020

    • Author(s)
      Fang Yuan、Akimoto Masaru、Mayanagi Kouta、Hatano Atsushi、Matsumoto Masaki、Matsuda Shigeru、Yasukawa Takehiro、Kang Dongchon
    • Journal Title

      Mitochondrion

      Volume: 53 Pages: 99-108

    • DOI

      10.1016/j.mito.2020.05.003

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] The Autism-Related Protein SETD5 Controls Neural Cell Proliferation through Epigenetic Regulation of rDNA Expression.2020

    • Author(s)
      Nakagawa T, Hattori S, Nobuta R, Kimura R, Nakagawa M, Matsumoto M, Nagasawa Y, Funayama R, Miyakawa T, Inada T, Osumi N, Nakayama KI, Nakayama K.
    • Journal Title

      iScience

      Volume: 23 Issue: 4 Pages: 101030-101030

    • DOI

      10.1016/j.isci.2020.101030

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Cell cycle-dependent localization of the proteasome to chromatin2020

    • Author(s)
      Kito Yuki、Matsumoto Masaki、Hatano Atsushi、Takami Tomoyo、Oshikawa Kiyotaka、Matsumoto Akinobu、Nakayama Keiichi I.
    • Journal Title

      Scientific Reports

      Volume: 10 Issue: 1 Pages: 5801-5801

    • DOI

      10.1038/s41598-020-62697-2

    • Related Report
      2020 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] 高速・高深度プロテオミクスが加速する生命科学研究2022

    • Author(s)
      松本雅記
    • Organizer
      日本糖尿病肥満動物学会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 高感度・ハイスループットプロテオミクスがもたらすタンパク質研究の新展開2022

    • Author(s)
      松本雅記
    • Organizer
      第22回日本蛋白質科学会年会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] 高密度・ハイスループットプロテオミクスによるタンパク質動態研究2022

    • Author(s)
      松本雅記
    • Organizer
      日本プロテオーム学会2022年大会
    • Related Report
      2022 Annual Research Report
  • [Presentation] 質量分析計を基盤とするがんのマルチオミクス解析2021

    • Author(s)
      松本 雅記
    • Organizer
      第80回日本癌学会学術総会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 定量プロテオミクスを用いたがん研究2021

    • Author(s)
      松本 雅記
    • Organizer
      第17回日本病理学会カンファレンス
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 質量分析計を用いた未開拓プロテオームへの挑戦2021

    • Author(s)
      松本 雅記
    • Organizer
      日本プロテオーム学会2021年大会
    • Related Report
      2021 Research-status Report
  • [Presentation] iMPAQT ver. 2: New platform for absolute quantification of proteins of interest2021

    • Author(s)
      Masaki Matsumoto
    • Organizer
      10th AOHUPO
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] 高感度・ハイスループットプロテオミクスによるがん代謝研究2021

    • Author(s)
      松本 雅記
    • Organizer
      第39回日本内分泌学会 内分泌代謝学サマーセミナー
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] ペプチドセントリックな定量プロテオミクスを用いた未開拓プロテオームの実体解明への挑戦2021

    • Author(s)
      松本 雅記
    • Organizer
      第94回日本生化学会大会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] ペプチド先導型プロテオミクス-精密で信頼性の高いタンパク質定量技術-2020

    • Author(s)
      松本雅記
    • Organizer
      CBI学会2020
    • Related Report
      2020 Research-status Report
    • Invited
  • [Presentation] 多重ターゲットプロテオミクスを用いたタンパク質動態解析2020

    • Author(s)
      松本雅記
    • Organizer
      第93回日本生化学会大会
    • Related Report
      2020 Research-status Report
    • Invited

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Published: 2020-08-03   Modified: 2024-01-30  

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