高出力絶対定量法の開発によるシグナル伝達経路定量マップの構築

• Project Area: Integrative understanding of biological signaling networks based on mathematical science
• Project/Area Number: 19H04969
• Research Category: Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)
• Allocation Type: Single-year Grants
• Review Section: Complex systems
• Research Institution: Niigata University
• Principal Investigator: 松本 雅記 新潟大学, 医歯学系, 教授 (60380531)
• Project Period (FY): 2019-04-01 – 2021-03-31
• Project Status: Discontinued (Fiscal Year 2020)
• Budget Amount: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000); Fiscal Year 2020: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2019: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
• Keywords: プロテオミクス / シグナル伝達 / タンパク質絶対定量

Outline of Research at the Start

細胞の増殖や運命決定などの本質的な生命現象は、細胞外刺激が引き起こす細胞内シグナル伝達によって規定されているが、いかなる原理に基づいてシグナル経路のアウトプットの多様性が生み出されているはほとんど不明である。これまで独自に開発してきた革新的なタンパク質絶対定量法iMPAQT法を駆使して、EGFシグナル経路などの構成成分の絶対定量やシグナル伝達のダイナミクス計測技術の開発に成功した。本研究では、現行のiMPAQT法が有するいくつかの技術的限界を完全に克服し、様々な細胞システムにおける広範なシグナル伝達経路の全体構造を定量的に記述する手法の確立を目指す。

Outline of Annual Research Achievements

１）シグナル伝達経路の定量技術の確立：　本年度は、ゲノムワイドなタンパク質リソースに対して、DIA (データ非依存取得)と呼ばれる手法によって、データ再取得を実施した。これらのデータをDIA-NNによるライブラリーフリーサーチを行い、従来の方法以上に多数のペプチドの同定を行うことが可能であった。DIAでは、定量に資するペプチドか否かの精査が可能であるため、その結果を用いてiMPAQTデータベースを更新した。次に、前年度完成させたiMPAQTver.2を用いて、様々なシグナル伝達経路タンパク質に対する内部標準タンパク質を作製した。さらに、個々の内部標準タンパク質自体を定量するためのバーコードタグの拡張を行い、100種類以上のタグの選定と合成、さらにはこれらを集約させた内々標準タンパク質であるQuantimerを五種類作製した。併せて、データ解析ソフトウェアの最適化など、本研究をより効率よく行うための情報基盤の整備をすすめた。また、DIAで検出できなかったタンパク質をparallel reaction monitoringと呼ばれる手法で再解析できる解析ワークフローを確立し、網羅的に多数のタンパク質の絶対定量が実施可能な基盤を構築した。
２）がん細胞パネルでの定量プロテオーム解析：　150種類以上のがん細胞パネルを構築し、これらを対象としてシグナル伝達関連タンパク質の絶対定量やリン酸化プロテオミクスを実施し、細胞特異的なシグナル伝達経路の定量マップの作成に成功した。本研究は途中廃止となったが、詳細なデータ解析を残して、ほとんどを予定通り進めることができた。

Research Progress Status

令和2年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

令和2年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Senolysis by glutaminolysis inhibition ameliorates various age-associated disorders (2021)
  • 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
  • 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 obesity (2020)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] A phospho-switch controls RNF43-mediated degradation of Wnt receptors to suppress tumorigenesis (2020)
  • 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
  • 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 topology (2020)
  • 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
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Cell cycle-dependent localization of the proteasome to chromatin (2020)
  • 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
  • Peer Reviewed / Open Access
• [Journal Article] Production of BBF2H7‐derived small peptide fragments via endoplasmic reticulum stress‐dependent regulated intramembrane proteolysis (2020)
  • Author(s): Matsuhisa Koji、Saito Atsushi、Cai Longjie、Kaneko Masayuki、Okamoto Takumi、Sakaue Fumika、Asada Rie、Urano Fumihiko、Yanagida Kanta、Okochi Masayasu、Kudo Yukitsuka、Matsumoto Masaki、Nakayama Keiichi I.、Imaizumi Kazunori
  • Journal Title: The FASEB Journal Volume: 34 Issue: 1 Pages: 865-880
  • DOI: 10.1096/fj.201901748r
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A Fail-Safe System to Prevent Oncogenesis by Senescence Is Targeted by SV40 Small T Antigen (2020)
  • Author(s): Kiyotaka Oshikawa, Masaki Matsumoto, Manabu Kodama, Hideyuki Shimizu, Keiichi I Nakayama
  • Journal Title: Oncogene Volume: 39 Issue: 10 Pages: 2170-2186
  • DOI: 10.1038/s41388-019-1139-1
  • Peer Reviewed / Open Access
• [Journal Article] In-line sample processing system with an immobilized trypsin-packed fused-silica capillary tube for proteomic analysis of a small number of mammalian cells. (2020)
  • Author(s): Hata K, Izumi Y*, Hara T, Matsumoto M*, Bamba T.
  • Journal Title: Anal. Chem. Volume: 92(4) Issue: 4 Pages: 2997-3005
  • DOI: 10.1021/acs.analchem.9b03993
  • Peer Reviewed
• [Journal Article] Novel localizations and interactions of intercellular bridge proteins revealed by proteomic profiling† (2020)
  • Author(s): Iwamori Tokuko、Iwamori Naoki、Matsumoto Masaki、Imai Hiroyuki、Ono Etsuro
  • Journal Title: Biology of Reproduction Volume: 0 Issue: 5 Pages: 1134-1144
  • DOI: 10.1093/biolre/ioaa017
  • Peer Reviewed
• [Journal Article] The role of Mediator and Little Elongation Complex in transcription termination (2020)
  • Author(s): Takahashi H, Ranjan A, Chen S, Suzuki H, Shibata M, Hirose T, Hirose H, Sasaki K, Abe R, Chen K, He Y, Zhang Y, Takigawa I, Tsukiyama T, Watanabe M, Fujii S, Iida M, Yamamoto J, Yamaguchi Y, Suzuki Y, Matsumoto M, Nakayama KI, Washburn P, Saraf A, Florens L, Sato S, Tomomori-Sato C, Conaway RC, Conaway JW, Hatakeyama S
  • Journal Title: Nature Communications Volume: 11 Issue: 1 Pages: 1-20
  • DOI: 10.1038/s41467-020-14849-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Tyrosine pre-transfer RNA fragments are linked to p53-dependent neuronal cell death via PKM2 (2020)
  • Author(s): Inoue Masanori、Hada Kazumasa、Shiraishi Hiroshi、Yatsuka Hiroyuki、Fujinami Hiroyuki、Morisaki Ikuko、Nishida Yoshihiro、Matsubara Etsuro、Ishitani Tohru、Hanada Reiko、Matsumoto Masaki、Penninger Josef M.、Ihara Kenji、Hanada Toshikatsu
  • Journal Title: Biochemical and Biophysical Research Communications Volume: May 3 Issue: 3 Pages: 155-163
  • DOI: 10.1016/j.bbrc.2020.02.157
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] A shift in glutamine nitrogen metabolism contributes to malignant progression of cancer. (2020)
  • Author(s): Kodama M, Oshikawa K, Shimizu H, Yoshioka S, Takahashi M, Izumi Y, Bamba T, Tateishi C, Tomonaga T, Matsumoto M*, Nakayama KI*.
  • Journal Title: Nat. Commun. Volume: 11 Issue: 1 Pages: 1320-1320
  • DOI: 10.1038/s41467-020-15136-9
  • Peer Reviewed / Open Access
• [Journal Article] Cell Stress Induced Stressome Release Including Damaged Membrane Vesicles and Extracellular HSP90 by Prostate Cancer Cells. (2020)
  • Author(s): Eguchi T, Sogawa C, Ono K, Matsumoto M, Tran MT, Okusha Y, Lang BJ, Okamoto K, Calderwood SK.
  • Journal Title: Cells. Volume: 9(3). Issue: 3 Pages: 755-755
  • DOI: 10.3390/cells9030755
  • NAID: 120006847416
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Frequent Detection of Pituitary-Derived PrPres in Human Prion Diseases (2019)
  • Author(s): Honda Hiroyuki、Matsumoto Masaki、Shijo Masahiro、Hamasaki Hideomi、Sadashima Shoko、Suzuki Satoshi O、Aishima Shinichi、Kai Keita、Nakayama Keiichi I、Sasagasako Naokazu、Iwaki Toru
  • Journal Title: Journal of Neuropathology & Experimental Neurology Volume: 78 Issue: 10 Pages: 922-929
  • DOI: 10.1093/jnen/nlz075
  • Peer Reviewed
• [Journal Article] The pericentromeric protein shugoshin 2 cooperates with HSF1 in heat shock response and RNA Pol II recruitment (2019)
  • Author(s): Takii Ryosuke、Fujimoto Mitsuaki、Matsumoto Masaki、Srivastava Pratibha、Katiyar Arpit、Nakayama Keiich I、Nakai Akira
  • Journal Title: The EMBO Journal Volume: 38 Issue: 24
  • DOI: 10.15252/embj.2019102566
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] iMPAQT ver.2: New platform for protein absolute quantification of proteins of interest. (2020)
  • Author(s): Masaki Matsumoto
  • Organizer: 29th Hot Spring Harbor Symposium
  • Int'l Joint Research / Invited