Method for determination of cellar pathway structure using multidimensional proteomics

• Project/Area Number: 25290078
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Partial Multi-year Fund
• Section: 一般
• Research Field: System genome science
• Research Institution: Kyushu University
• Principal Investigator: Masaki Matsumoto 九州大学, 生体防御医学研究所, 准教授 (60380531)
• Co-Investigator(Renkei-kenkyūsha): NAKAYAMA Keiichi 九州大学生体防御医学研究所, 教授 (80291508)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥18,460,000 (Direct Cost: ¥14,200,000、Indirect Cost: ¥4,260,000); Fiscal Year 2015: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2014: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000); Fiscal Year 2013: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
• Keywords: 代謝 / プロテオミクス / シグナル伝達

Outline of Final Research Achievements

In this study, we originally developed a novel platform for targeted proteomics, iMPAQT (in vitro proteome assisted MRM for protein absolute quantification) using genome-wide recombinant protein library and applied this method to obtain quantitative structure of the pathways in biological system. We subjected more than 18000 recombinant proteins to LC-MS/MS analysis and obtained information for targeted proteomics to construct database. Using this platform, we performed absolute quantification of proteins associated with metabolism and signal-transduction pathway　across various cell lines and succeeded to obtain the quantitative structure of biochemical pathways.

Research Products

• [Journal Article] Akt1-mediated Gata3 phosphorylation controls the repression of IFNγ in memory-type Th2 cells. (2016)
  • Author(s): Hosokawa H, Tanaka T, Endo Y, Kato M, Shinoda K, Suzuki A, Motohashi S, Matsumoto M, Nakayama K, Nakayama T.
  • Journal Title: Nat Commun. Volume: - Issue: 1 Pages: 11289-11289
  • DOI: 10.1038/ncomms11289
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Truncation mutants of ASXL1 observed in myeloid malignancies are expressed at detectable protein levels. (2016)
  • Author(s): Inoue D, Matsumoto M, Nagase R, Saika M, Fujino T, Nakayama KI, Kitamura T.
  • Journal Title: Exp Hematol. Volume: 44 Issue: 3 Pages: 172-176
  • DOI: 10.1016/j.exphem.2015.11.011
  • Peer Reviewed
• [Journal Article] A New Screen for Tuberculosis Drug Candidates Utilizing a Luciferase-Expressing Recombinant Mycobacterium bovis Bacillus Calmette-Guéren. (2015)
  • Author(s): 2)Ozeki Y, Igarashi M, Doe M, Tamaru A, Kinoshita N, Ogura Y, Iwamoto T, Sawa R, Umekita M, Enany S, Nishiuchi Y, Osada-Oka M, Hayashi T, Niki M, Tateishi Y, Hatano M, Matsumoto S.
  • Journal Title: PLoS One Volume: 10 Pages: 214-221
  • DOI: 10.1016/j.jprot.2016.01.008
  • Peer Reviewed / Open Access
• [Journal Article] UV Damage-Induced Phosphorylation of HBO1 Triggers CRL4DDB2-Mediated Degradation To Regulate Cell Proliferation. (2015)
  • Author(s): Matsunuma R, Niida H, Ohhata T, Kitagawa K, Sakai S, Uchida C, Shiotani B, Matsumoto M, Nakayama KI, Ogura H, Shiiya N, Kitagawa M.
  • Journal Title: Mol Cell Biol. Volume: 36 Issue: 3 Pages: 394-406
  • DOI: 10.1128/mcb.00809-15
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Tissue-specific expression of histone H3 variants diversified after species separation. (2015)
  • Author(s): Maehara K, Harada A, Sato Y, Matsumoto M, Nakayama KI, Kimura H, Ohkawa Y.
  • Journal Title: Epigenetics Chromatin Volume: 8 Issue: 1 Pages: 1-17
  • DOI: 10.1186/s13072-015-0027-3
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Reconstruction of insulin signal flow from phosphoproteome and metabolome data (2014)
  • Author(s): Yugi, K., Kubota, H., Toyoshima, Y., Noguchi, R., Kawata, K., Komori, Y., Uda, S., Kunida, K., Tomizawa, Y., Funato, Y., Miki, H., Matsumoto, M., Nakayama, K.I., Kashikura, K., Endo, K., Ikeda, K., Soga, T., Kuroda, S.
  • Journal Title: Cell Rep. Volume: 8 Issue: 4 Pages: 1171-1183
  • DOI: 10.1016/j.celrep.2014.07.021
  • NAID: 120005537752
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] FBXL21 Regulates Oscillation of the Circadian Clock through Ubiquitination and Stabilization of Cryptochromes (2013)
  • Author(s): Arisa Hirano, Kanae Yumimoto, Ryosuke Tsunematsu, Masaki Matsumoto, Masaaki Oyama, Hiroko Kozuka-Hata, Tomoki Nakagawa, Darin Lanjakornsiripan, Keiichi I. Nakayama, and Yoshitaka Fukada
  • Journal Title: Cell Volume: 152 Issue: 5 Pages: 1106-1118
  • DOI: 10.1016/j.cell.2013.01.054
  • Peer Reviewed
• [Journal Article] F-box and WD repeat domain containing-7 (Fbxw7) targets endoplasmic reticulum-anchored osteogenic and chondrogenic transcriptional factors for degradation (2013)
  • Author(s): Yumimoto K., Matsumoto M., Onoyama I., Imaizumi K., Nakayama KI.
  • Journal Title: J. Biol. Chem. Volume: 288 Issue: 40 Pages: 28488-502
  • DOI: 10.1074/jbc.m113.465179
  • Peer Reviewed
• [Presentation] 大規模定量プロテオミクスで挑むがん代謝の実体解明 (2015)
  • Author(s): 松本 雅記、中山 敬一
  • Organizer: 第38回日本分子生物学会年会/第88回日本生化学会大会 合同大会
  • Place of Presentation: 神戸
  • Year and Date: 2015-12-01
• [Presentation] ハイスループットかつ精密な定量プロテオームのための試料調整法開発 (2015)
  • Author(s): 松本 雅記
  • Organizer: 日本プロテオーム学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2015-07-23
• [Presentation] 次世代ターゲットプロテオミクスによるヒト全代謝経路の絶対定量マッピング (2014)
  • Author(s): 松本 雅記, 押川 清孝, 松崎 芙美子, 五島 直樹, 夏目 徹, 中山 敬一
  • Organizer: 第87回日本生化学会大会
  • Place of Presentation: 国立京都国際会館
  • Year and Date: 2014-10-15 – 2014-10-18
  • Invited
• [Presentation] プロテオーム研究を支えるインフォマティクス (2014)
  • Author(s): 松本 雅記
  • Organizer: 生命医薬情報学連合大会
  • Place of Presentation: 仙台国際センター
  • Year and Date: 2014-10-02 – 2014-10-03
  • Invited
• [Presentation] 羅的ターゲットプロテオミクスによるヒトプロテオーム定量マップ作成 (2014)
  • Author(s): 松本 雅記, 中山 敬一
  • Organizer: 日本プロテオーム学会大会2014年会
  • Place of Presentation: つくば国際会議場
  • Year and Date: 2014-07-17 – 2014-07-18
• [Presentation] リン酸化定量プロテオミクスによるシグナル伝達研究 (2014)
  • Author(s): 松本 雅記、中津海 洋一、中山 敬一
  • Organizer: 第１４回蛋白質科学会年会
  • Place of Presentation: ワークピア横浜
  • Year and Date: 2014-06-25 – 2014-06-27
  • Invited
• [Presentation] 組み換えタンパク質を利用した大規模絶対定量 (2013)
  • Author(s): 松本 雅記
  • Organizer: 日本生化学会
  • Place of Presentation: 横浜
  • Invited
• [Presentation] 定量プロテオミクスの実際～装置と試料の取り扱い～ (2013)
  • Author(s): 松本 雅記
  • Organizer: Biological Mass Spectrometry Conference
  • Place of Presentation: 宮崎
  • Invited
• [Remarks] 九州大学生体防御医学研究所分子医科学分野
  • URL: http://www.bioreg.kyushu-u.ac.jp/saibou/index.html