Use of genome-wide RNAi screening to identify modes of action of bioactive compounds

• Project/Area Number: 15K12759
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Chemical biology
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Matsumoto Ken 国立研究開発法人理化学研究所, 吉田化学遺伝学研究室, 専任研究員 (60222311)
• Project Period (FY): 2015-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2015: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: 化合物 / RNAi / スクリーニング / 標的同定 / shRNAスクリーニング / 化合物標的

Outline of Final Research Achievements

Genome-wide RNA interference (RNAi) with pooled and barcoded short-hairpin RNA (shRNA) libraries provides a powerful tool for identifying cellular components that are relevant to the modes/mechanisms of action of bioactive compounds. We used multiplex barcode sequencing technology which enables parallel analysis of multiple samples. An shRNA library screen with this system revealed that downregulation of ATP1A1, a catalytic subunit of Na+/K+ ATPase, conferred significant sensitivity to aurilide B, a natural marine product that induces mitochondria-mediated apoptosis. Combined treatment with ouabain which inhibits Na+/K+ ATPase by targeting catalytic subunits potentiated sensitivity to aurilide B.

Research Products

• [Journal Article] A quantitative shRNA screen identifies ATP1A1 as a gene that regulates cytotoxicity by aurilide B. (2017)
  • Author(s): Takase, S., Kurokawa, R., Arai, D., Kanto, K. K., Okino, T., Nakao, Y., Kushiro, T., Yoshida, M., and Matsumoto, K.
  • Journal Title: Scientific Reports Volume: 印刷中
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] YBX1 gene silencing inhibits migratory and invasive potential via CORO1C in breast cancer in vitro (2017)
  • Author(s): Lim, J. P., Shyamasundar, S., Gunaratne, J., Scully, O. J., Matsumoto, K., and Bay, B.-H.
  • Journal Title: BMC Cancer Volume: 17 Issue: 1 Pages: 201-201
  • DOI: 10.1186/s12885-017-3187-7
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] PRAS40 deregulates apoptosis in Ewing sarcoma family tumors by enhancing the insulin receptor/Akt and mTOR signaling pathways. (2016)
  • Author(s): Lv, D., Liu, J., Guo, L., Wu, D., Matsumoto, K., and Huang, L.
  • Journal Title: American Journal of Cancer Research Volume: 6 Pages: 486-497
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of the determinants of 2-deoxyglucose sensitivity in cancer cells by shRNA library screening (2015)
  • Author(s): Kobayashi, H. et al.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 467 Issue: 1 Pages: 121-127
  • DOI: 10.1016/j.bbrc.2015.09.106
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] 網羅的shRNAスクリーニングによる海洋天然物aurilide Bの作用に関わる遺伝子の同定 (2017)
  • Author(s): 高瀬翔平、黒川留美、新井大祐、中尾洋一、久城哲夫、吉田 稔、松本 健
  • Organizer: 日本薬学会第137年会
  • Place of Presentation: 仙台国際センター（宮城県・仙台市）
  • Year and Date: 2017-03-24
• [Presentation] shRNAスクリーニング法の改良による化合物の標的経路の同定の効率化 (2017)
  • Author(s): 高瀬翔平、黒川留美、新井大祐、中尾洋一、久城哲夫、松本 健、吉田 稔
  • Organizer: 日本農芸化学会2017年度大会
  • Place of Presentation: 京都女子大学（京都府・京都市）
  • Year and Date: 2017-03-17
• [Remarks] 研究者ホームページ
  • URL: http://www.riken.jp/matsumok/index.html
• [Remarks] ホームページ
  • URL: http://www.riken.jp/matsumok/index.html