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Systems biology of ERK signaling networks

Research Project

Project/Area Number 18200021
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionThe University of Tokyo

Principal Investigator

KURODA Shinya  The University of Tokyo, 大学院・理学系研究科, 教授 (50273850)

Project Period (FY) 2006 – 2008
Project Status Completed (Fiscal Year 2008)
Budget Amount *help
¥49,010,000 (Direct Cost: ¥37,700,000、Indirect Cost: ¥11,310,000)
Fiscal Year 2008: ¥14,300,000 (Direct Cost: ¥11,000,000、Indirect Cost: ¥3,300,000)
Fiscal Year 2007: ¥14,300,000 (Direct Cost: ¥11,000,000、Indirect Cost: ¥3,300,000)
Fiscal Year 2006: ¥20,410,000 (Direct Cost: ¥15,700,000、Indirect Cost: ¥4,710,000)
Keywordsシグナル伝達 / システム生物学 / ERK / シミュレーション / シミュレーションモデル
Research Abstract

ERK signaling networks can regulate various cellular processes. One of the remarkable features of signaling networks is that the same signaling networks can regulate multiple cellular functions. In PC12 cells, EGF and NGF induces transient and sustained ERK activation, leading to cell proliferation and differentiation, respectively. In this study, we analyzed how ERK signaling networks can regulate cell proliferation and differentiation, depending on the distinct temporal activation patterns by use of systems biology approach. First, we tried to analyze the differentiation processes. We performed a discontinuous stimulation assay consisting of a first transient stimulation followed by an interval and then a second sustained stimulation and quantified the neurite extension level (Chung, J. et al, 2010). Consequently, we observed a timing-dependent action of NGF on cell differentiation, and discontinuous NGF stimulation similarly induced differentiation. The first stimulation did not ind … More uce neurite extension, whereas the second stimulation induced fast neurite extension ; therefore, the first stimulation is likely required as a prerequisite condition. These observations indicate that the action of NGF can be divided into two processes : an initial stimulation-driven latent process and a second stimulation-driven extension process. The latent process appears to require the activities of ERK and transcription, but not PI3K, whereas the extension-process requires the activities of ERK and PI3K, but not transcription. We screened the possible genes involved in the latent process, and identified 3 genes as a possible candidates. We developed a fully automatable assay technique, termed quantitative image cytometry, which integrates a quantitative immunostaining technique and a high precision image-processing algorithm for cell identification (Ozaki, Y. et al, 2010). With the aid of an automated sample preparation system, this device can quantify protein expression, phosphorylation and localization with subcellular resolution at one-minute intervals. We will investigate the signaling dynamics of the ERK pathway in PC12 cells, demonstrating using QIC. Less

Report

(4 results)
  • 2008 Annual Research Report   Final Research Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (29 results)

All 2010 2009 2008 2007 2006 Other

All Journal Article (7 results) (of which Peer Reviewed: 3 results) Presentation (18 results) Book (2 results) Remarks (1 results) Patent(Industrial Property Rights) (1 results)

  • [Journal Article] A quantitative image cytometry technique for time series or population analyses of signaling networks2010

    • Author(s)
      Ozaki Y, Uda S, Saito TH, Chung J, Kubota H, Kuroda S.
    • Journal Title

      PLoS ONE

    • Related Report
      2008 Final Research Report
  • [Journal Article] Timing-dependent actions of NGF required for cell differentiation2010

    • Author(s)
      Chung J, Kubota H, Ozaki Y, Uda S, Kuroda S.
    • Journal Title

      PLoS ONE

    • Related Report
      2008 Final Research Report
  • [Journal Article] Timing-Dependent Actions of NGF Required for Cell Differentiation2010

    • Author(s)
      Jaehoon Chung, Hiroyuki Kubota, Yu-ichi Ozaki, Shinsuke Uda, Shinya Kuroda
    • Journal Title

      PLoS ONE 5

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A quantitative image cytometry technique for time series or population analyses of signaling networks2010

    • Author(s)
      Yu-ichi Ozaki, Shinsuke Uda, Takeshi H.Saito, Jaehoon Chung, Hiroyuki Kubota, Shinya Kuroda
    • Journal Title

      PLoS ONE (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Specific features of transient Ras and sustained Rapl activation2009

    • Author(s)
      Ozaki, Y., Uda, S., Kuroda, S.
    • Journal Title

      In Systems Biology, the Challenge of Complexity Springer

      Pages: 121-127

    • Related Report
      2008 Final Research Report
  • [Journal Article] A Mass Conserved Reaction-Diffusion System Captures Propertles of Cell Polarity2007

    • Author(s)
      Otsuji, M., et. al.
    • Journal Title

      PloS.Comput.Biol 2

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics of the Ras/ERK MAP kinase casacade as monitored by fluorescence probes.2006

    • Author(s)
      Fujioka, A et al.
    • Journal Title

      J. Biol. Chem. 281

      Pages: 8917-8926

    • Related Report
      2006 Annual Research Report
  • [Presentation] Temporal coding of ERK and Akt signaling pathway2010

    • Author(s)
      黒田真也
    • Organizer
      第13回国際細胞膜研究フォーラム
    • Place of Presentation
      招待講演、京都
    • Year and Date
      2010-01-27
    • Related Report
      2008 Final Research Report
  • [Presentation] Temporal coding of ERK and AKT signaling pathway2010

    • Author(s)
      Shinya Kuroda
    • Organizer
      Shanghai, Invited
    • Place of Presentation
      Sino-Japan Workshop
    • Related Report
      2008 Final Research Report
  • [Presentation] NGF-dependent differentiation requires two distinct processes ; ERK-and transcription- driven protentiation process and ERK-and P13K-driven neurtie-extension process2009

    • Author(s)
      Jaehoon Chung, Hiroyuki Kubota, Yu-ichi Ozaki, Shinsuke Uda. Shinva Kuroda
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      ポスター、横浜
    • Year and Date
      2009-12-12
    • Related Report
      2008 Final Research Report
  • [Presentation] High throughput quantification of single cellular signaling events by use of immunostaining and image cytometry2009

    • Author(s)
      Yu-ichi Ozaki, Shinsuke Uda, Takeshi Saito, Chung Jeahoon, Hiroyuki Kubota, Shinva Kuroda
    • Organizer
      第32回日本分子生物学会年会
    • Place of Presentation
      招待講演、口頭、横浜
    • Year and Date
      2009-12-11
    • Related Report
      2008 Final Research Report
  • [Presentation] Low-pass filter characteristics of the Akt pathway decouple EGF receptor and downstream phosphorylation2009

    • Author(s)
      Fujita, K., Toyoshima, Y., Uda, S., Ozaki, Y., Kubota, H. Kuroda, S.
    • Organizer
      The 10th International Conference on Systems Biology
    • Place of Presentation
      CA, USA, Poster
    • Year and Date
      2009-08-30
    • Related Report
      2008 Final Research Report
  • [Presentation] システムズバイオロジー : 本質は複雑でなくシンプル!2009

    • Author(s)
      黒田真也
    • Organizer
      第61回日本細胞生物学会大会
    • Place of Presentation
      口頭・招待講演演、名古屋
    • Year and Date
      2009-06-02
    • Related Report
      2008 Final Research Report
  • [Presentation] ERK経路のシステム生物学2009

    • Author(s)
      黒田真也, 尾崎裕一
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      口頭・招待講演、熊本
    • Year and Date
      2009-05-22
    • Related Report
      2008 Final Research Report
  • [Presentation] ERK経路のシステム生物学2009

    • Author(s)
      黒田真也, 尾崎裕一
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本
    • Year and Date
      2009-05-22
    • Related Report
      2008 Annual Research Report
  • [Presentation] Tsukuba, Invited Temporal coding of ERK and AKT signaling pathway2009

    • Author(s)
      Shinya Kuroda
    • Organizer
      International symposium on cellular signaling-principles and functions-
    • Place of Presentation
      Tsukuba, Invited
    • Related Report
      2008 Final Research Report
  • [Presentation] Temporal coding of Akt signaling networks2009

    • Author(s)
      Shinva Kuroda, Kazuhiro Fujita, Yu Toyoshima
    • Organizer
      Dynamics of signal transduction and of gene-protein regulatory networks
    • Place of Presentation
      Ohio, USA Oral, Poster
    • Related Report
      2008 Final Research Report
  • [Presentation] Systems analysis of ERK signaling networks using automated immunofluorescent cytometry2009

    • Author(s)
      Shines Kuroda, Yu-ichi Ozaki
    • Organizer
      Computational Cell Biology
    • Place of Presentation
      Cold Spring Harbor, NY, USA, Oral
    • Related Report
      2008 Final Research Report
  • [Presentation] Systems analysis of ERK signaling network using automated immunofluorescence method2008

    • Author(s)
      尾崎裕一, 黒田真也
    • Organizer
      第31回日本分子生物学会年会 第81回日本生化学会大会 合同大会 (BMB2008)
    • Place of Presentation
      口頭
    • Year and Date
      2008-12-10
    • Related Report
      2008 Final Research Report
  • [Presentation] Temporal coding of ERK signaling network2008

    • Author(s)
      Shinya Kuroda
    • Organizer
      NIBB-EMBL-CRG Workshop on Systems Biology
    • Place of Presentation
      Barcelona
    • Related Report
      2008 Final Research Report
  • [Presentation] Systems biology of ERK signaling networks2008

    • Author(s)
      Shines Kuroda
    • Organizer
      Japan-Taiwan Young Researchers Conference on Computational and Systems Biology
    • Place of Presentation
      Taiwan
    • Related Report
      2008 Final Research Report
  • [Presentation] Temporal coding of ERK signaling networks2008

    • Author(s)
      Shines Kuroda
    • Organizer
      FCSB2008 International Workshop on Future Challenges for Systems Biology
    • Place of Presentation
      Tokyo
    • Related Report
      2008 Final Research Report
  • [Presentation] 自動化免疫染色法を用いたERK経路のシステム解析2007

    • Author(s)
      尾崎裕一, 黒田真也
    • Organizer
      第30回日本分子生物学会年会, 第80回日本生化学会大会 合同大会
    • Place of Presentation
      ポスター
    • Year and Date
      2007-12-11
    • Related Report
      2008 Final Research Report
  • [Presentation] ERK経路のシステム生物学2007

    • Author(s)
      黒田真也, 尾崎裕一
    • Organizer
      第30回日本分子生物学会年会, 第80回日本生化学会大会 合同大会
    • Place of Presentation
      招待講演
    • Year and Date
      2007-12-11
    • Related Report
      2008 Final Research Report
  • [Presentation] Temporal coding of ERK signaling network2007

    • Author(s)
      黒田 真也
    • Organizer
      2007EPA International Science Forum
    • Place of Presentation
      Durham,NC,USA
    • Year and Date
      2007-05-15
    • Related Report
      2007 Annual Research Report
  • [Book] 現代生物科学入門 第8巻2010

    • Author(s)
      システムバイオロジー
    • Publisher
      岩波書店
    • Related Report
      2008 Final Research Report
  • [Book] 現代生物科学入門8システムバイオロジー2010

    • Author(s)
      近藤滋, 北野宏明, 金子邦彦, 黒田真也
    • Total Pages
      176
    • Publisher
      岩波書店
    • Related Report
      2008 Annual Research Report
  • [Remarks]

    • Related Report
      2008 Final Research Report
  • [Patent(Industrial Property Rights)] 測定対象分子の定量的解析方法及び装置2010

    • Inventor(s)
      尾崎裕一, 黒田真也
    • Industrial Property Rights Holder
      尾崎裕一, 黒田真也
    • Industrial Property Number
      2010-050910
    • Filing Date
      2010-03-08
    • Related Report
      2008 Annual Research Report

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Published: 2006-04-01   Modified: 2016-04-21  

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