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Data assimilation prediction of cell motility processes driven by cooperative molecular information and forces

Research Project

Project/Area Number 19K20400
Research Category

Grant-in-Aid for Early-Career Scientists

Allocation TypeMulti-year Fund
Review Section Basic Section 62010:Life, health and medical informatics-related
Research InstitutionFujita Health University (2021-2022)
Nara Institute of Science and Technology (2019-2020)

Principal Investigator

Kunida Katsuyuki  藤田医科大学, 医学部, 講師 (40709888)

Project Period (FY) 2019-04-01 – 2023-03-31
Project Status Completed (Fiscal Year 2022)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2021: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2020: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2019: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords細胞運動 / Rho GTPase / 逆相関解析 / 数理モデリング / システム同定 / 分子活性 / 生物物理 / Rho活性 / シグナル伝達 / 力学モデル / データ同化
Outline of Research at the Start

細胞運動は胚発生やがん細胞浸潤など様々な場面で見られる基本的な生命現象の1つである。本研究では細胞運動を協調的に制御しているGタンパク質(Cdc42/Rac1/RhoA)の活性情報と力学に基づく物理モデルを用いて、細胞の移動を精密に予測する解析アルゴリズムを開発する。生細胞イメージングで計測されたGタンパク質活性データと細胞-基質間の相互作用を考慮した物理モデルを用いてベイズ推論に基づくシステム同定を行い、形態の変化を予測する(データ同化予測)。観測が困難な細胞膜張力も同時に推定する。協調的なGタンパク質活性と膜張力の情報がどのようにして細胞形態変化へ変換されるのかをシステムとして理解する。

Outline of Final Research Achievements

First, a Motion-Triggered Average (MTA) method was developed to integrate individually measured data from live cell imaging. Based on inverse correlation analysis, we collected the average activity time series for the same movement of the edges. We then identified a mathematical model to convert the activity time series of the three Rho GTPases (Cdc42/Rac1/RhoA) into an edge velocity series. System identification analysis was performed on the regression model derived from biophysical modeling of morphological changes and molecular activities, and revealed that there is a mathematical formula that quantitatively predicts edge velocity from the three Rho GTPase activity levels, which consists of the sum of the activity levels and their time derivatives.

Academic Significance and Societal Importance of the Research Achievements

本研究で得られた数理モデルから、細胞の移動方法の普遍的な制御メカニズムが解明される可能性がある。MTAとシステム同定を他の細胞株に適用することで細胞種ごとの移動方法が解明され、メカニズムの違いから新たな生物学的発見が得られることが期待できる。さらにMTAのデータ前処理法は、原因と結果の時系列があれば、ヒトや植物、微生物など様々な生命現象に適用可能であり、複数因子による制御システムの原理解明に繋がる。

Report

(5 results)
  • 2022 Annual Research Report   Final Research Report ( PDF )
  • 2021 Research-status Report
  • 2020 Research-status Report
  • 2019 Research-status Report
  • Research Products

    (14 results)

All 2023 2022 2021 2019 Other

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (11 results) (of which Int'l Joint Research: 6 results,  Invited: 1 results) Remarks (2 results)

  • [Journal Article] Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities2023

    • Author(s)
      Katsuyuki Kunida Nobuhiro Takagi Kazuhiro Aoki Kazushi Ikeda Takeshi Nakamura Yuichi Sakumura
    • Journal Title

      Cell Reports

      Volume: 42 Issue: 2 Pages: 1-16

    • DOI

      10.1016/j.celrep.2023.112071

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] 細胞内分子ネットワークの可制御性を決定付ける特徴要因の探索2023

    • Author(s)
      村山毅
    • Organizer
      Spring School for Theoretical Biology 2023
    • Related Report
      2022 Annual Research Report
  • [Presentation] 代謝物 -酵素間ネットワークのデータ駆動型推定法の開発2023

    • Author(s)
      衣笠智裕
    • Organizer
      Spring School for Theoretical Biology 2023
    • Related Report
      2022 Annual Research Report
  • [Presentation] Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities2022

    • Author(s)
      Katsuyuki Kunida, Yuichi Sakumrua
    • Organizer
      第74回日本細胞生物学会年会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities2022

    • Author(s)
      Katsuyuki Kunida, Yuichi Sakumrua
    • Organizer
      The 21st International Conference on Systems Biology (ICSB 2022)
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Design of optimal input for state transition from non-oscillation to oscillation in glycolytic system2022

    • Author(s)
      Tomohiro Kinugasa, Masaaki Nagahara, Yuichi Sakumura, Katsuyuki Kunida
    • Organizer
      第72回バイオ情報学研究発表会
    • Related Report
      2022 Annual Research Report
  • [Presentation] Design of control input for optimal transition from non-oscillation to oscillation in glycolytic system2021

    • Author(s)
      Kinugasa T, Nagahara M, Sakumura Y, Kunida K
    • Organizer
      SICE Annual Conference 2021
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research
  • [Presentation] Optimal Control of Adaptive Response in Intracellular Molecular Network Based on Particle Filter2021

    • Author(s)
      Murayama T, Sakumura Y, Kunida K
    • Organizer
      SICE Annual Conference 2021
    • Related Report
      2021 Research-status Report
  • [Presentation] Extraction of biomolecular signals controlling complex cellular behavior based on reverse correlation analysis2019

    • Author(s)
      Kunida K
    • Organizer
      Asia-Pacific Signal and Information Processing Association (APSIPA) BioSiPS Workshop 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] Novel extraction method of molecular activity patterns that control cell morphological changes based on reverse correlation analysis2019

    • Author(s)
      Kunida K, Sakumura Y
    • Organizer
      SICE Annual Conference 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Extraction of Biomolecular Signals Controlling Complex Behavior of Biological Cells2019

    • Author(s)
      Sakumura Y, Kunida K
    • Organizer
      Asia-Pacific Signal and Information Processing Association Annual Summit and Conference (APSIPA ASC) 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Presentation] Novel extraction method of molecular activity patterns controlling the cell morphological changes based on reverse correlation analysis2019

    • Author(s)
      Kunida K, Sakumura Y
    • Organizer
      American Society for Cell Biology (ASCB) 2019
    • Related Report
      2019 Research-status Report
    • Int'l Joint Research
  • [Remarks] 細胞の変形・運動に複数のタンパク質が協調して関わる仕組みを数式で解明

    • URL

      https://www.fujita-hu.ac.jp/news/j93sdv000000hjjh.html

    • Related Report
      2022 Annual Research Report
  • [Remarks] 細胞の変形・運動に複数のタンパク質が協調して関わる仕組みを数式で解明

    • URL

      https://bsw3.naist.jp/research/index.php?id=2639

    • Related Report
      2022 Annual Research Report

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Published: 2019-04-18   Modified: 2024-01-30  

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