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Kunida K, Takagi N, Aoki K, Ikeda K, Nakamura T, Sakumura Y. Decoding cellular deformation from pseudo-simultaneously observed Rho GTPase activities. Cell Rep 2023; 42:112071. [PMID: 36764299 DOI: 10.1016/j.celrep.2023.112071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 10/31/2022] [Accepted: 01/19/2023] [Indexed: 02/11/2023] Open
Abstract
Limitations in simultaneously observing the activity of multiple molecules in live cells prevent researchers from elucidating how these molecules coordinate the dynamic regulation of cellular functions. Here, we propose the motion-triggered average (MTA) algorithm to characterize pseudo-simultaneous dynamic changes in arbitrary cellular deformation and molecular activities. Using MTA, we successfully extract a pseudo-simultaneous time series from individually observed activities of three Rho GTPases: Cdc42, Rac1, and RhoA. To verify that this time series encoded information on cell-edge movement, we use a mathematical regression model to predict the edge velocity from the activities of the three molecules. The model accurately predicts the unknown edge velocity, providing numerical evidence that these Rho GTPases regulate edge movement. Data preprocessing using MTA combined with mathematical regression provides an effective strategy for reusing numerous individual observations of molecular activities.
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Affiliation(s)
- Katsuyuki Kunida
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; School of Medicine, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Nobuhiro Takagi
- Graduate School of Information Science and Technology, Aichi Prefectural University, Nagakute, Aichi 480-1342, Japan
| | - Kazuhiro Aoki
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Aichi 444-8787, Japan; Department of Basic Biology, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Aichi 444-8787, Japan
| | - Kazushi Ikeda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; RIKEN Center for Advanced Intelligence Project (RIKEN AIP), Kyoto 619-0288, Japan
| | - Takeshi Nakamura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Noda, Chiba 278-0022, Japan
| | - Yuichi Sakumura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan; Data Science Center, Nara Institute of Science and Technology, Ikoma, Nara 8916-5, Japan.
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