Deciphering positive and negative selection in thymocyte from information theoretic approach

• Project/Area Number: 18H02431
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Review Section: Basic Section 43060:System genome science-related
• Research Institution: Kyushu University
• Principal Investigator: Uda Shinsuke 九州大学, 生体防御医学研究所, 准教授 (20599609)
• Co-Investigator(Kenkyū-buntansha): 幡野 敦 新潟大学, 医歯学系, 助教 (30755533) ; 比嘉 綱己 九州大学, 生体防御医学研究所, 学術研究員 (60826238)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000); Fiscal Year 2020: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2019: ¥5,200,000 (Direct Cost: ¥4,000,000、Indirect Cost: ¥1,200,000); Fiscal Year 2018: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
• Keywords: 情報理論 / システム生物学 / 胸腺T細胞 / シグナル伝達 / 生命科学 / 情報 / 正負の選択

Outline of Final Research Achievements

We measured and acquired the data set to analyze signal transduction in thymocyte at single cell level by information theory. The data set is composed of 6000 cells per time point, because the analysis base on information theory requires a large sample size. The result suggests that dynamics of information transmission of S6 is specific compared to another signaling molecules. We developed the quantitative visualization method of communication channel of signaling molecules and applied to the data set. We found that the communication channel of S6 was different from another signaling molecules.

Academic Significance and Societal Importance of the Research Achievements

胸腺T細胞の正負の選択におけるシグナル伝達の情報理論的解析はなく，生物学的にも情報伝達の全貌は未解明のままである．本研究により，情報量という定量的尺度を導入した解析によって，新たな知見が得られる可能性は高い．特に，通信路の観点からのシグナル伝達系の解析はほとんどなく，通信路の違いの可視化は本研究の実験系だけでなく，一般の系にも適用可能で広く応用できる可能性がある．

Research Products

• [Journal Article] Transomics analysis reveals allosteric and gene regulation axes for altered hepatic glucose-responsive metabolism in obesity (2020)
  • Author(s): Kokaji Toshiya、Hatano Atsushi、Ito Yuki、et al.
  • Journal Title: Science Signaling Volume: 13 Issue: 660 Pages: 1236-1236
  • DOI: 10.1126/scisignal.aaz1236
  • Peer Reviewed / Open Access
• [Journal Article] Single-Cell Information Analysis Reveals That Skeletal Muscles Incorporate Cell-to-Cell Variability as Information Not Noise (2020)
  • Author(s): Wada Takumi、Hironaka Ken-ichi、Wataya Mitsutaka、Fujii Masashi、Eto Miki、Uda Shinsuke、Hoshino Daisuke、Kunida Katsuyuki、Inoue Haruki、Kubota Hiroyuki、Takizawa Tsuguto、Karasawa Yasuaki、Nakatomi Hirofumi、Saito Nobuhito、Hamaguchi Hiroki、Furuichi Yasuro、Manabe Yasuko、Fujii Nobuharu L.、Kuroda Shinya
  • Journal Title: Cell Reports Volume: 32 Issue: 9 Pages: 108051-108051
  • DOI: 10.1016/j.celrep.2020.108051
  • Peer Reviewed / Open Access
• [Journal Article] Application of information theory in systems biology (2020)
  • Author(s): Shinsuke Uda
  • Journal Title: Biophysical Review Volume: - Issue: 2 Pages: 377-384
  • DOI: 10.1007/s12551-020-00665-w
  • Peer Reviewed / Open Access
• [Journal Article] Trans-omics impact of thymoproteasome in cortical thymic epithelial cells. (2019)
  • Author(s): Ohigashi I, Tanaka Y, Kondo K, Fujimori S, Kondo H, Palin A, Hoffmann V, Kozai M, Matsushita Y, Uda S, Motosugi R, Hamazaki J, Kubota H, Murata S, Tanaka K, Katagiri T, Kosako H, Takahama Y
  • Journal Title: Cell Reports Volume: 29 Issue: 9 Pages: 2901-2916
  • DOI: 10.1016/j.celrep.2019.10.079
  • NAID: 120006894616
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data (2018)
  • Author(s): Kawata Kentaro、Yugi Katsuyuki、Hatano Atsushi、Kokaji Toshiya、Tomizawa Yoko、Fujii Masashi、Uda Shinsuke、Kubota Hiroyuki、Matsumoto Masaki、Nakayama Keiichi I.、Kuroda Shinya
  • Journal Title: Genes to Cells Volume: 24 Issue: 1 Pages: 82-93
  • DOI: 10.1111/gtc.12655
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] Comparison of hepatic responses to glucose perturbation between normal and obese mice using edge ontology (2020)
  • Author(s): Yuki Ito, Shinsuke Uda, Toshiya Kokaji, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Shinya Kuroda and Hiroyuki Kubota
  • Organizer: Fusion of Mathematics and Biology
  • Int'l Joint Research
• [Presentation] Comparison of hepatic metabolome and transcriptome responses to oral glucose tolerance test between normal and obese mice by information theoretic approach (2019)
  • Author(s): Yuki Ito, Shinsuke Uda, Toshiya Kokaji, Akiyoshi Hirayama, Tomoyoshi Soga, Yutaka Suzuki, Shinya Kuroda and Hiroyuki Kubota
  • Organizer: 第42回日本分子生物学会年会