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Analysis of cell-to-cell variability in pluripotent stem cells by single-cell gene expression analysis and mathematical modeling

Research Project

Project/Area Number 16KT0139
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section特設分野
Research Field Mathematical Sciences in Search of New Cooperation
Research InstitutionOsaka University (2018-2019)
Kyoto University (2016-2017)

Principal Investigator

Nakamura Naotoshi  大阪大学, 数理・データ科学教育研究センター, 特任准教授(常勤) (30554472)

Co-Investigator(Kenkyū-buntansha) 中村 正裕  東京大学, 大学院工学系研究科(工学部), 特任助教 (40634449)
Project Period (FY) 2016-07-19 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Keywords1細胞 / 遺伝子発現のゆらぎ / 1細胞遺伝子発現解析 / ヘテロジェネイティ / 心筋分化 / 多能性幹細胞 / 力学系 / 擬似時間軸
Outline of Final Research Achievements

The aim of this study was to describe and understand the fluctuations in gene expression in stem cells at the single cell level, using mathematical modeling based on the concept of intrinsic and extrinsic noise and actual experimental data. In order to obtain the number of cells needed for mathematical modeling at a viable research cost, it became necessary to develop a better and novel instrument. The co-investigator was able to develop it successfully and obtain pilot data using stem cells. He presented his results in a poster presentation at an international conference in Singapore, and also had an opportunity to present the results orally at an event organized by BD. The principal investigator has published a paper on the newly developed LAVENDER method.

Academic Significance and Societal Importance of the Research Achievements

由来の同じ細胞であっても、細胞の示す実際の姿(表現型)には各細胞ごとにばらつきがあることが知られており、そのばらつきの原因や制御法を理解することは、細胞生物学として重要な研究テーマであるのみならず、細胞治療などの応用場面で細胞を有効に活用するためにも必須であるといえる。本研究では、近年開発された実験技術および研究者独自の実験技術・新規解析手法を用いて、そのばらつきの程度を可視化し、詳細に解析することに成功した。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (12 results)

All 2019 2018 2017 2016 Other

All Journal Article (3 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (8 results) (of which Int'l Joint Research: 3 results,  Invited: 4 results) Remarks (1 results)

  • [Journal Article] LAVENDER: latent axes discovery from multiple cytometry samples with non-parametric divergence estimation and multidimensional scaling reconstruction2019

    • Author(s)
      Nakamura Naotoshi、Okada Daigo、Setoh Kazuya、Kawaguchi Takahisa、Higasa Koichiro、Tabara Yasuharu、Matsuda Fumihiko、Yamada Ryo
    • Journal Title

      bioRxiv

      Volume: 1 Pages: 673434-673434

    • DOI

      10.1101/673434

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Precision Health (プレシジョン・ヘルス, 精密保健)の実現に向けて2018

    • Author(s)
      中村正裕
    • Journal Title

      IoMT学会誌(メディカルレビュー社)

      Volume: 1

    • Related Report
      2018 Research-status Report
  • [Journal Article] 心筋分化過程を描写するシングルセル遺伝子発現解析2017

    • Author(s)
      中村正裕、吉田善紀、渡辺亮
    • Journal Title

      細胞

      Volume: 5月増刊号

    • Related Report
      2016 Research-status Report
  • [Presentation] Heterogeneity and its hierarchy of Prrx1-positive cells during limb development2019

    • Author(s)
      Masahiro Nakamura
    • Organizer
      Cell Symposia (Single Cells: Technology to Biology)
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 距離に基づく細胞間不均一性の解析2019

    • Author(s)
      Naotoshi Nakamura
    • Organizer
      第11回光塾
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] 実空間や情報空間の『形』を観る方法の開発2019

    • Author(s)
      Naotoshi Nakamura
    • Organizer
      日本応用数理学会研究部会連合会発表会
    • Related Report
      2019 Annual Research Report
    • Invited
  • [Presentation] Heterogeneity and its hierarchy of Prrx1-positive cells during limb development2019

    • Author(s)
      Nakamura M, Hojo H, Kawabe.K, Takarada.T
    • Organizer
      Cell Symposia "Single Cells: Technology to Biology"
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] 実空間や情報空間の「形」を観る方法の開発2019

    • Author(s)
      中村直俊
    • Organizer
      生理研研究会「シグナル動態の可視化と操作に基づく多階層機能解析の新展開」
    • Related Report
      2018 Research-status Report
    • Invited
  • [Presentation] 季節性インフルエンザワクチンに対する免疫応答から個人差を抽出する+細胞の動く軌跡の空間の形2018

    • Author(s)
      中村直俊
    • Organizer
      第5回先進イメージング医学研究会(第15回生体イメージング研究会)
    • Related Report
      2017 Research-status Report
  • [Presentation] LAVENDER extracts individual variability in the immune response to seasonal influenza vaccination2018

    • Author(s)
      Naotoshi Nakamura
    • Organizer
      From Molecules and Cells to Human Health: Ideas and concepts
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] シングルセルマルチオミックス~心筋分化におけるシングルセル発現解析とオープンクロマチン解析~2016

    • Author(s)
      中村正裕
    • Organizer
      第39回日本分子生物学会
    • Place of Presentation
      横浜
    • Year and Date
      2016-12-01
    • Related Report
      2016 Research-status Report
    • Invited
  • [Remarks] LAVENDER extracts individual variability

    • URL

      https://www.youtube.com/watch?v=3f3Et2ToM1s

    • Related Report
      2017 Research-status Report

URL: 

Published: 2016-07-20   Modified: 2023-03-08  

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