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Measurement of single-cell dynamics with nanoelectroporation

Research Project

Project/Area Number 21K18194
Research Category

Grant-in-Aid for Challenging Research (Pioneering)

Allocation TypeMulti-year Fund
Review Section Medium-sized Section 28:Nano/micro science and related fields
Research InstitutionKyoto University (2023)
Institute of Physical and Chemical Research (2021-2022)

Principal Investigator

Shintaku Hirofumi  京都大学, 医生物学研究所, 教授 (80448050)

Co-Investigator(Kenkyū-buntansha) 口丸 高弘  自治医科大学, 医学部, 准教授 (10570591)
錦井 秀和  筑波大学, 医学医療系, 准教授 (30512834)
塩見 晃史  国立研究開発法人理化学研究所, 開拓研究本部, 基礎科学特別研究員 (60880557)
金子 泰洸ポール  国立研究開発法人理化学研究所, 開拓研究本部, 特別研究員 (80873504)
鳥井 孝太郎  国立研究開発法人理化学研究所, 開拓研究本部, 特別研究員 (80878463)
Project Period (FY) 2021-07-09 – 2024-03-31
Project Status Completed (Fiscal Year 2023)
Budget Amount *help
¥25,870,000 (Direct Cost: ¥19,900,000、Indirect Cost: ¥5,970,000)
Fiscal Year 2023: ¥9,490,000 (Direct Cost: ¥7,300,000、Indirect Cost: ¥2,190,000)
Fiscal Year 2022: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2021: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Keywords1細胞 / RNA-sequencing / マイクロ流体工学 / オミクス / 電気泳動 / 造血幹細胞
Outline of Research at the Start

1細胞RNA-sequencing (scRNA-seq)は,基本的にエンドポイント解析である.そのため,scRNA-seqより得られる遺伝子発現情報は瞬時の状態量に過ぎず,時々刻々状態変化する真のダイナミクス解析は実現できていない.本研究では1細胞の生存状態を維持したまま時系列の網羅的遺伝子発現情報を取得する方法を構築し,それに基づく真の1細胞ダイナミクス計測を実現する.

Outline of Final Research Achievements

Single-cell omics approaches are fundamentally endpoint measurements, interrupting the biological activity of a single cell at the time of measurement. Current methods track the consensus dynamics of single cells by ensemble averaging omics data from a large number of cells. Consequently, these methods cannot link the individual dynamics of single cells to their specific omics states. To overcome this challenge and track the dynamics of individual single cells from an omics perspective, we have developed techniques that utilize nanoelectroporation for the extraction or delivery of charged molecules with minimal invasiveness. Here, we present ELASTomics, live-organismal transcriptomics, and opto-combinatorial indexing, which respectively link individual cellular dynamics with their transcriptomics profiles.

Academic Significance and Societal Importance of the Research Achievements

ヒトは受精卵と呼ばれる1つの細胞から始まり、最終的に数十兆の細胞から構成される生命体へと変化します。1細胞オミクス解析は、そのダイナミクスを生み出す分子の量を1細胞解像度で捉える強力なツールですが、ほとんどの場合、対象の1細胞を計測時により損なってしまいます。本研究で開発したELASTomics、Live-organismal transcriptomicsおよびopto-combinatorial indexingはそのような1細胞オミクス解析の根源的課題を解決し得る1細胞オミクス解析法群であり、例えば、非殺傷的に受精卵の遺伝子発現を計測しながら発生過程を観察することが可能です。

Report

(5 results)
  • 2023 Annual Research Report   Final Research Report ( PDF )
  • 2022 Research-status Report
  • 2021 Comments on the Screening Results   Research-status Report
  • Research Products

    (28 results)

All 2024 2023 2022 2021 Other

All Journal Article (2 results) (of which Peer Reviewed: 2 results,  Open Access: 1 results) Presentation (24 results) (of which Int'l Joint Research: 8 results,  Invited: 9 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Opto-combinatorial indexing enables high-content transcriptomics by linking cell images and transcriptomes2024

    • Author(s)
      Tsuchida Arata、Kaneko Taikopaul、Nishikawa Kaori、Kawasaki Mayu、Yokokawa Ryuji、Shintaku Hirofumi
    • Journal Title

      Lab on a Chip

      Volume: TBA Issue: 8 Pages: 2287-2297

    • DOI

      10.1039/d3lc00866e

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] High-throughput mechanical phenotyping and transcriptomics of single cells2024

    • Author(s)
      Shiomi Akifumi、Kaneko Taikopaul、Nishikawa Kaori、Tsuchida Arata、Isoshima Takashi、Sato Mayuko、Toyooka Kiminori、Doi Kentaro、Nishikii Hidekazu、Shintaku Hirofumi
    • Journal Title

      Nature Communications

      Volume: 15 Issue: 1 Pages: 1-13

    • DOI

      10.1038/s41467-024-48088-5

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Presentation] Micro- and nanoscale electrokinetics for single-cell multimodal analyses2024

    • Author(s)
      Hirofumi Shintaku
    • Organizer
      uTAStic
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] ELASTomics: High-throughput mechanical phenotyping and transcriptomics of single cells2023

    • Author(s)
      Akifumi Shiomi, Taikopaul Kaneko, Kaori Nishikawa, and Hirofumi Shintaku
    • Organizer
      The 27th International Conference on Miniaturized Systems for Chemistry and Life Sciences (uTAS 2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Microgels for a large-scale screening and longitudinal observations of cancer cell dormancy2023

    • Author(s)
      Misa Minegishi and Hirofumi Shintaku
    • Organizer
      The 27th International Conference on Miniaturized Systems for Chemistry and Life Sciences (uTAS 2023)
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Opto-combinatorial indexing enables high content transcriptomics by linking cell images and the whole transcriptome2023

    • Author(s)
      Arata Tsuchida, Taikopaul Kaneko, Mayu Kawasaki, Kaori Nishikawa, and Hirofumi Shintaku
    • Organizer
      Physics and Chemistry of Microfluidics, Gordon Research Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ELASTomics: Combined analysis of mechanical phenotype of cellular surface and transcriptome at single-cell resolution2023

    • Author(s)
      Akifumi Shiomi, Taikopaul Kaneko, Kaori Nishikawa, Hirofumi Shintaku
    • Organizer
      Physics and Chemistry of Microfluidics Gordon Research Seminar
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ELASTomics: Combined analysis of mechanical phenotype of cellular surface and transcriptome at single-cell resolution2023

    • Author(s)
      Akifumi Shiomi, Taikopaul Kaneko, Kaori Nishikawa, Hirofumi Shintaku
    • Organizer
      Physics and Chemistry of Microfluidics Gordon Research Conference
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nanopore electroporation enables profiling cell surface tension and gene expression at single-cell resolution2023

    • Author(s)
      Hirofumi Shintaku, Akifumi Shiomi, Taikopaul Kaneko, Kaori, Nishikawa
    • Organizer
      the 61th Annual Meeting of the Biophysical Society of Japan
    • Related Report
      2023 Annual Research Report
    • Invited
  • [Presentation] Micro- and nanoscale electroporation for single-cell multiomics2023

    • Author(s)
      Hirofumi Shintaku
    • Organizer
      The 29th EAJS -East Asia Joint Symposium
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 1細胞の表現型と遺伝子発現をつなぐ2023

    • Author(s)
      新宅博文
    • Organizer
      電気学会全国大会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] Live-cell RNA-seq links time-evolving fluctuations between cellular phenotypes and gene regulation2023

    • Author(s)
      鳥井 孝太郎,渡邊 慶子,西川 香里,武石 明佳,新宅 博文
    • Organizer
      第64回日本植物生理学会年会
    • Related Report
      2022 Research-status Report
  • [Presentation] マイクロ・ナノエレクトロポレーションと1細胞オミクス解析2022

    • Author(s)
      新宅博文
    • Organizer
      定量生物学の会年会
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] マイクロ・ナノ電場を活用した1細胞マルチオミクス解析2022

    • Author(s)
      新宅博文
    • Organizer
      シングルゲノミクス研究会2022
    • Related Report
      2022 Research-status Report
    • Invited
  • [Presentation] 揺らぐ遺伝子ネットワークと表現型の因果を結ぶLive cell RNA-seq法の開発2022

    • Author(s)
      鳥井 孝太郎,渡邉 慶子,西川 香里,武石 明佳,新宅 博文
    • Organizer
      シングルゲノミクス研究会2022
    • Related Report
      2022 Research-status Report
  • [Presentation] 微小電気穿孔法を用いた細胞の膜張力と遺伝子発現の統合解析2022

    • Author(s)
      塩見 晃史,金子 泰洸ポール,西川 香里,新宅 博文
    • Organizer
      シングルゲノミクス研究会2022
    • Related Report
      2022 Research-status Report
  • [Presentation] 近接細胞蛍光標識技術を用いたがん細胞と相互作用した細胞の1細胞トランスクリプトーム解析2022

    • Author(s)
      峯岸 美紗,西川 香里,新宅 博文,口丸 高弘
    • Organizer
      シングルゲノミクス研究会2022
    • Related Report
      2022 Research-status Report
  • [Presentation] DNAバーコード技術を用いた1細胞画像・遺伝子発現量解析の統合1細胞多階層相関解析2022

    • Author(s)
      土田 新,金子 泰洸ポール,川崎 真由,横川 隆司,新宅 博文
    • Organizer
      日本機械学会 2022年度年次大会
    • Related Report
      2022 Research-status Report
  • [Presentation] 細胞の機械特性と遺伝子発現の統合解析2022

    • Author(s)
      塩見 晃史,金子 泰洸ポール,西川 香里,新宅 博文
    • Organizer
      第95回日本生化学会大会
    • Related Report
      2022 Research-status Report
  • [Presentation] 老化における細胞の膜張力と遺伝子発現の統合解析2022

    • Author(s)
      塩見 晃史,金子 泰洸ポール,西川 香里,新宅 博文
    • Organizer
      第13回マイクロ・ナノ工学シンポジウム
    • Related Report
      2022 Research-status Report
  • [Presentation] A combined analysis of membrane-mechanical phenotyping and transcriptomics using nanoelectroporation2021

    • Author(s)
      塩見 晃史,金子 泰洸ポール,西川 香里,新宅 博文
    • Organizer
      第59回日本生物物理学会年会
    • Related Report
      2021 Research-status Report
  • [Presentation] 1細胞電気泳動および遺伝子発現の統合解析に向けた並列マイクロ流体システムの開発2021

    • Author(s)
      土田 新,マハムド N. アブディルモエズ,金子 泰洸ポール,横川 隆司,新宅 博文
    • Organizer
      第12回マイクロ・ナノ工学シンポジウム
    • Related Report
      2021 Research-status Report
  • [Presentation] トランスクリプトーム解析を組み合わせた細胞膜の機械特性計測2021

    • Author(s)
      塩見 晃史,金子 泰洸ポール,西川 香里,新宅 博文
    • Organizer
      日本機械学会 2021年度年次大会
    • Related Report
      2021 Research-status Report
  • [Presentation] マイクロ・ナノ電気穿孔を用いた1細胞ダイナミクス分析2021

    • Author(s)
      新宅 博文
    • Organizer
      日本機械学会 2021年度 年次大会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] 核と細胞質に存在するトランスクリプトノイズの1細胞定量2021

    • Author(s)
      新宅 博文
    • Organizer
      情報計算化学生物学会 2021年大会
    • Related Report
      2021 Research-status Report
    • Invited
  • [Presentation] Exploring transcriptional noise in subcellular compartments with on-chip electrophoretic fractionation of cytoplasmic versus nuclear RNAs2021

    • Author(s)
      Hirofumi Shintaku
    • Organizer
      Human Cell Atlas Asia General Meeting 2021
    • Related Report
      2021 Research-status Report
    • Int'l Joint Research / Invited
  • [Book] A SINC-Seq Protocol for the Analysis of Subcellular Gene Expression in Single Cells, Single Cell Assays2023

    • Author(s)
      Mahmoud N. Abdelmoez and Hirofumi Shintaku
    • Total Pages
      11
    • Publisher
      Springer
    • Related Report
      2023 Annual Research Report
  • [Remarks] LiMe Nano Bioengineering Lab

    • URL

      https://www.hshintaku.com/

    • Related Report
      2023 Annual Research Report

URL: 

Published: 2021-07-13   Modified: 2025-01-30  

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