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Microfluidic approach to single cell transcriptome analysis and its applications

Research Project

Project/Area Number 16H06328
Research Category

Grant-in-Aid for Scientific Research (S)

Allocation TypeSingle-year Grants
Research Field Nanobioscience
Research InstitutionThe University of Tokyo

Principal Investigator

FUJII Teruo  東京大学, 生産技術研究所, 教授 (30251474)

Co-Investigator(Kenkyū-buntansha) 長阪 一憲  帝京大学, 医学部, 教授 (30624233)
PLESSY Charles  沖縄科学技術大学院大学, ゲノム・遺伝子制御システム科学ユニット, グループリーダー (60391984)
Kim SooHyeon  東京大学, 生産技術研究所, 講師 (80709189)
Project Period (FY) 2016-05-31 – 2021-03-31
Project Status Completed (Fiscal Year 2021)
Budget Amount *help
¥177,580,000 (Direct Cost: ¥136,600,000、Indirect Cost: ¥40,980,000)
Fiscal Year 2020: ¥29,250,000 (Direct Cost: ¥22,500,000、Indirect Cost: ¥6,750,000)
Fiscal Year 2019: ¥31,850,000 (Direct Cost: ¥24,500,000、Indirect Cost: ¥7,350,000)
Fiscal Year 2018: ¥27,560,000 (Direct Cost: ¥21,200,000、Indirect Cost: ¥6,360,000)
Fiscal Year 2017: ¥50,830,000 (Direct Cost: ¥39,100,000、Indirect Cost: ¥11,730,000)
Fiscal Year 2016: ¥38,090,000 (Direct Cost: ¥29,300,000、Indirect Cost: ¥8,790,000)
Keywordsマイクロ流体デバイス / 1細胞解析 / ゲノム工学 / 単一細胞解析 / トランスクリプトーム解析 / 誘電泳動 / 1細胞解析 / トランスクリプートム解析
Outline of Final Research Achievements

By integrating microfluidics and CMOS technologies, a novel microfluidic system has been developed for trapping single cells and/or microparticles into designated locations, followed by parallelized analysis of trapped single cells. Moreover, a new protocol for cap analysis of gene expression has been established by utilizing combinatorial DNA barcodes for efficient labeling of single cells. By using these methods, clinical samples from cervical cancer patients were successfully analyzed, and it was confirmed that the cervical cancer could be detected by analyzing RNA or protein expression level.

Academic Significance and Societal Importance of the Research Achievements

細胞を一つずつ解析可能な1細胞解析は、細胞の多様性を把握できるため基礎研究が活発に進められている。本研究では、臨床検体を1細胞レベルで確実に捕捉する方法を確立するとともに、トランスクリプトーム解析が医療分野へ応用できることを確認した。これらにより、病態と各細胞の性質との関係を理解することが可能になれば、細胞の多様性に基づく新しい診断方法の創出が期待できる。

Assessment Rating
Verification Result (Rating)

A

Assessment Rating
Result (Rating)

B: Progress in the research is delayed than the initial goal. Further efforts are necessary.

Report

(11 results)
  • 2022 Research Progress Assessment (Verification Result) ( PDF )
  • 2021 Final Research Report ( PDF )
  • 2020 Annual Research Report
  • 2019 Annual Research Report   Abstract(Research Progress Assessment) ( PDF )   Research Progress Assessment (Result) ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Abstract ( PDF )   Comments on the Screening Results ( PDF )   Annual Research Report
  • Research Products

    (37 results)

All 2022 2021 2020 2019 2018 2017 2016

All Journal Article (10 results) (of which Int'l Joint Research: 6 results,  Peer Reviewed: 10 results,  Open Access: 2 results) Presentation (16 results) (of which Int'l Joint Research: 9 results,  Invited: 1 results) Patent(Industrial Property Rights) (11 results)

  • [Journal Article] Automated phenol-chloroform extraction of high molecular weight genomic DNA for use in long-read single-molecule sequencing2022

    • Author(s)
      Liu Andrew W.、Villar-Briones Alejandro、Luscombe Nicholas M.、Plessy Charles
    • Journal Title

      F1000Research

      Volume: 11 Pages: 240-240

    • DOI

      10.12688/f1000research.109251.1

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Multi-omics analysis of hiPSCs-derived HLCs matured on-chip revealed patterns typical of liver regeneration2021

    • Author(s)
      Danoy M, Tauran Y, Poulain S, Jellali R, Bruce J, Leduc M, Gall M, Koui Y, Arakawa H, Gilard F, Kato Y, Kido T, Miyajima A, Sakai Y, Leclerc E
    • Journal Title

      Biotechnology & Bioengineering

      Volume: 118 Issue: 10 Pages: 3716-3732

    • DOI

      10.1002/bit.27667

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Machine-driven parameter screen of biochemical reactions2020

    • Author(s)
      Poulain Stephane、Arnaud Ophelie、Kato Sachi、Chen Iris、Ishida Hiro、Carninci Piero、Plessy Charles
    • Journal Title

      Nucleic Acids Research

      Volume: 48 Issue: 7 Pages: e37-e37

    • DOI

      10.1093/nar/gkaa079

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages2020

    • Author(s)
      Taguchi A, Nagasaka K, Plessy C, Nakamura H, Kawata Y, Kato S, Hashimoto K, Nagamatsu T, Oda K, Kukimoto I, Kawana K, Carninci P, Osuga Y, Fujii T.
    • Journal Title

      Sci Rep

      Volume: 10 Issue: 1 Pages: 17991-17991

    • DOI

      10.1038/s41598-020-75133-2

    • Related Report
      2020 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Sequential Cell-Processing System by Integrating Hydrodynamic Purification and Dielectrophoretic Trapping for Analyses of Suspended Cancer Cells2019

    • Author(s)
      Park Jongho、Komori Takayuki、Uda Toru、Miyajima Keiichi、Fujii Teruo、Kim Soo Hyeon
    • Journal Title

      Micromachines

      Volume: 11 Issue: 1 Pages: 47-47

    • DOI

      10.3390/mi11010047

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On-chip immunofluorescence analysis of single cervical cells using an electroactive microwell array with barrier for cervical screening2019

    • Author(s)
      Takeuchi Makoto、Nagasaka Kazunori、Yoshida Mina、Kawata Yoshiko、Miyagawa Yuko、Tago Saori、Hiraike Haruko、Wada-Hiraike Osamu、Oda Katsutoshi、Osuga Yutaka、Fujii Tomoyuki、Ayabe Takuya、Kim Soo Hyeon、Fujii Teruo
    • Journal Title

      Biomicrofluidics

      Volume: 13 Issue: 4 Pages: 044107-044107

    • DOI

      10.1063/1.5089796

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Cancer marker-free enrichment and direct mutation detection in rare cancer cells by combining multi-property isolation and microfluidic concentration2019

    • Author(s)
      Kim Soo Hyeon、Ito Hiroshi、Kozuka Masahiro、Takagi Hidenori、Hirai Mitsuharu、Fujii Teruo
    • Journal Title

      Lab on a Chip

      Volume: 19 Issue: 5 Pages: 757-766

    • DOI

      10.1039/c8lc00772a

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Localization of low-abundant cancer cells in a sharply expanded microfluidic step-channel using dielectrophoresis2017

    • Author(s)
      Kim Soo Hyeon、Ito Hiroshi、Kozuka Masahiro、Hirai Mitsuharu、Fujii Teruo
    • Journal Title

      Biomicrofluidics

      Volume: 11 Issue: 5 Pages: 054114-054114

    • DOI

      10.1063/1.4998756

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Label-free single-cell separation and imaging of cancer cells using an integrated microfluidic system2017

    • Author(s)
      Antfolk Maria、Kim Soo Hyeon、Koizumi Saori、Fujii Teruo、Laurell Thomas
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 46507-46507

    • DOI

      10.1038/srep46507

    • Related Report
      2017 Annual Research Report 2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Efficient Analysis of a Small Number of Cancer Cells at the Single-cell Level using Electroactive Double-well Array2016

    • Author(s)
      Kim, S.-H., and Fujii, T.
    • Journal Title

      Lab on a Chip

      Volume: 16 Issue: 13 Pages: 2440-2449

    • DOI

      10.1039/c6lc90066f

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Presentation] Two-dimensional flow cytometry realized by using an array of time-gated single photon avalanche diodes2021

    • Author(s)
      S. Tago, K. Iizuka, T. Mitsunaka, D. Sato, T. Shindo, T. Fujii and S. H. Kim
    • Organizer
      MicroTAS2021
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Parallelized flow cytometry realized by array of time-gated single photon avalanche diodes2020

    • Author(s)
      C. Trzeciakowski, D. Sato, T. Shindo, T. Mitsunaka, Y. Fujimoto, K. Iizuka, S. Tago, T. Fujii and S. H. Kim
    • Organizer
      MicroTAS2020
    • Related Report
      2020 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ntegration of on-chip cluster purification and compartmentalization for rna-seq analysis of cluster2019

    • Author(s)
      H. Saito, S. H. Kim, I. Tsuchiya, S. Nagasawa, M. Seki, Y. Komazaki, T. Torii, Y. Suzuki and T. Fujii
    • Organizer
      International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2019)
    • Related Report
      2019 Annual Research Report
  • [Presentation] Efficient pairing of single cells using trap-and-drop microwell array2018

    • Author(s)
      S. H. Kim, M. Yoshida, S. Tago and T. Fujii
    • Organizer
      International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2018)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Electroactive microwell array for separate trapping of single cells and clusters2018

    • Author(s)
      C. J. Park, S. H. Kim, T. Fujii
    • Organizer
      International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2018)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Machine-driven parameter-space exploration of biochemical reactions2018

    • Author(s)
      C. Plessy, S. Poulain, S. Kato, O. Arnaud, P. Carninci
    • Organizer
      41st annual meeting of the Molecular Biology Society of Japan (MBSJ)
    • Related Report
      2018 Annual Research Report
  • [Presentation] Addressable electroactive microwell array capable of deterministic combinatorial trapping of single cells2017

    • Author(s)
      S. H. Kim, T. Mitsunaka, Y. Fujimoto, K. Iizuka and T. Fujii
    • Organizer
      Proceedings of International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Highly efficient rare cancer cells isolation and concentration by combining label-free isolation and dielectrophoretic concentration in a microfluidic step-channel2017

    • Author(s)
      S. H. Kim, H. Ito, M. Kozuka, H. Takagi, M. Hirai and T. Fujii
    • Organizer
      Proceedings of International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Highly efficient trapping and analysis of rare cells using an electroactive microwell array with barriers2017

    • Author(s)
      M. Takeuchi, S. H. Kim, K. Nagasaka, M. Yoshida, Y. Kawata, K. Oda and T. Fujii
    • Organizer
      Proceedings of International Conference on Miniaturized Systems for Chemistry and Life Sciences (MicroTAS2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Highly efficient compartmentalization of multiple single cells using addressable electroactive microwell array2017

    • Author(s)
      S. H. Kim, T. Mitsunaka, Y. Fujimoto, K. Iizuka and T. Fujii
    • Organizer
      2017 meeting on Single Cell Analyses
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Label-free selective trapping of single cancer cells using electroactive microwell array2017

    • Author(s)
      S. H. Kim, M. Yoshida, and T. Fujii
    • Organizer
      Proceedings of 9th International Symposium on Microchemistry and Microsystems (ISMM 2017)
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Highly Efficient Trapping and Analysis of Rare Cells using an Electroactive Microwell Array with Barriers2017

    • Author(s)
      M. Takeuchi, S. H. Kim, K. Nagasaka, M. Yoshida, Y. Kawata, K. Oda, T. Fujii
    • Organizer
      The 76th Annual Meeting of the Japanese Cancer Association
    • Related Report
      2017 Annual Research Report
  • [Presentation] Microfluidics for Innovative Biological Experimentations - from Single Cell Analysis to Organ-on-a-Chip2017

    • Author(s)
      T. Fujii
    • Organizer
      The 9th International Symposium on Microchemistry and Microsystems
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 希少細胞の1細胞解析を実現するマイクロ流体デバイスの開発2016

    • Author(s)
      金秀炫,藤井輝夫
    • Organizer
      第75回日本癌学会学術総会
    • Related Report
      2016 Annual Research Report
  • [Presentation] Electroactive trap-well array coupled with PDMS reaction-well array allows highly efficient single-cell trapping followed by on-chip analysis with a controllable dilution ratio of cell lysates2016

    • Author(s)
      Ogata,K., Kim, S.-H., and Fujii, T.
    • Organizer
      MicroTAS2016 conference
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Presentation] An integrated acousto- and dielectrophoresis device for tumor cell separation, concentration, and single-cell trapping2016

    • Author(s)
      Antfolk, M., Kim, S.-H., Saori, K., Kaneda, S., Fujii, T., and Laurell, T.
    • Organizer
      MicroTAS2016 conference
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Patent(Industrial Property Rights)] 生体粒子捕集装置2019

    • Inventor(s)
      満仲健、飯塚邦彦、幡井徹也、藤井輝夫、金秀炫
    • Industrial Property Rights Holder
      満仲健、飯塚邦彦、幡井徹也、藤井輝夫、金秀炫
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2019-192797
    • Filing Date
      2019
    • Related Report
      2019 Annual Research Report
  • [Patent(Industrial Property Rights)] 流路デバイスおよび流体中粒子解析システム2019

    • Inventor(s)
      満仲健、飯塚邦彦、幡井徹也、藤井輝夫、金秀炫
    • Industrial Property Rights Holder
      満仲健、飯塚邦彦、幡井徹也、藤井輝夫、金秀炫
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2019-180308
    • Filing Date
      2019
    • Related Report
      2019 Annual Research Report
  • [Patent(Industrial Property Rights)] 細胞捕捉装置2018

    • Inventor(s)
      藤井輝夫、金秀炫、朴致済
    • Industrial Property Rights Holder
      藤井輝夫、金秀炫、朴致済
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2018-210761
    • Filing Date
      2018
    • Related Report
      2018 Annual Research Report
  • [Patent(Industrial Property Rights)] 対象物捕捉装置、および対象物捕捉装置ユニット2017

    • Inventor(s)
      飯塚邦彦、満仲健、藤本義久、藤井輝夫、金秀炫
    • Industrial Property Rights Holder
      東京大学、シャープ株式会社
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-085579
    • Filing Date
      2017
    • Related Report
      2017 Annual Research Report
  • [Patent(Industrial Property Rights)] 液体中微粒子分析システムおよび液体中微粒子分析方法2017

    • Inventor(s)
      飯塚邦彦、藤本義久、満仲健、藤井輝夫、金秀炫
    • Industrial Property Rights Holder
      東京大学、シャープ株式会社
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-149018
    • Filing Date
      2017
    • Related Report
      2017 Annual Research Report
  • [Patent(Industrial Property Rights)] 細胞捕捉装置2017

    • Inventor(s)
      小森隆幸、金秀炫、藤井輝夫
    • Industrial Property Rights Holder
      東京大学、NOK株式会社
    • Industrial Property Rights Type
      特許
    • Industrial Property Number
      2017-193145
    • Filing Date
      2017
    • Related Report
      2017 Annual Research Report
  • [Patent(Industrial Property Rights)] 粒子捕捉用マイクロデバイス、試料中の粒子を捕捉する方法及びそれを用いた粒子の濃縮、観察又は回収方法2016

    • Inventor(s)
      藤井輝夫、金秀炫、伊藤博史
    • Industrial Property Rights Holder
      藤井輝夫、金秀炫、伊藤博史
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016
    • Acquisition Date
      2022
    • Related Report
      2020 Annual Research Report
  • [Patent(Industrial Property Rights)] 蛍光検査システム及び細胞検査手法2016

    • Inventor(s)
      飯塚邦彦、藤本義久、金秀炫、藤井輝夫
    • Industrial Property Rights Holder
      東京大学、シャープ(株)
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016
    • Related Report
      2016 Annual Research Report
  • [Patent(Industrial Property Rights)] 蛍光検査システム2016

    • Inventor(s)
      飯塚邦彦、藤本義久、金秀炫、藤井輝夫
    • Industrial Property Rights Holder
      東京大学、シャープ(株)
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016
    • Related Report
      2016 Annual Research Report
  • [Patent(Industrial Property Rights)] 誘電泳動デバイス2016

    • Inventor(s)
      飯塚邦彦、藤本義久、金秀炫、藤井輝夫
    • Industrial Property Rights Holder
      東京大学、シャープ(株)
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016
    • Related Report
      2016 Annual Research Report
  • [Patent(Industrial Property Rights)] DEPピンセット2016

    • Inventor(s)
      佐藤大紀、飯塚邦彦、齊藤晶、満仲健、金秀炫、藤井輝夫
    • Industrial Property Rights Holder
      東京大学、シャープ(株)
    • Industrial Property Rights Type
      特許
    • Filing Date
      2016
    • Related Report
      2016 Annual Research Report

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Published: 2016-06-01   Modified: 2023-10-16  

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