Kubota Shimpei 久保田晋平

Researcher Number	90808859
Other IDs
Affiliation (Current)	2025: 名古屋大学, 医学系研究科, 特任講師 2025: 北海道大学, 遺伝子病制御研究所, 客員研究員
Affiliation (based on the past Project Information) *help	2025: 名古屋大学, 医学系研究科, 特任講師 2021 – 2023: 北海道大学, 遺伝子病制御研究所, 特任講師 2020: 東京大学, 大学院医学系研究科(医学部), 特任研究員
Review Section/Research Field	Principal Investigator Basic Section 49030:Experimental pathology-related
Keywords	Principal Investigator システム生物学 / 組織透明化 / 病理学 / 神経免疫連関 / 全細胞解析 / システムズバイオロジー / 免疫学 / シングルセルバイオロジー / 癌転移 / がん転移 / がん微小環境 / 全身全細胞解析

Whole-body analysis of tumor stromal heterogeneityPrincipal Investigator
- Principal Investigator
  
  久保田晋平
- Project Period (FY)
  2025 – 2029
- Research Category
  
  Grant-in-Aid for Scientific Research (B)
- Review Section
  
  Basic Section 49030:Experimental pathology-related
- Research Institution
  Nagoya University
微小炎症ネットワークの解明に資する全身全細胞解析技術の開発Principal Investigator
- Principal Investigator
  
  久保田晋平
- Project Period (FY)
  2022 – 2024
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 49030:Experimental pathology-related
- Research Institution
  Hokkaido University
Whole-body/organ pathology of cancer microenvironmentPrincipal Investigator
- Principal Investigator
  
  Kubota Shimpei
- Project Period (FY)
  2020 – 2021
- Research Category
  
  Grant-in-Aid for Early-Career Scientists
- Review Section
  
  Basic Section 49030:Experimental pathology-related
- Research Institution
  Hokkaido University
  The University of Tokyo

All 2024 2023 2022 2021 2020

All Journal Article Presentation Book

[Book] シングルセル解析でなにがわかるか2020
- Author(s)
  久保田晋平　他多数
- Total Pages
  200
- Publisher
  化学同人
- ISBN
  9784759817348
- Data Source
  KAKENHI-PROJECT-20K16212
[Journal Article] Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing2024
- Author(s)
  Daichi M. Sakamoto; Iori Tamura; Bo Yi; Sho Hasegawa; Yutaro Saito; Naoki Yamada; Yoichi Takakusagi; Shimpei I. Kubota; Minoru Kobayashi; Hiroshi Harada; Kenjiro Hanaoka; Masayasu Taki; Masaomi Nangaku; Kazuki Tainaka; Shinsuke Sando
- Journal Title
  
  ACS Nano
  
  Volume: 18 Issue: 6 Pages: 5176-5179
- DOI
  10.1021/acsnano.3c12716
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-23K18274, KAKENHI-PROJECT-21K16159, KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-21K07727, KAKENHI-PROJECT-21KK0144, KAKENHI-ORGANIZER-21H05258, KAKENHI-PLANNED-21H05262, KAKENHI-PROJECT-23K24198, KAKENHI-PROJECT-23K27304, KAKENHI-PROJECT-23K27546
[Journal Article] Calcineurin inhibitor inhibits tolerance induction by suppressing terminal exhaustion of donor T cells after allo-HCT2023
- Author(s)
  Senjo Hajime、Harada Shinpei、Kubota Shimpei I.、Tanaka Yuki、Tateno Takahiro、Zhang Zixuan、Okada Satomi、Chen Xuanzhong、Kikuchi Ryo、Miyashita Naoki、Onozawa Masahiro、Goto Hideki、Endo Tomoyuki、Hasegawa Yuta、Ohigashi Hiroyuki、Ara Takahide、Hasegawa Yoshinori、Murakami Masaaki、Teshima Takanori、Hashimoto Daigo
- Journal Title
  
  Blood
  
  Volume: 142 Issue: 5 Pages: 477-492
- DOI
  10.1182/blood.2023019875
- Peer Reviewed / Open Access / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-23K18296, KAKENHI-PROJECT-21K16259, KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-21K08409, KAKENHI-PROJECT-20K17366, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-23K21439
[Journal Article] High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore2023
- Author(s)
  Murakami Kaoru、Kubota Shimpei I.、Tanaka Kumiko、Tanaka Hiroki、Akabane Keiichiroh、Suzuki Rigel、Shinohara Yuta、Takei Hiroyasu、Hashimoto Shigeru、Tanaka Yuki、Hojyo Shintaro、Sakamoto Osamu、Naono Norihiko、Takaai Takayui、（１０名省略）、Taniguchi Masateru、Murakami Masaaki
- Journal Title
  
  Lab on a Chip
  
  Volume: 23 Issue: 22 Pages: 4909-4918
- DOI
  10.1039/d3lc00572k
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-22K07203, KAKENHI-PROJECT-20K15766, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-23H00471
[Journal Article] GM-CSF Promotes the Survival of Peripheral-Derived Myeloid Cells in the Central Nervous System for Pain-Induced Relapse of Neuroinflammation2023
- Author(s)
  Matsuyama Shiina、Yamamoto Reiji、Murakami Kaoru、Takahashi Nobuhiko、Nishi Rieko、Ishii Asuka、Nio Kobayashi Junko、Abe Nobuya、Tanaka Kumiko、Jiang Jing Jing、Kawamoto Tadafumi、Iwanaga Toshihiko、Shinohara Yuta、（４名省略）、Kubota Shimpei I、（４名省略）、Murakami Masaaki
- Journal Title
  
  The Journal of Immunology
  
  Volume: 211 Issue: 1 Pages: 34-42
- DOI
  10.4049/jimmunol.2200567
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-22K07203, KAKENHI-PROJECT-21K06727, KAKENHI-PROJECT-21K07062, KAKENHI-PROJECT-21K07075, KAKENHI-PROJECT-20K15766, KAKENHI-PROJECT-20H00502
[Journal Article] Computer model of IL-6-dependent rheumatoid arthritis in F759 mice2023
- Author(s)
  Yamamoto Reiji、Yamada Satoshi、Atsumi Toru、Murakami Kaoru、Hashimoto Ari、Naito Seiichiro、Tanaka Yuki、Ohki Izuru、Shinohara Yuta、Iwasaki Norimasa、Yoshimura Akihiko、Jiang Jing-Jing、Kamimura Daisuke、Hojyo Shintaro、Kubota Shimpei I、Hashimoto Shigeru、Murakami Masaaki
- Journal Title
  
  International Immunology
  
  Volume: 35 Issue: 9 Pages: 403-421
- DOI
  10.1093/intimm/dxad016
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-22K06890, KAKENHI-PROJECT-22K07203, KAKENHI-PROJECT-21K12131, KAKENHI-PROJECT-20K15766, KAKENHI-PROJECT-20H00502
[Journal Article] Combination therapy with bevacizumab and CCR2 inhibitor for women with ovarian cancer: in vivo validation study2023
- Author(s)
  Tianyue Zhai, Takashi Mitamura, Lei Wang, Shimpei I Kubota, Masaaki Murakami, Shinya Tanaka, Hidemichi Watari
- Journal Title
  
  Cancer Medicine
  
  Volume: - Issue: 8 Pages: 9697-9708
- DOI
  10.1002/cam4.5674
- Peer Reviewed
- Data Source
  KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-21K19364, KAKENHI-PROJECT-19H01171
[Journal Article] Dupuytren's contracture-associated SNPs increase SFRP4 expression in nonimmune cells including fibroblasts to enhance inflammation development2023
- Author(s)
  Kida H, Jiang JJ, Matsui Y, Takahashi I, Hasebe R, Kawamura D, Endo T, Shibayama H, Kondoh M, Nishio Y, Nishida K, Matsuno Y, Oikawa T, Kubota S, Hojyo S, Iwasaki N, Hashimoto S, Tanaka Y, Murakami M.
- Journal Title
  
  Int Immunol.
  
  Volume: dxad004 Issue: 7 Pages: 303-312
- DOI
  10.1093/intimm/dxad004
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K07075, KAKENHI-PROJECT-22K07203, KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-21K19364, KAKENHI-PROJECT-23K14551
[Journal Article] In situ Microinflammation Detection Using Gold Nanoclusters and a Tissue-clearing Method2023
- Author(s)
  Naim Fayrouz、Hasebe Rie、Hojyo Shintaro、Shichibu Yukatsu、Ishii Asuka、Tanaka Yuki、Tainaka Kazuki、Kubota Shimpei、Konishi Katsuaki、Murakami Masaaki
- Journal Title
  
  BIO-PROTOCOL
  
  Volume: 13 Issue: 7 Pages: 7-7
- DOI
  10.21769/bioprotoc.4644
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-21K07062, KAKENHI-PROJECT-21K07075, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-23K24198
[Journal Article] Zoobiquity experiments show the importance of the local MMP9-plasminogen axis in inflammatory bowel diseases in both dogs and patients.2023
- Author(s)
  Takeshi Yamasaki, Noriyuki Nagata, Toru Atsumi, Rie Hasebe, Yuki Tanaka, Izuru Ohki, Shimpei Kubota, Yuta Shinohara, Yong Bin Teoh, Nozomu Yokoyama, Noboru Sasaki, Kensuke Nakamura, Hiroshi Ohta, Takehiko Katsurada, Yoshihiro Matsuno, Shintaro Hojyo, Shigeru Hashimoto, Mitsuyoshi Takiguchi, Masaaki Murakami.
- Journal Title
  
  International immunology
  
  Volume: - Issue: 7 Pages: 313-326
- DOI
  10.1093/intimm/dxad006
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K07062, KAKENHI-PROJECT-21K07075, KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-20H00502, KAKENHI-PROJECT-20K06423, KAKENHI-PROJECT-21K19364, KAKENHI-PROJECT-23K14551, KAKENHI-PROJECT-22K07203, KAKENHI-PROJECT-20K15766
[Journal Article] An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis2022
- Author(s)
  Takahashi K, Abe K, Kubota SI, Fukatsu N, Morishita Y, Yoshimatsu Y, Satoshi Hirakawa, Yoshiaki Kubota, Tetsuro Watabe, Shogo Ehata, Hiroki R. Ueda, Teppei Shimamura, Kohei Miyazono
- Journal Title
  
  Nature Communiactions
  
  Volume: 13 Issue: 1 Pages: 5239-5239
- DOI
  10.1038/s41467-022-32848-2
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-21K07094, KAKENHI-PROJECT-22K15435, KAKENHI-PROJECT-22H04925, KAKENHI-PROJECT-18H05270, KAKENHI-PROJECT-20H03851, KAKENHI-PROJECT-20H04281, KAKENHI-PROJECT-20K21832, KAKENHI-PUBLICLY-22H04839, KAKENHI-PLANNED-17H06326, KAKENHI-ORGANIZER-19H05794, KAKENHI-PROJECT-20H00513
[Journal Article] A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues2022
- Author(s)
  Glaser AK, Bishop KW, Barner LA, Susaki EA , Kubota SI, ..., Huang H, Reder NP, Wilson JJ, Sivakumar R, Shamskhou E, Stoltzfus CR, Wei X, Hempton AK, Pende M, Murawala P, Dodt HU, Imaizumi T, Shendure J, Beliveau BJ, Gerner MY, Xin L, Zhao H, Tru LD, Reid RC, Chandrashekar J, Ueda HR, Svoboda K, Liu JTC
- Journal Title
  
  Nature Methods
  
  Volume: 19 Issue: 5 Pages: 613-619
- DOI
  10.1038/s41592-022-01468-5
- Peer Reviewed / Int'l Joint Research
- Data Source
  KAKENHI-PROJECT-22K15435
[Journal Article] Whole-organ analysis of TGF-β-mediated remodelling of the tumour microenvironment by tissue clearing.2021
- Author(s)
  Kubota SI, Takahashi K, Mano T, Matsumoto K, Katsumata T, Shi S, Tainaka K, Ueda HR, Ehata S, Miyazono K.
- Journal Title
  
  Commun. Biol.
  
  Volume: 4 Issue: 1 Pages: 294-294
- DOI
  10.1038/s42003-021-01786-y
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K21246, KAKENHI-PROJECT-15H05774, KAKENHI-PLANNED-17H06326, KAKENHI-PUBLICLY-20H04700, KAKENHI-PROJECT-18H02105, KAKENHI-PROJECT-18H02540, KAKENHI-PROJECT-19J13071, KAKENHI-PROJECT-20K16212, KAKENHI-ORGANIZER-17H06324, KAKENHI-PROJECT-19K16487, KAKENHI-PLANNED-20H05903
[Journal Article] Heterogenous expression of endoglin marks advanced renal cancer with distinct tumor microenvironment fitness.2021
- Author(s)
  Yusaku Momoi, Jun Nishida, Kosuke Miyakuni, Masafumi Kuroda, Shimpei I Kubota, Kohei Miyazono, Shogo Ehata
- Journal Title
  
  Cancer science
  
  Volume: 112 Issue: 8 Pages: 3136-3149
- DOI
  10.1111/cas.15007
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K16212, KAKENHI-PROJECT-21J12321, KAKENHI-PROJECT-19K07684, KAKENHI-PLANNED-17H06326
[Journal Article] Visualization of the cancer cell cycle by tissue-clearing technology using the Fucci reporter system.2021
- Author(s)
  Kei Takahashi, Ryo Tanabe, Shogo Ehata, Shimpei I Kubota, Yasuyuki Morishita, Hiroki R Ueda, Kohei Miyazono
- Journal Title
  
  Cancer science
  
  Volume: 112 Issue: 9 Pages: 3796-3809
- DOI
  10.1111/cas.15034
- Peer Reviewed / Open Access
- Data Source
  KAKENHI-PROJECT-20K16212, KAKENHI-PROJECT-20H00513, KAKENHI-PLANNED-17H06326
[Presentation] 組織透明化技術を用いた三次元空間解析2023
- Author(s)
  久保田晋平
- Organizer
  第一回北海道バイオ"Mix-up"
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 組織透明化技術を用いた全細胞解析2023
- Author(s)
  久保田晋平
- Organizer
  量子生命科学先端フォーラム2023 夏の研究会
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 組織透明化技術を基盤とした三次元病理学解析2022
- Author(s)
  久保田晋平
- Organizer
  iSeminar
- Invited
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 光シート顕微鏡を用いた三次元病理学解析2022
- Author(s)
  久保田晋平、村上正晃
- Organizer
  光シート顕微鏡ワークショップ
- Invited
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 組織透明化を用いたがん微小環境の全細胞解析2022
- Author(s)
  久保田晋平
- Organizer
  遺伝子・デリバリー研究会第21回シンポジウム
- Invited
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] がん組織不均一性に資する全身全細胞解析技術の構築2022
- Author(s)
  久保田晋平, 高橋恵生, 西田純, 江幡正悟, 田井中一貴, 上田泰己, 宮園浩平
- Organizer
  第111回日本病理学会総会
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] ゲートウェイ反射による組織特異的な炎症性疾患の誘導機構2022
- Author(s)
  久保田晋平、長谷部理絵、村上薫、田中勇希、村上正晃
- Organizer
  第102回　北海道医学大会　病理分科会
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 組織透明化による一細胞解像度での病理学解析2022
- Author(s)
  久保田晋平
- Organizer
  第81回日本癌学会学術総会
- Data Source
  KAKENHI-PROJECT-22K15435
[Presentation] 三次元病理解析に資する組織透明化手法の開発2021
- Author(s)
  久保田晋平、高橋恵生、田井中一貴、江幡正悟、上田泰己、宮園浩平
- Organizer
  第110回日本病理学会総会
- Invited
- Data Source
  KAKENHI-PROJECT-20K16212
[Presentation] Whole-organ quantitative analysis of the tumor microenvironment by tissue clearing2021
- Author(s)
  Kubota Shimpei I.、Takahashi Kei、Mano Tomoyuki、Matsumoto Katsuhiko、Katsumata Takahiro、Shi Shoi、Tainaka Kazuki、Ueda Hiroki R.、Ehata Shogo、Miyazono Kohei
- Organizer
  第93回日本薬理学会
- Data Source
  KAKENHI-PROJECT-20K16212
[Presentation] Whole-organ quantitative analysis of cancer metastasis with single cell resolution2020
- Author(s)
  Kubota Shimpei I.、Takahashi Kei、Nishida Jun、Ehata Shogo、Miyazono Kohei
- Organizer
  第79回日本癌学会
- Data Source
  KAKENHI-PROJECT-20K16212

1. HASEBE Rie

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
2. 田井中一貴

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
3. 豊嶋崇徳

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# of Collaborated Products: 1 results
4. 原田浩

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# of Collaborated Products: 1 results
5. 小林稔

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# of Collaborated Products: 1 results
6. 吉松康裕

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results
7. 北條慎太郎

# of Collaborated Projects: 0 results

# of Collaborated Products: 1 results

Kubota Shimpei 久保田 晋平

Research Projects

Research Products

Co-Researchers

Whole-body analysis of tumor stromal heterogeneityPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

微小炎症ネットワークの解明に資する全身全細胞解析技術の開発Principal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

Whole-body/organ pathology of cancer microenvironmentPrincipal Investigator

Principal Investigator

Project Period (FY)

Research Category

Review Section

Research Institution

[Book] シングルセル解析でなにがわかるか2020

Author(s)

Total Pages

Publisher

ISBN

Data Source

[Journal Article] Whole-Body and Whole-Organ 3D Imaging of Hypoxia Using an Activatable Covalent Fluorescent Probe Compatible with Tissue Clearing2024

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Calcineurin inhibitor inhibits tolerance induction by suppressing terminal exhaustion of donor T cells after allo-HCT2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] High-precision rapid testing of omicron SARS-CoV-2 variants in clinical samples using AI-nanopore2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] GM-CSF Promotes the Survival of Peripheral-Derived Myeloid Cells in the Central Nervous System for Pain-Induced Relapse of Neuroinflammation2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Computer model of IL-6-dependent rheumatoid arthritis in F759 mice2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Combination therapy with bevacizumab and CCR2 inhibitor for women with ovarian cancer: in vivo validation study2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Dupuytren's contracture-associated SNPs increase SFRP4 expression in nonimmune cells including fibroblasts to enhance inflammation development2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] In situ Microinflammation Detection Using Gold Nanoclusters and a Tissue-clearing Method2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] Zoobiquity experiments show the importance of the local MMP9-plasminogen axis in inflammatory bowel diseases in both dogs and patients.2023

Author(s)

Journal Title

DOI

Data Source

[Journal Article] An analysis modality for vascular structures combining tissue-clearing technology and topological data analysis2022

Author(s)

Journal Title

DOI

Data Source

[Journal Article] A hybrid open-top light-sheet microscope for versatile multi-scale imaging of cleared tissues2022

Author(s)

Kubota Shimpei 久保田晋平

[Presentation] ゲートウェイ反射による組織特異的な炎症性疾患の誘導機構2022