チームディレクター
城口克之 Ph.D.

細胞システム動態予測研究チーム

E-mail katsuyuki.shiroguchi@riken.jp

生物物理学を含めた複合的なアプローチにより新しい視点から生命を理解し、医科学への貢献もめざす

光学顕微鏡を用いた蛋白質１分子動態観察と次世代シークエンサ関連の手法開発の経験を基に、バイオイメージング・シークエンシング・機械学習を組み合わせた新規１細胞計測法を開発し、三次元空間計測へも展開しています。DNA分子バーコード法の開発により、高精度にRNA 分子を定量できるDigital RNA sequencing (dRNA-seq）を実現し、また、細菌の種類を高精度で区別して１細胞レベルで定量できる、新しい細菌叢解析法も開発しました。これらの技術開発を基盤として、生命システムの理解や、幹細胞・オルガノイドを用いた研究などにより医科学への貢献を目指しています。免疫に関わる細胞などを対象に、たくさんの共同研究も行っています。

研究テーマ

幹細胞・オルガノイド
免疫細胞
空間細胞計測
細菌叢解析
DNA分子バーコード法

主要論文

Wataru Ise, Takuya Koike, Nozomi Shimada , et al.
KLF2 expression in IgG plasma cells at their induction site regulates the migration program
J Exp Med 222 (5):e20241019, (2025) doi: 10.1084/jem.20241019

Kanaya T, Jinnohara T, Sakakibara S, et al.
RelB and C/EBPα critically regulate the development of Peyer’s patch mononuclear phagocytes
Mucosal Immunology (2024) doi: 10.1016/j.mucimm.2024.10.005

Jin J, Liu X, Shiroguchi K.
Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization
iMetaOmics (2024) doi: 10.1002/imo2.9

Nakai-Futatsugi Y, Jin J, Ogawa T, et al.
Pigmentation level of human iPSC-derived retinal pigment epithelium cell does not indicate a specific gene expression profile
eLife 12, RP92510 (2024) doi: 10.7554/eLife.92510

Takahashi S, Ochiai S, Jin J, et al.
Sensory neuronal STAT3 is critical for IL-31 receptor expression and inflammatory itch
Cell Reports (2023) doi: /10.1016/j.celrep.2023.113433

Jin J, Yamamoto R, Shiroguchi K, et al.
High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ
Nature Protocols (2023) doi: /10.1038/s41596-023-00906-8

Cui G, Shimba A, Jin J, et al.
CD45 Alleviates Airway Inflammation and Lung Fibrosis by Limiting Expansion and Activation of ILC2s.
Proceedings of the National Academy of Sciences of the United States of America 120(36), e2215941120 (2023) doi: 10.1073/pnas.2215941120

Fujimura T, Enomoto Y, Katsura H, et al.
Identifying a Lung Stem Cell Subpopulation by Combining Single-Cell Morphometrics, Organoid Culture, and Transcriptomics.
Stem Cells 41(8), 809-820 (2023) doi: 10.1093/stmcls/sxad044

Jin J, Ogawa T, Hojo N, et al.
Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes.
Proceedings of the National Academy of Sciences of the United States of America 120(1), e2210283120 (2023) doi: 10.1073/pnas.2210283120

Cui G, Shimba A, Jin J, et al.
A circulating subset of iNKT cells mediates antitumor and antiviral immunity.
Science Immunology 7(76), eabj8760 (2022) doi: 10.1126/sciimmunol.abj8760

Jin J, Yamamoto R, Takeuchi T, et al.
High-throughput identification and quantification of single bacterial cells in the microbiota.
Nature Communications 13, 863 (2022) doi: 10.1038/s41467-022-28426-1

Zhang B, Vogelzang A, Miyajima M, et al.
B cell-derived GABA elicits IL-10⁺ macrophages to limit anti-tumour immunity.
Nature 599(7885), 471-476 (2021) doi: 10.1038/s41586-021-04082-1

Nishida M, Yamashita N, Ogawa T, et al.
Mitochondrial reactive oxygen species trigger metformin-dependent antitumor immunity via activation of Nrf2/mTORC1/p62 axis in tumor-infiltrating CD8T lymphocytes.
Journal for immunotherapy of cancer 9, e002954 (2021) doi: 10.1136/jitc-2021-002954