
チームリーダー
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[at]riken.jp
[at]を@に変えてください
採用情報
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ています。これらの技術開発を基盤として、生命システムの理解や、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
- DNA分子バーコード法の開発
- デジタルRNAシークエンシング
- 新規細菌叢解析法の開発
- バイオイメージング、シークエンシング、機械学習の融合
- オルガノイド計測
- 細胞間相互作用
主要論文
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
Aso H, Nagaoka S, Kawakami E, et al.
Multiomics investigation revealing the characteristics 1 of HIV-1-infected cells.
Cell Reports
32, 107887 (2020)
Kimura S, Nakamura Y, Kobayashi N, et al.
Osteoprotegerin-dependent M cell self-regulation balances gut infection and immunity.
Nature Communications
11, 234 (2020)
doi: 10.1038/s41467-019-13883-y
Yazaki J, Kawashima Y, Ogawa T, et al.
HaloTag-based conjugation of proteins to barcoding-oligonucleotides.
Nucleic Acids Research
48, e8 (2020)
doi: 10.1093/nar/gkz1086
Miyamoto C, Kojo S, Yamashita M, et al.
Runx/Cbfβ complexes protect group 2 innate lymphoid cells from exhausted-like hyporesponsiveness during allergic airway inflammation.
Nature Communications
10, 447 (2019)
doi: 10.1038/s41467-019-08365-0
Ise W, Fujii K, Shiroguchi K, et al.
T follicular helper cell-germinal center B cell interaction strength regulates entry into plasma cell or recycling GC cell fate.
Immunity
48, 702-715 (2018)
doi: 10.1016/j.immuni.2018.03.027
Tenno M, Kojo S, Lawir DF, et al.
Cbfβ2 controls differentiation of and confers homing capacity to prethymic progenitors.
Journal of Experimental Medicine
215, 595-610 (2018)
doi: 10.1084/jem.20171221
Ogawa T*, Kryukov K*, Imanishi T, Shiroguchi K.
The efficacy and further functional advantages of random-base molecular barcodes for absolute and digital quantification of nucleic acid molecules.
Scientific Reports
7, 13576 (2017)
doi: 10.1038/s41598-017-13529-3
Tenno M, Shiroguchi K, Muroi S, et al.
Cbfβ2-deficiency preserves Langerhans cell precursors by lack of selective TGFβ receptor signaling.
Journal of Experimental Medicine
214(10), 2933-2946 (2017)
doi: 10.1084/jem.20170729
Suzuki H, Mitsuno K, Shiroguchi K, et al.
One-step micromolding of complex 3D microchambers for single-cell analysis.
Lab on a Chip
17(4), 647-652 (2017)
doi: 10.1039/c6lc01313a
Chen HY*, Shiroguchi K*, Ge H, Xie XS.
Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli.
Molecular Systems Biology
11(1), 781 (2015)
doi: 10.15252/msb.20145794
Miyazaki M, Kinosita K, Shiroguchi K.
Accurate polarity control and parallel alignment of actin filaments for myosin-powered transport systems.
Rsc Advances
3(23), 8728-8733 (2013)
doi: 10.1039/c3ra41112e
Shiroguchi K, Jia TZ, Sims PA, Xie XS.
Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes.
Proceedings of the National Academy of Sciences of the United States of America
109(4), 1347-1352 (2012)
doi: 10.1073/pnas.1118018109
Shiroguchi K, Chin HF, Hannemann DE, et al.
Direct Observation of the Myosin Va Recovery Stroke That Contributes to Unidirectional Stepping along Actin.
PLOS Biology
9(4), e1001031 (2011)
doi: 10.1371/journal.pbio.1001031
Shiroguchi K, Kinosita K.
Myosin V walks by lever action and Brownian motion.
Science
316(5828), 1208-1212 (2007)
doi: 10.1126/science.1140468