Team Director
Katsuyuki Shiroguchi
Ph.D.
Laboratory for Prediction of Cell Systems Dynamics
Location Kobe / Developmental Biology Buildings
E-mailkatsuyuki.shiroguchi@riken.jp
I had been working on single molecule observation of molecular motors by optical microscopy, and have jumped into the genomics research field. Based on these experiences, we are making a new platform enabled by the combination of imaging, sequencing, and machine learning, and also developing the three-dimension spatial analysis. Using these systems, we are studying stem cells, organoids, and immune-related cells, etc. We have developed other techniques as well, for example, molecular barcoding which provides digital RNA sequencing (dRNA-seq), and a novel bacterial microbiota analysis based on single-base identification and single-cell level quantification. We often collaborate with biologists and/or medical scientists in order to study immune-related cells and diseases. We would like to understand biological systems, and to contribute to medical sciences.
Research Theme
- Stem cells・Organoids
- Immune cells
- Spatial cell analysis
- Bacterial microbiota analysis
- DNA molecular barcodes
Selected Publications
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
