RIKEN Center for Biosystems Dynamics Research Laboratory for Prediction of Cell Systems Dynamics
Team Director: Katsuyuki Shiroguchi (Ph.D.)
Research Summary
“Unraveling biological systems and contributing to medical sciences by combination of multidisciplinary approaches including biophysics”
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.
Main Research Fields
- Biological Sciences
Related Research Fields
- Engineering
- Informatics
- Complex Systems
- Interdisciplinary Science & Engineering
- Biophysics
- Systems biology
Keywords
- Stem cells / Organoids
- Immune cells
- Spatial cell analysis
- Bacterial microbiota analysis
- DNA molecular barcodes
Selected Publications
Papers with an asterisk(*) are based on research conducted outside of RIKEN.
- 1.
Jin J, Liu X, Shiroguchi K.:
"Long journey of 16S rRNA-amplicon sequencing toward cell-based functional bacterial microbiota characterization"
iMetaOmics (2024). - 2.
Nakai-Futatsugi Y., Jin J., Ogawa T., Sakai N., Maeda A., Hironaka K., Fukuda M., Danno H., Tanaka Y., Hori S., Shiroguchi K., Takahashi M.:
"Pigmentation level of human iPSC-derived retinal pigment epithelium cell does not indicate a specific"
eLife 12 RP92510 (2024). - 3.
Takahashi S., Ochiai S., Jin J., Takahashi N., Toshima S., Ishigame H., Kabashima K., Kubo M., Nakayama M., Shiroguchi K., Okada T.:
"Sensory neuronal STAT3 is critical for IL-31 receptor expression and inflammatory itch"
Cell Reports 42 (12) 113433 (2023). - 4.
Jin J., Yamamoto R., Shiroguchi K.:
"High-throughput identification and quantification of bacterial cells in the microbiota based on 16S rRNA sequencing with single-base accuracy using BarBIQ"
Nature Protocols 19, 207 (2024). - 5.
Jin J.§, Ogawa T.§, Hojo N., Kryukov K., Shimizu K., Ikawa T., Imanishi T., Okazaki T., Shiroguchi K.: (§equally contributed)
"Robotic data acquisition with deep learning enables cell image-based prediction of transcriptomic phenotypes"
Proc. Natl. Acad. Sci. USA. 120 (1) e2210283120 (2023). - 6.
Cui G, Shimba A, Jin J, Ogawa T, Muramoto Y, Miyachi H, Abe S, Asahi T, Tani-Ichi S, Dijkstra JM, Iwamoto Y, Kryukov K, Zhu Y, Takami D, Hara T, Kitano S, Xu Y, Morita H, Zhang M, Zreka L, Miyata K, Kanaya T, Okumura S, Ito T, Hatano E, Takahashi Y, Watarai H, Oike Y, Imanishi T, Ohno H, Ohteki T, Minato N, Kubo M, Hollander GA, Ueno H, Noda T, Shiroguchi K, Ikuta K.:
"A circulating subset of iNKT cells mediates antitumor and antiviral immunity"
Sci. Immunol. 7, eabj8760 (2022). - 7.
Jin J., Yamamoto R., Takeuchi T., Cui G., Miyauchi E., Hojo N., Ikuta K., Ohno H., Shiroguchi K.:
"High-throughput identification and quantification of single bacterial cells in the microbiota"
Nat. Commun. 13, 863 (2022). - 8.
Zhang B., Vogelzang A., Miyajima M., Sugiura Y., Wu Y., Chamoto K., Nakano R., Hatae R., Menzies R.J., Sonomura K., Hojo N., Ogawa T., Kobayashi W., Tsutsui Y., Yamamoto S., Maruya M., Narushima S., Suzuki K., Sugiya H., Murakami K., Hashimoto M., Ueno H., Kobayashi T., Ito K., Hirano T., Shiroguchi K., Matsuda F., Suematsu M., Honjo T., Fagarasan S.:
"B cell-derived GABA elicits IL-10+ macrophages to limit anti-tumour immunity"
Nature 599, 471-476 (2021). - 9.
*Shiroguchi, K.*, Chin, H.F., Hannemann, D.E., Muneyuki, E., De La Cruz, E.M.*, Kinosita Jr. K.:
"Direct observation of the Myosin Va recovery stroke that contributes to unidirectional stepping along actin"
PLoS Biol. 9: e1001031 (2011) *Corresponding author. - 10.
*Shiroguchi K., Kinosita Jr. K.:
"Myosin V walks by lever action and Brownian motion"
Science, 316, 1208-1212 (2007).
Recent Research Results
Related Links
Lab Members
Principal investigator
- Katsuyuki Shiroguchi
- Team Director
Core members
- Wakako Oda
- Assistant
- Kaori Fukuhara
- Technical Staff I
- Reiko Yamamoto
- Technical Staff I
- Nozomi Hojo
- Research Scientist
- Yungyu Tsai
- Research Scientist