Team Leader
Katsuyuki Shiroguchi
Ph.D.
Laboratory for Prediction of Cell Systems Dynamics
LocationOsaka / Quantitative Biology Buildings
E-mailkatsuyuki.shiroguchi[at]riken.jp
Please replace [at] with @.
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. Using this system, we would like to understand biological systems, and to contribute to medical sciences. 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 cells and diseases.
Research Theme
- Molecular barcodes for digital quantification of nucleic acid molecules
- Digital RNA sequencing (dRNA-seq)
- Novel bacterial microbiota analysis
- Combination of bio-imaging, sequencing, and machine learning
- Organoid studies
- Cell-Cell interaction
Selected Publications
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
