Laboratory for Prediction of Cell Systems Dynamics | RIKEN BDR

Laboratory for Prediction of Cell Systems Dynamics

Team Leader

Katsuyuki ShiroguchiPh.D.

Photo of principal investigator

  • Location:Osaka / Quantitative Biology Buildings
  • E-mail:
    katsuyuki.shiroguchi[at]riken.jpPlease replace [at] with @.
  • Lab Website

Unraveling biological systems and contributing to medical sciences by a combination of biophysics and quantitative genomics.

Research Summary

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

Main Publications List

  • Zhang B, Vogelzang A, Miyajima M, et al.
    B cell-derived GABA elicits IL-10+ macrophages to limit anti-tumour immunity.
    Nature (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 of HIV-1-infected cells In Vivo.
    Cell Reports 32, 107887 (2020) doi: 10.1016/j.celrep.2020.107887
  • 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

All Publications