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Realization of cellomics to dive into the whole-body or whole-organ cell cloud

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Tissues, organs and organ systems are composed of interacting cells (the cellome). We discuss the emergence of an omics approach that we refer to as cellomics. It enables cellome-wide analysis in whole-organ or whole-body specimens, based on advanced three-dimensional imaging and image analysis technology. We think that cellomics will pave the way for the incorporation of cellular, intercellular and spatial information across millions of cells in our body.

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Fig. 1: The concept and possible workflow of cellomics.
Fig. 2: Application of cellomics.

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Acknowledgements

We thank T. Mano (OIST) and the Ueda lab members, particularly S. Harada, K. Yamaura and F. Kinoshita, for their advice in enhancing the manuscript. This study was supported by grants from the JST ERATO JPMJER2001 (to H.R.U.); JST CREST JPMJCR23B7 (to E.A.S.); MEXT QLEAP JPMXS0120330644 (to H.R.U.); JST Moonshot R&D JPMJMS2023 (to K.M.); AMED/MEXT JPMJER2001 (to H.R.U.); JP22ama221517, JP20gm6210027, JP21ak0101181 and JP21wm0425003 (to E.A.S.); the JSPS KAKENHI JP18H05270 (to H.R.U.), 20K06885 (to K.M.), 22H02824, 22H04926 and 23K20044 (to E.A.S.), and 20K16498 (to T.T.M.); grants-in-aid from the Human Frontier Science Program (to H.R.U.);Operating Costs Subsidies for Private Universities (to E.A.S.); Takeda Science Foundation, UTEC-UTokyo, Uehara Memorial Foundation and Nakatani Foundation (to E.A.S.).

Author information

Author notes

  1. These authors contributed equally: Tomoki T. Mitani, Etsuo A. Susaki.

Authors and Affiliations

  1. Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan

    Tomoki T. Mitani, Etsuo A. Susaki, Katsuhiko Matsumoto & Hiroki R. Ueda

  2. Department of Systems Biology, Graduate School of Medicine, Osaka University, Osaka, Japan

    Tomoki T. Mitani

  3. Department of Neurology, Graduate School of Medicine, Osaka University, Osaka, Japan

    Tomoki T. Mitani

  4. Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan

    Etsuo A. Susaki

  5. Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan

    Etsuo A. Susaki

  6. Department of Systems Pharmacology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan

    Katsuhiko Matsumoto & Hiroki R. Ueda

Authors
  1. Tomoki T. Mitani
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  2. Etsuo A. Susaki
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  3. Katsuhiko Matsumoto
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  4. Hiroki R. Ueda
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Contributions

E.A.S. and H.R.U. came up with the concept of cellomics. T.T.M. and E.A.S. prepared the manuscript and figures. K.M. and H.R.U. were involved in revising the content and manuscript.

Corresponding author

Correspondence to Hiroki R. Ueda.

Ethics declarations

Competing interests

CUBICStars Inc., which H.R.U. founded and where T.T.M., K.M. and E.A.S. are employed, has filed patents regarding CUBIC-HV and CUBIC-Cloud. The company also provides CUBIC-Cloud web services. H.R.U., E.A.S., T.T.M. and K.M. are co-inventors on patents and patent applications owned or filed by RIKEN covering the CUBIC reagents and/or MOVIE. E.A.S. receives collaboration funding from Kantum Ushikata Co., LTD., that is related to the development of devices for cellomics.

Peer review

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Nature Methods thanks Raju Tomer and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Mitani, T.T., Susaki, E.A., Matsumoto, K. et al. Realization of cellomics to dive into the whole-body or whole-organ cell cloud. Nat Methods 21, 1138–1142 (2024). https://doi.org/10.1038/s41592-024-02307-5

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