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MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution

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  • Till Fabian Mertens

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Alina Tabea Liebheit

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute
    Freie Universität Berlin)

  • Johanna Ehl

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Ralf Köhler

    (Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Asylkhan Rakhymzhan

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Andrew Woehler

    (Max Delbrück Center for Molecular Medicine
    Janelia Research Campus, Howard Hughes Medical Institute)

  • Lukas Katthän

    (Miltenyi Biotec B.V. and Co. Bertha-von-Suttner-Straße 5)

  • Gernot Ebel

    (Miltenyi Biotec B.V. and Co. Bertha-von-Suttner-Straße 5)

  • Wjatscheslaw Liublin

    (Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Ana Kasapi

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Antigoni Triantafyllopoulou

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

  • Tim Julius Schulz

    (German Institute of Human Nutrition (DIfE) Potsdam-Rehbruecke
    German Center for Diabetes Research (DZD))

  • Raluca Aura Niesner

    (Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute
    Freie Universität Berlin)

  • Anja Erika Hauser

    (Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin
    Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute)

Abstract

Analyzing immune cell interactions in the bone marrow is vital for understanding hematopoiesis and bone homeostasis. Three-dimensional analysis of the complete, intact bone marrow within the cortex of whole long bones remains a challenge, especially at subcellular resolution. We present a method that stabilizes the marrow and provides subcellular resolution of fluorescent signals throughout the murine femur, enabling identification and spatial characterization of hematopoietic and stromal cell subsets. By combining a pre-processing algorithm for stripe artifact removal with a machine-learning approach, we demonstrate reliable cell segmentation down to the deepest bone marrow regions. This reveals age-related changes in the marrow. It highlights the interaction between CX3CR1+ cells and the vascular system in homeostasis, in contrast to other myeloid cell types, and reveals their spatial characteristics after injury. The broad applicability of this method will contribute to a better understanding of bone marrow biology.

Suggested Citation

  • Till Fabian Mertens & Alina Tabea Liebheit & Johanna Ehl & Ralf Köhler & Asylkhan Rakhymzhan & Andrew Woehler & Lukas Katthän & Gernot Ebel & Wjatscheslaw Liublin & Ana Kasapi & Antigoni Triantafyllop, 2024. "MarShie: a clearing protocol for 3D analysis of single cells throughout the bone marrow at subcellular resolution," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-45827-6
    DOI: 10.1038/s41467-024-45827-6
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    References listed on IDEAS

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    1. Jingtan Zhu & Xiaomei Liu & Zhang Liu & Yating Deng & Jianyi Xu & Kunxing Liu & Ruiying Zhang & Xizhi Meng & Peng Fei & Tingting Yu & Dan Zhu, 2024. "SOLID: minimizing tissue distortion for brain-wide profiling of diverse architectures," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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