Novel Hexb-based tools for studying microglia in the CNS

An Author Correction to this article was published on 11 August 2020

This article has been updated


Microglia and central nervous system (CNS)-associated macrophages (CAMs), such as perivascular and meningeal macrophages, are implicated in virtually all diseases of the CNS. However, little is known about their cell-type-specific roles in the absence of suitable tools that would allow for functional discrimination between the ontogenetically closely related microglia and CAMs. To develop a new microglia gene targeting model, we first applied massively parallel single-cell analyses to compare microglia and CAM signatures during homeostasis and disease and identified hexosaminidase subunit beta (Hexb) as a stably expressed microglia core gene, whereas other microglia core genes were substantially downregulated during pathologies. Next, we generated HexbtdTomato mice to stably monitor microglia behavior in vivo. Finally, the Hexb locus was employed for tamoxifen-inducible Cre-mediated gene manipulation in microglia and for fate mapping of microglia but not CAMs. In sum, we provide valuable new genetic tools to specifically study microglia functions in the CNS.

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Fig. 1: scRNA-seq during de- and remyelination and FNX reveals Hexb as a stably expressed microglia core gene.
Fig. 2: Steady high expression of Hexb in microglia but not CAMs during homeostasis and autoimmune neuroinflammatory conditions.
Fig. 3: Generation and characterization of HexbtdTomato mice.
Fig. 4: Continuous detection of HexbtdT microglia during neurodegeneration and autoimmune demyelination.
Fig. 5: In vivo dynamics of HexbtdT microglia.
Fig. 6: Generation and comparative analysis of HexbCreERT2 mice.
Fig. 7: Fate mapping following CNS macrophage depletion using HexbCreERT2/CreERT2 R26yfp/yfp mice.
Fig. 8: Effects of Csf1r deletion on microglia but not CAMs.

Data availability

Raw data for new scRNA-seq or bulk RNA-seq have been deposited in the Gene Expression Omnibus, and are available at the following accession numbers: GSE148405 (scRNA-seq) and GSE148413 (bulk RNA-seq). All other data are published previously or are available from the corresponding authors on reasonable request.

Change history

  • 11 August 2020

    An amendment to this paper has been published and can be accessed via a link at the top of the paper.


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We thank E. Barleon for excellent technical assistance and the Center for Animal Resource and Development (CARD, Kumamoto University) for providing research material. T. Masuda was supported by the KANAE Foundation for the Promotion of Medical Science and the Japan Society for the Promotion of Science (JSPS) as the JSPS Postdoctoral Fellow for Research Abroad. M.P. was supported by the Sobek Foundation, the Ernst-Jung Foundation, the German Research Foundation (DFG) (grant nos. SFB 992, SFB1160, SFB/TRR167, Reinhart-Koselleck-Grant and the Gottfried Wilhelm Leibniz-Prize) and the Ministry of Science, Research and Arts, Baden-Wuerttemberg (Sonderlinie ‘Neuroinflammation’). This study was supported by the DFG under Germany’s Excellence Strategy (grant no. CIBSS—EXC-2189, Project ID390939984). J.P. was supported by the DFG (grant nos. SFB/TRR167 B05 and B07), and the UK DRI Momentum Award. C.B. was supported by the DFG (grant no. SFB/TRR167 B05).

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T. Masuda, L.A., P.E., M.L., N.S., T. Misgeld, R.S., O.S., M.J.C.J., C.B., K.K., D.G., A.V. and K.P.K. conducted experiments and analyzed the data. M.P., K.P.K., S.J., M.M.L. and J.P. analyzed the data, contributed to the in vivo studies and provided mice or reagents. T. Masuda and M.P. supervised the project and wrote the manuscript, J.P. edited the manuscript.

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Correspondence to Takahiro Masuda or Marco Prinz.

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Masuda, T., Amann, L., Sankowski, R. et al. Novel Hexb-based tools for studying microglia in the CNS. Nat Immunol 21, 802–815 (2020).

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