Cross-organ single-cell transcriptome profiling reveals macrophage and dendritic cell heterogeneity in zebrafish
Qiuxia Zhou,
Changlong Zhao,
Zhiyong Yang,
Rui Qu,
Yunbo Li,
Yining Fan,
Jinlin Tang,
Ting Xie,
Zilong Wen
Affiliations
Qiuxia Zhou
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Changlong Zhao
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Zhiyong Yang
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Rui Qu
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Yunbo Li
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Yining Fan
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Jinlin Tang
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Ting Xie
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China
Zilong Wen
Division of Life Science, State Key Laboratory of Molecular Neuroscience, the Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China; Greater Bay Biomedical Innocenter, Shenzhen Bay Laboratory, Shenzhen 518055, China; Department of Immunology and Microbiology, School of Life Science, Southern University of Science and Technology, Shenzhen 518055, China; Corresponding author
Summary: Tissue-resident macrophages (TRMs) and dendritic cells (DCs) are highly heterogeneous and essential for immunity, tissue regeneration, and homeostasis maintenance. Here, we comprehensively profile the heterogeneity of TRMs and DCs across adult zebrafish organs via single-cell RNA sequencing. We identify two macrophage subsets: pro-inflammatory macrophages with potent phagocytosis signatures and pro-remodeling macrophages with tissue regeneration signatures in barrier tissues, liver, and heart. In parallel, one conventional dendritic cell (cDC) population with prominent antigen presentation capacity and plasmacytoid dendritic cells (pDCs) featured by anti-virus properties are also observed in these organs. Remarkably, in addition to a single macrophage/microglia population with potent phagocytosis capacity, a pDC population and two distinct cDC populations are identified in the brain. Finally, we generate specific reporter lines for in vivo tracking of macrophage and DC subsets. Our study depicts the landscape of TRMs and DCs and creates valuable tools for in-depth study of these cells in zebrafish.
