Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity

The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of kidney in fish immune systems remain to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cell types from zebrafish kidney via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in kidney, suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system, and highlighted the multifaced biology of kidney in ancient vertebrates. ### Competing Interest Statement The authors have declared no competing interest. * SVCV : spring viremia of carp virus scRNA-seq : single-cell RNA sequencing HSPCs : hematopoietic stem and progenitor cells AID : activation-induced cytidine deaminase Igs : immunoglobulins APCs : antigen-presenting cells IFNs : interferons MAST : Model-based Analysis of Single-cell Transcriptomics DEs : dual expressers SHM : somatic hypermutation DCs : dendritic cells EPC : Epithelioma papulosum cyprinid CPE : cytopathic effect TCID50 : 50% tissue culture infective dose PCA : principal component analysis t-SNE : t-Distributed Stochastic Neighbor Embedding GO : Gene Ontology KEGG : Kyoto Encyclopedia of Genes and Genomes cDC : classical DC pDC : plasmacytoid DCs DEGs : differentially expressed genes BCG : Bacillus Calmette-Guerin HSCs : hematopoietic stem cells MPPs : multipotent progenitors CMLPs : common myeloid-lymphoid progenitors CMMEPs : common myeloid-megakaryocyte-erythroid progenitors MACS : magnetic-activated cell sorting RT-qPCR : quantitative real-time PCR.