Clonal lineage tracing reveals shared origin of conventional and plasmacytoid dendritic cells

Developmental origins of dendritic cells (DCs) including conventional DCs (cDCs, comprising cDC1 and cDC2 subsets) and plasmacytoid DCs (pDCs) remain unclear. We studied DC development in unmanipulated adult mice using inducible lineage tracing combined with clonal DNA “barcoding” and single-cell transcriptome and phenotype analysis (CITE-seq). Inducible tracing of Cx3cr1+ hematopoietic progenitors in the bone marrow showed that they simultaneously produce all DC subsets including pDCs, cDC1s, and cDC2s. Clonal tracing of hematopoietic stem cells (HSCs) and of Cx3cr1+ progenitors revealed clone sharing between cDC1s and pDCs, but not between the two cDC subsets or between pDCs and B cells. Accordingly, CITE-seq analyses of differentiating HSCs and Cx3cr1+ progenitors identified progressive stages of pDC development including Cx3cr1+ Ly-6D+ pro-pDCs that were distinct from lymphoid progenitors. These results reveal the shared origin of pDCs and cDCs and suggest a revised scheme of DC development whereby pDCs share clonal relationship with cDC1s. [Display omitted] •FlipJump allows Cre-inducible DNA barcoding and clonal cell tracing in naive mice•Lineage tracing reveals cDC and pDC development from Cx3cr1+ progenitors•DNA barcoding suggests shared clonal origin of pDC and cDC1 subsets•CITE-seq identifies a hierarchy of pDC development from Cx3cr1+ DC progenitors The origin and lineage affiliation of plasmacytoid dendritic cells (pDCs) remain controversial. Feng et al. show that pDCs originate from the same pool of bone marrow progenitors as conventional dendritic cells (cDCs) and are clonally related to the cDC1 subset of cDCs.