Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

INTRODUCTION

Dendritic cells (DCs) and monocytes consist of multiple specialized subtypes that play a central role in pathogen sensing, phagocytosis, and antigen presentation. However, their identities and interrelationships are not fully understood, as these populations have historically been defined by a combination of morphology, physical properties, localization, functions, developmental origins, and expression of a restricted set of surface markers.

RATIONALE

To overcome this inherently biased strategy for cell identification, we performed single-cell RNA sequencing of ~2400 cells isolated from healthy blood donors and enriched for HLA-DR⁺ lineage⁻ cells. This single-cell profiling strategy and unbiased genomic classification, together with follow-up profiling and functional and phenotypic characterization of prospectively isolated subsets, led us to identify and validate six DC subtypes and four monocyte subtypes, and thus revise the taxonomy of these cells.

RESULTS

Our study reveals:

1) A new DC subset, representing 2 to 3% of the DC populations across all 10 donors tested, characterized by the expression of AXL, SIGLEC1, and SIGLEC6 antigens, named AS DCs. The AS DC population further divides into two populations captured in the traditionally defined plasmacytoid DC (pDC) and CD1C⁺ conventional DC (cDC) gates. This split is further reflected through AS DC gene expression signatures spanning a spectrum between cDC-like and pDC-like gene sets. Although AS DCs share properties with pDCs, they more potently activate T cells. This discovery led us to reclassify pDCs as the originally described “natural interferon-producing cells (IPCs)” with weaker T cell proliferation induction ability.

2) A new subdivision within the CD1C⁺ DC subset: one defined by a major histocompatibility complex class II–like gene set and one by a CD14⁺ monocyte–like prominent gene set. These CD1C⁺ DC subsets, which can be enriched by combining CD1C with CD32B, CD36, and CD163 antigens, can both potently induce T cell proliferation.

3) The existence of a circulating and dividing cDC progenitor giving rise to CD1C⁺ and CLEC9A⁺ DCs through in vitro differentiation assays. This blood precursor is defined by the expression of CD100⁺CD34^int and observed at a frequency of ~0.02% of the LIN^–HLA-DR⁺ fraction.

4) Two additional monocyte populations: one expressing classical monocyte genes and cytotoxic genes, and the other with unknown functions.

5) Evidence for a relationship between blastic plasmacytoid DC neoplasia (BPDCN) cells and healthy DCs.

CONCLUSION

Our revised taxonomy will enable more accurate functional and developmental analyses as well as immune monitoring in health and disease. The discovery of AS DCs within the traditionally defined pDC population explains many of the cDC properties previously assigned to pDCs, highlighting the need to revisit the definition of pDCs. Furthermore, the discovery of blood cDC progenitors represents a new therapeutic target readily accessible in the bloodstream for manipulation, as well as a new source for better in vitro DC generation. Although the current results focus on DCs and monocytes, a similar strategy can be applied to build a comprehensive human immune cell atlas.

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