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Single-Cell RNA-Seq Reveals New Dendritic Cell, Monocyte Subtypes

NEW YORK (GenomeWeb) – An international team led by researchers from the Broad Institute of MIT and Harvard have used single-cell RNA sequencing to identify six dendritic cell (DC) and four monocyte subtypes in human blood. Of these, three of the six DC subtypes were new and two of the four monocyte subtypes were new.

The team believes the identification of these new subtypes sheds light on these cells' role in tissues, inflammation, and disease. It could also help better pinpoint and refine therapeutic targeting using these cells. 

"Dendritic cells and monocytes play a central role in pathogen sensing, phagocytosis, and antigen presentation and consist of multiple specialized subtypes," the researchers wrote in the study published today in Science. "However, their identities and interrelationships are not fully understood."

To unravel the mystery of these cells' mechanics, the researchers collected fresh blood samples from healthy donors recruited from the Boston-based PhenoGenetic project — a resource for fresh and stored biological samples from 1,000 subjects aged 18 to 50 from different ethnic backgrounds — and the Newcastle community in UK.

The team isolated approximately 2,400 peripheral blood mononuclear cells (PBMCs) from samples by performing flow cytometry and fluorescence-activated cell sorting. Then they conducted single-cell RNA sequencing on the samples using the previously described Smart-Seq2 protocol, and analyzed the raw data to quantify gene expression levels. The researchers then performed a DC differentiation assay in culture to identify cell subsets. 

Based on their analysis, the team made several key findings: the identification of circulating CD100hiCD34int progenitors, which provide a well-defined cell type for generating DCs in vitro and for therapeutic targeting; a new strategy for isolating pure plasmacytoid DCs; their use of the DC atlas to understand blastic plasmacytoid dendritic cell neoplasm cells, which illustrate how single-cell analysis can pinpoint relationships of diseased cells to healthy cells;  and that susceptibility genes identified in previous human genetics association studies were expressed in the DCs and monocyte subsets defined in this study.

Overall, they noted, single-cell transcriptome profiling to deconvolute admixtures of cell types, reveal rare cell types, and elucidate complex relationships between cell types — "thus addressing limitations in the existing classification that relies on a small number of markers." 

However, the researchers did note that some DC and monocyte subtypes were likely missed, since "they do not express MHC class II at rest, can only be defined by non-RNA molecules, are distinguished by low-abundance transcripts, or are only present during inflammation, disease, or within tissues." They therefore conclude that future studies will need to address these issues in order for the community to build a comprehensive immune cell atlas.