Characterization of Dendritic Cell Subtypes in Human Cord Blood by Single-Cell Sequencing

Dendritic cells (DCs) are professional antigen-presenting cells (APCs). The key functions of DCs include engulfing, processing and presenting antigens to T cells and regulating the activation of T cells. There are two major DC subtypes in human blood: plasmacytoid DCs (pDCs) and conventional DCs (cDCs). To define the differences between the adult and infant immune systems, especially in terms of DC constitution, we enriched dendritic cells from human cord blood and generated single-cell RNA sequencing data from ~7,000 cells using the 10X Genomics Single Cell 3’ Solution. After incorporating the differential expression analysis method in our clustering process, we identified all known dendritic cell subsets. Interestingly, we also found a group of DCs with gene expression that was a mix of megakaryocytes and pDCs. Further, we verified the expression of selected genes at both the RNA level by PCR and the protein level by flow cytometry. This study further demonstrates the power of single-cell RNA sequencing in dendritic cell research. To acquire enriched DCs from cord blood mononuclear cells (CBMCs), we labeled T cells, B cells, NK cells and monocytes with the lineages-specific markers CD3, CD19, CD16 and CD14, respectively, followed by magnetic bead depletion. Then, we applied single-cell RNA sequencing on all lineage-negative cells.