Transcriptional basis of mouse and human dendritic cell heterogeneity revealed by single-cell profiling

Dendritic cells (DCs) play a critical role in orchestrating adaptive immune responses due to their unique ability to serve as a principal antigen-presenting cell type capable of initiating T cell responses. Classical dendritic cells have been divided into two subsets, cDC1 and cDC2, based on phenotypic markers and their distinct abilities to prime CD8 and CD4 T cells and direct their differentiation into effectors. Whilst the transcriptional features of the cDC1 subset have been well characterized, the heterogeneity of cDC2 and the development and function of distinct cell types comprising this subset remain poorly understood. Unbiased single-cell RNA sequencing analysis of DCs, combined with genetic reporter expression and fate-mapping revealed two principal cDC2 lineages, their developmental pathways and transcriptional regulators, including the expression of T-bet and RORt, two key transcription factors known to define functional adaptive and innate lymphocyte subsets. The cDC2 lineages were characterized by distinct metabolic and functional programs with phenotypic conservation observed across tissues. Extending the findings in mice to humans revealed conserved characteristics of DC heterogeneity and the presence of the newly defined DC subsets in human autoimmune disease and cancer. Single-cell RNA sequencing was performed on mouse and human splenic dendritic cells. Two samples of mouse dendritic cells were FACS purified based on Tbx21Cre-RFP reporter expression. Single-cell RNA sequencing was also performed on CD45-positive cells in melanoma tumors from two patients.