Transcriptional identity and function of human dendritic cells is dictated by origin not tissue microenvironment

It has been well established that murine myeloid and plasmacytoid dendritic cells (DCs) derive from a separate hematopoietic precursor before they migrate via the blood stream to peripheral tissues. Moreover, two classes of murine conventional DCs (cDC1 and cDC2 DCs) and one class of plasmacytoid DCs (pDCs) were shown to be transcriptionally and functionally distinct entities. In humans, these DC subtypes have also been identified based on the cell surface markers CD1c (cDC2), CD141 (cDC1), and CD303 (pDCs), albeit it still remains elusive whether DC functionality is mainly determined by ontogeny or the tissue microenvironment. Moreover, an in-depth analysis of their transcriptome in different human tissues has not been established. By phenotypic and transcriptional profiling of these three DC subtypes in different human tissues derived from a larger number of human individuals, we here demonstrate that DC subpopulations – in contrast to macrophages – are more strongly defined by ontogeny rather than their localization. We provide a compendium of novel markers distinguishing DCs in different human tissues. Furthermore, bioinformatical modeling revealed a network of DC subtype-specific transcriptional regulators (TRs). Particularly CD141+ DCs were underrepresented in previous data as determined by gene set enrichment analysis using ImmuneSigDB signatures. Collectively, the data provided in this study should serve the community as a rich resource guiding further studies into human DC biology during homeostasis and inflammation. Single cell suspensions were generated from freshly isolated human tissues, namely blood, spleen and thymus; subpopulations of each 10.000 cells CD1c+ DCs, CD141+ DCs, pDCs, CD3+CD4+ T cells, CD3+CD8+ T cells, CD19+CD20+ B cells, and CD14+CD11b+ monocytes were FACS sorted and cells were directly snap frozen upon sorting. RNA preparation, super amplification and RNA quality control, and hybridization onto Whole Human Genome Oligo Microarray Agilent 8X60K was performed by Miltenyi Biotech (Bergisch-Gladbach, Germany)