Single-cell analysis of signalling and transcriptional responses to type I interferons

Abstract Type I interferons (IFNs) play crucial roles in antiviral defence, autoinflammation and cancer immunity. The human genome encodes 17 different type I IFNs that all signal through the same receptor. Non-redundant functions have been reported for some type I IFNs. However, whether different type I IFNs induce different responses remains largely unknown. Here, we stimulate human peripheral blood mononuclear cells (PBMCs) with recombinant type I IFNs to address this question in multiple types of primary cells. We analyse signalling responses by mass cytometry and changes in gene expression by bulk and single-cell RNA sequencing. We find cell-type specific changes in the phosphorylation of STAT transcription factors and in the gene sets induced and repressed upon type I IFN exposure. We further report that the magnitude of these responses varies between different type I IFNs, while qualitatively different responses to type I IFN subtypes are not apparent. Taken together, we provide a rich resource mapping signalling responses and IFN-regulated genes in immune cells.