An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development

Abstract

Abstract Classical type 1 dendritic cells (cDC1) are required for anti-viral and anti-tumor immunity, motivating a need to understand their development. We recently discovered that the development of the cDC1 progenitor requires an E protein-dependent +41 kb Irf8 enhancer, but its maturation instead requires a BATF3-dependent +32 kb Irf8 enhancer. To identify the genetic circuitry underlying this switch, we performed single-cell RNA-sequencing of the multipotent common dendritic cell progenitor (CDP). We found a cluster of cells within the CDP that already expressed transcription factors influencing cDC1 development, including Nfil3, Id2, and Zeb2. Genetic epistasis between these factors revealed a hierarchy of action in which Nfil3 expression is required for a transition from Zeb2hi and Id2lo CDPs into Zeb2lo and Id2hi CDPs, which represent the earliest committed cDC1 progenitors. This genetic circuit blocks E protein activity to exclude pDC potential within this progenitor and also explains the switch in Irf8 enhancer usage during cDC1 development.