Single-cell RNA-Seq analysis reveals dual sensing of HIV-1 in blood Axl positive dendritic cells

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Flavien Brouiller, Francesca Nadalin, Ouardia Aït Mohamed, Pierre-Emmanuel Bonté, Constance Delaugerre, Jean-Daniel Lelièvre, Florent Ginhoux, Nicolas Ruffin, Philippe Benaroch

AbstractSensing of incoming viruses represents one of the pivotal tasks of dendritic cells (DC). Human primary blood DC encompass various subsets that are diverse in their susceptibility and response to HIV-1. The recent identification of Axl+DC, a new blood DC subset, endowed with unique capacities to bind, replicate, and transmit HIV-1 prompted us to evaluate its anti-viral response. We show that HIV-1 induced two main broad and intense transcriptional programs in different Axl+DC potentially induced by different sensors; a NF-κB-mediated program that led to DC maturation and efficient antigen-specific CD4+T cell activation, and a program mediated by STAT1/2 that activated type I IFN and an ISG response. These responses were absent from cDC2 exposed to HIV-1 except when viral replication occurred. Finally, Axl+DC actively replicating HIV-1 identified by quantification of viral transcripts exhibited a mixed NF-κB/ISG innate response. Our results suggest that the route of HIV-1 entry may dictate different innate sensing pathway by DC.