Ablation of Adar1 in myeloid cells imprints a global antiviral state in the lung and heightens early immunity against SARS-CoV-2 [scRNA-Seq]

Under normal homeostatic conditions, self double-stranded RNA (self-dsRNA) is modified by adenosine deaminase acting on RNA 1 (ADAR1) to prevent the induction of a type I interferon (IFN) mediated inflammatory cascade. Antigen presenting cells (APCs) sense pathogen associated molecular patterns (PAMPs), such as dsRNA, to activate the immune response. The impact of ADAR1 on the function of APCs and the consequences on immunity is poorly understood. Here, we show that ADAR1 deletion in CD11c+ APCs leads to: (i) a skewed myeloid cell compartment enriched in inflammatory cDC2s (inf-cDC2) like cells; (ii) enhanced numbers of activated tissue resident memory T cells (TRMs) in the lung; and (iii) the imprinting of a broad antiviral transcriptional signature across both immune and non-immune cells. Further the resulting changes can be partially reversed by blocking IFNAR1 signaling and promote early resistance against SARS-CoV-2 infection. Our study provides insight into the consequences of self-dsRNA sensing in APCs on the immune system in the context of viral challenge. Overall design: Given the impact of ADAR1 ablation in APCs on APC and T cell homeostasis, we sought to characterize the broader consequences of ADAR1 deficient APCs on the immune system. To this end, we combined the 10x Chromium Single Cell RNA sequencing (scRNAseq) platform with a FACS based enrichment strategy to uncover minor cell populations such as AMs and DCs . Single cell suspensions were stained with a panel of cell surface marker antibodies. Sorted T cells, alveolar macrophages (AMs), and CD11c+SiglecF- cells, and other immune cells were pooled at a ratio 15:15:5:65, respectively, and subjected to 10x single cell RNAseq.