scRNA-seq of TNF receptor-deficient NK cells during Salmonella Typhimurium infection

Natural killer (NK) cell function is regulated by a balance of activating and inhibitory signals, however the role of tumor necrosis factor (TNF) on NK cells remains poorly understood. The goal of this study was to use single-cell RNA sequencing to delineate the transcriptional changes induced in NK cells by TNF signalling through either TNFR1 or TNFR2. Our findings highlight the different regulatory pathways induced by each receptor which play dichotomous roles on the outcome of NK cell function and anti-bacterial immunity. Overall design: We generated novel mouse models of NK specific TNF signalling deficiency by crossing Ncr1cre mice to either TNFR1 or TNFR2 flox mice. These mice, along with Ncr1cre used as WT controls, were infected with 5 x 10^6 Salmonella Typhimurium SL3261 by i.p. infection to induce systemic infection. At day four post infection, NK cells were isolated from mouse spleens. Each biological replicate (n = 3-4) were stained with TotalSeq HTO antibodies (Biolegend), pooled, and processed for 10x scRNA-seq.