Effect of FcRγ on gene expression profile of naïve and IL-15 treated NK cells

Here, we aimed to study the NK cell molecular signatures under the control of FcRγ and how these signatures are regulated by IL-15 and the tumour microenvironment (TME). To investigate this, we obtained purified splenic NK cells from naïve wild-type (WT) and FcRγ-deficient (FcRγ–/–, KO) mice cultured in the presence or absence of IL-15 for three days. To obtain NK cells from the TME, NK cells were purified from tumour-bearing lungs of WT and KO (FcRγ–/–) mice, which were intravenously injected with B16F10 cells two weeks earlier. Naïve NK cells (without any IL-15 treatment) were used as the control group. Next, we performed bulk RNA sequencing (RNA-seq) on six groups of NK cells for gene expression profiling: naive WT, naive KO (FcRγ–/–), IL-15-treated WT, IL-15-treated KO (FcRγ–/–), tumour WT, and tumour KO (FcRγ–/–). Bulk RNA-seq data were obtained from spleen derived NK cells from four experimental conditions (naïve WT, naïve KO, IL-15-treated WT, IL-15-treated KO), and tumour bearing lung derived NK cells from two experimental conditions (tumour WT and tumour KO). Each condition had four biological replicates each, therefore RNA-seq data were obtained from a total of 24 samples: splenic NK samples (n = 16) and NK samples isolated from tumour-bearing lung (n = 8).