scRNA-Seq of negatively enriched NK cells 4 days post MCMV infection

Ly49G2+ NK cells mediate essential control of murine cytomegalovirus (MCMV) infection in mice which express the H-2Dk class I molecule. As a cognate ligand for specific Ly49G2 inhibitory receptor allotypes, H-2Dk also licenses Ly49G2+ NK cells in naïve and MCMV-infected mice. These findings suggest Ly49G2 may promote antiviral NK cell activities during MCMV infection. Indeed, in mice lacking the Ly49G2 receptor, MCMV resistance is fully abrogated. Additionally, NK cells expressing Ly49R, an NK cell associated activation receptor that also recognizes H-2Dk, have their function augmented by Ly49G2 and are required for MCMV resistance. Overall design: Since Ly49G2 promoted enhanced Ly49R+ NK cell effector responses during viral infection, we examined it's influence on NK cell gene expression day 4 PI. Single cell RNA sequencing (scRNA-Seq) was used to evaluate transcriptomic differences in single NK cells responding to MCMV across mouse strains expressing either, Ly49G2, H-2Dk or both. We also ascertained whether strain-specific differences in NK cell gene expression were simply due to different extrinsic signals based on host environment. scRNA-Seq analysis revealed that both extrinsic and intrinsic factors determined NK cell gene expression, such that expression of both receptor and ligand resulted in increased cell cycle regulation and proliferation during MCMV infection. In comparison, NK cells lacking self-MHC Dk recognition via Ly49G2 had significantly higher expression of inflammatory response pathways.