Transcriptional and epigenetic control of Natural Killer cells during viral infection

Natural killer (NK) cells are circulating group 1 innate lymphocytes (ILCs) that play a critical role during herpesvirus infection in mice and humans1-3. Although historically categorized as innate immune cells, circulating and tissue-resident group 1 ILCs can exhibit memory responses to mouse cytomegalovirus (MCMV)-associated glycoproteins through expression of germline encoded activating receptors4-6. NK cells possess traits of adaptive immunity, such as memory formation. However, the molecular mechanisms by which NK cells persist to form memory cells are not well understood. In chapter 2, we used single cell RNA sequencing to identify two distinct effector NK cell (NKeff) populations following mouse cytomegalovirus (MCMV) infection. Ly6C- memory precursor NK cells displayed enhanced survival during the contraction phase in a Bcl2-dependent manner, and differentiated into Ly6C+ memory NK cells. MP NK cells exhibited distinct transcriptional and epigenetic signatures compared to Ly6C+ NKeff cells, with a core epigenetic signature shared with MP CD8+ T cells enriched in ETS1 and Fli1 DNA-binding motifs. Until recent years, studying gene function intrinsic to innate immune cell function was limited to Cre-inducible murine models. In order to increase the speed at which we can study gene function, we developed a novel method in Chapter 3 to study gene function in multiple innate immune cell linages during viral infection using a quick and robust protocol. Using this method, we were able to identify Fli1, a transcription factor, which controls memory precursor (MP) Natural Killer cell formation during viral infection. Fli1 was induced by STAT5 signaling ex vivo, and increased Bim levels in early effector NK cells following viral infection. Collectively, these results suggest that a NK cell-intrinsic checkpoint controlled by Fli1 limits MP NK formation by regulating early effector NK cell fitness during viral infection. In addition to transcriptional regulation, NK cells undergo dynamic chromatin remodeling during development and in response to viral infection6,7. However, the epigenetic regulators that are responsible for these genome-wide chromatin changes are unknown. In chapter 4, we identify ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX) as a critical regulator of the NK cell regulome. Deletion of UTX in NK cells results in global transcriptional changes and differences in chromatin accessibility at several gene loci involved in NK cell development, homeostasis, and effector function. Together, these results identify UTX as a critical epigenetic regulator of NK cells in mice. In summary, our work has developed a method for studying gene function in innate immune cells, identified novel transcriptional regulation of MP NK cells during memory NK cell formation and profiled epigenetic regulation of NK cell effector function during viral infection