Combined IL-12, IL-15 and IL-18 activation induces epigenetic changes in human NK cells during the memory-like state transition

Abstract

NK cells exhibit memory properties after activation with haptens, viral infection, or cytokines with each stimulus having distinct biology. Memory-like (ML) NK cells differentiate over one week after brief activation with combined IL-12/15/18, and have augmented responses upon restimulation by cytokines, activating receptor, or tumor targets. While much is known about their functional characteristics, there are large gaps in our understanding of the molecular mechanisms involved in programming conventional (c)NK cells into ML NK cells. As ML NK cells have enhanced ability to produce IFN-γ after multiple cell divisions, this suggests that the IFNG gene, and others, may be epigenetically poised. Therefore, we hypothesize that activation with IL-12/15/18 triggers epigenetic remodeling of cNK cells to ML NK cells that drives enhanced functionality. To test this, we performed ATAC-seq on baseline cNK cells, IL-12/15/18 activated NK cells, and in vitro differentiated cNK and ML NK cells after one week. Activation with IL-12/15/18 induces dramatic early epigenetic remodeling with >10,000 differentially accessible regions (DARs) compared to cNK cells. Moreover, ML differentiation generates epigenetically distinct ML NK cells (>1,000 DARs) compared to in vitro differentiated cNK cells, including increased IFNG locus accessibility, suggesting epigenetic mechanisms regulate their enhanced functionality. Also, ML NK cells are markedly different from IL-12/15/18 activated NK cells (>15,000 DARs) suggesting not all epigenetic changes are immediately induced, and time is required for full implementation of the memory-like state. Together, this supports that ML NK cells rely on epigenetic programming for enhanced function. Supported by grants from NIH (P50CA171963, R01CA205239, P30CA91842, 1F31GM146361-01).