Cytomegalovirus Infection Drives Adaptive Epigenetic Diversification of NK Cells with Altered Signaling and Effector Function

The mechanisms underlying human natural killer (NK) cell phenotypic and functional heterogeneity are unknown. Here, we describe the emergence of diverse subsets of human NK cells selectively lacking expression of signaling proteins after human cytomegalovirus (HCMV) infection. The absence of B and myeloid cell-related signaling protein expression in these NK cell subsets correlated with promoter DNA hypermethylation. Genome-wide DNA methylation patterns were strikingly similar between HCMV-associated adaptive NK cells and cytotoxic effector T cells but differed from those of canonical NK cells. Functional interrogation demonstrated altered cytokine responsiveness in adaptive NK cells that was linked to reduced expression of the transcription factor PLZF. Furthermore, subsets of adaptive NK cells demonstrated significantly reduced functional responses to activated autologous T cells. The present results uncover a spectrum of epigenetically unique adaptive NK cell subsets that diversify in response to viral infection and have distinct functional capabilities compared to canonical NK cell subsets. •HCMV infection induces adaptive NK cell subsets with diversified signaling potential•Adaptive NK cells share molecular features of differentiation with CTLs•Adaptive NK cells lose the ability to kill autologous, activated immune cells•Gain of adaptive NK cell functions correlates with silencing of PLZF expression Cytomegalovirus infection can shape the NK cell receptor repertoire. Schlums, Cichocki, and colleagues dig deeper and demonstrate that cytomegalovirus infection induces a genome-wide epigenetic diversification of NK cell subsets, paralleling T cell differentiation and leading to changes in NK cell specificity and function.