Global profiling of human blood ILC subtypes reveals that NK cells produce homeostatic cytokine amphiregulin and sheds light on HIV-1 pathogenesis

Abstract The interrelatedness of human blood innate lymphoid cell (ILC) subsets, and how they are perturbed by HIV-1, remains unclear. Transcriptional and chromatin profiling separated blood ILCs into ILC2s, ILCPs, one cluster that included CD56 dim and CD56 − NK cells, and CD56 hi NK cells that have features of both CD56 dim/– NK cells and ILCs. In contrast to mice, human NK cells expressed tissue repair protein amphiregulin (AREG), with greater production by CD56 hi NK cells than by ILCs. AREG was induced by TCF7/WNT signaling, IL-2, or IL-15, but not by inflammatory cytokines, and was inhibited by TGFB1, a cytokine elevated in people living with HIV-1. NK cell knockout of the TGFB1-stimulated WNT antagonist RUNX3 increased AREG production. In people living with HIV-1, AREG + NK cell percentage correlated with numbers of ILCs and CD4 + T cells, and correlated inversely with inflammatory cytokine IL-6. RNA-Seq showed increased antiviral gene expression in all ILC subsets from people who were HIV-1 viremic, and increased expression of anti-inflammatory gene MYDGF in CD56 hi NK cells from elite controllers. Functionally-defective CD56 − NK cells were increased in people living with HIV-1 in inverse correlation with CD56 dim NK cells, ILCs, and CD4 + T cells. Experiments with human PBMCs ex vivo and in humanized mice revealed that CD4 + T cells and their production of IL-2 prevented CD56 dim transition to CD56 − NK cells by activating mTOR, and, in people living with HIV-1, plasma IL-2 correlated with CD4 + T cell number but not with CD8 + T cells. These studies clarify how ILC subsets are interrelated and provide insight into how HIV-1 infection disrupts NK cells, including homeostatic functions of NK cells discovered here. Graphical Abstract