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

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.