Global mRNA and chromatin accessibility profiling elucidate how HIV-1 perturbs ILC and NK cell subsets

HIV-1 infection is associated with depletion of gut ILC3s, blood ILC2s and conventional CD56dim natural killer (NK) cells, as well as with expansion of CD56-NK cells. These cell types derive from a common precursor (ILCP) yet their interrelationship remains unclear. Bulk and single cell RNA-Seq and ATAC-Seq showed that blood ILCs cluster into ILC2s, ILCPs, a mixed cluster of both CD56dimNK cells and CD56-NK cells, and a distinct cluster of CD56hiNK cells which shares features of both ILCs and CD56dimNK cells. In surprising contrast to mice, tissue repair factor AREG was produced by human NK cells, with even higher levels in CD56hiNK cells than in ILCs. AREG production was promoted by TCF7/WNT signaling and inhibited by TGFB1, a cytokine elevated in people living with HIV-1. Knockout of RUNX3, a WNT antagonist acting downstream of TGFB1, increased AREG production. Transcriptional profiling revealed that, when CD4+T cells were depleted, or when MTOR was inhibited, CD56dimNK cells shifted to become metabolically-defective CD56-NK cells; in either case, exogenous IL-2 prevented this transition. These findings establish the interrelatedness of ILC populations disrupted by HIV-1 infection and provide insight into how disruption of these cells contributes to chronic inflammation in people living with HIV-1.