Single-cell sequencing reveals NK cell dysregulation during chronic HIV infection and identifies transitional NK cell cytotoxicity related to HIV reservoir decay.

Abstract

Natural killer (NK) cells, as an integral component of the innate immune system, assume a pivotal role in combating viral infections. Our understanding of how human immunodeficiency virus (HIV) infection affects NK cell heterogeneity remains limited. We conducted single-cell RNA sequencing (scRNA-seq) on peripheral blood NK cells from five healthy controls and seventeen male people living with HIV (PLWH), both before and after antiretroviral therapy (ART). Biological sex was extracted from medical records, and gender identity was not collected. O-link proteomic analysis was employed to quantify alterations in plasma inflammatory cytokines. Cell-associated HIV-DNA was measured in CD4⁺ T cells. Among ten identified NK cell subsets, c7-Type I interferon (IFN)-responding cells were increased in untreated participants, correlating negatively with CD4⁺ T cell counts and positively with inflammation. The c3-CD56^dim NK-IRS2 subset, enriched in lipopolysaccharide (LPS) response genes, markedly declined and showed extensive transcriptional remodelling following HIV infection. Two proliferating NK cell subsets, c8-CD56^dim NK-STMN1 and c9-CD56^dim NK-MKI67, increased following HIV infection, enriched in S and G2/M phases cells, respectively, with distinct metabolic profiles. Notably, the cytotoxicity score of the c5-Transitional NK subset before ART was associated with HIV-DNA decline over time. Our findings offer a comprehensive understanding of the cellular and molecular heterogeneity of NK cell immune response during HIV infection and offer insights for NK cell-based immunotherapies. Supported by grants from the National Natural Science Foundation of China (No. 82371766, 82572006, 82101837, and 82271857).