Background
For most people with HIV (PWH) on antiretroviral therapy (ART), cessation of ART results in rapid rebound of viremia. However, in rare individuals, called post-treatment controllers (PTCs), HIV is controlled through poorly understood mechanisms. The objective of this study was to leverage multiomics single-cell sequencing approaches to assess the extent to which the transcriptomic and epigenetic features of immune cells in PTCs differ between those non-controllers (NCs).
Methods
A total of 6 PTCs and 7 NCs were identified from the UCSF OPTIONS cohort. PTCs were defined as PWH who upon ART interruption maintained viral loads ≤400 copies/mL for at least two-thirds of the time points while off ART for ≥24 weeks. NCs, by contrast, were defined as PWH who upon ART interruption experienced viral rebound to viral loads exceeding 400 copies/mL within 24 weeks. We performed multiomics single-cell assay for transposase-accessible chromatin (scATAC) and single-cell RNA (scRNA) sequencing on PBMCs collected from these individuals immediately prior to their undergoing treatment interruption. As prior evidence suggests that Natural Killer (NK) cells influence the timing of viral rebound, our analysis specifically focused on these cells.
Results
Analysis of scRNA-seq data revealed 447 genes that were differentially expressed (p<0.05; |log2(fold change)|>0.5) in NK cells from PTCs compared to NCs. Genes involved in the NF-kappa-B signaling pathway, including NFKB1 and RELB, were significantly elevated (p<0.05; |log2(fold change)|>0.5) in NK cells from PTCs, in both the cytolytic CD56dimCD16+ and cytokine-producing CD56brightCD16- NK cell subsets. scATAC-seq analysis revealed increased accessibility of NF-kappa-B transcription factor family binding motifs in NK cells from PTCs, particularly within the CD56brightCD16- NK cell subset. Given the critical role of NF-kappa-B signaling in NK cell effector functions, these findings suggest that CD56brightCD16- NK cells from PTCs may be primed for heightened immune responses, including increased IFN-gamma production.
Conclusions
Upregulation of genes within the NF-kappa-B signaling pathway among PTCs suggests that highly functional NK cells could play a critical role in mediating ART-free control of HIV. Further investigation of how NF-kappa-B influences NK cell function and recognition of HIV-infected cells may inform the development of therapeutic strategies aimed at enhancing immune-mediated control of HIV.