Single-cell transcriptome profiling reveals immunological fitness of HIV long-term non-progressors

Long-term non-progressors (LTNPs) represent a valuable model to investigate immunological features associated with non-progression in chronic HIV infection. In this study, single-cell RNA sequencing was performed on peripheral blood mononuclear cells obtained from 12 individuals, including 4 LTNPs, 4 typical progressors (TPs), and 4 healthy donors (HDs). Compared with TPs, LTNPs exhibited a higher percentage of naive T cells, whereas TPs showed a higher percentage of CD8⁺ Effector-GNLY cells. LTNPs also exhibited lower gene-expression scores related to T-cell activation, cytotoxicity, inflammation, and interferon-alpha response across multiple effector-state T-cell subsets. GO enrichment analysis showed that compared with HDs and TPs, LTNPs exhibited downregulation of migration, translation, and antiviral response pathways in both CD4⁺ and CD8⁺ T cells, with upregulation of stress/inflammatory response and differentiation programs in CD4⁺ T cells and of immune differentiation/activation pathways in CD8⁺ T cells. High-dimensional weighted gene co-expression network analysis (hdWGCNA) further revealed higher module eigengene expression of innate and myeloid-related modules and lower expression of B-cell and cytotoxicity-related modules in LTNPs compared with TPs. Additionally, HIV-1 RNA⁺ cells were detected more frequently in TPs than in LTNPs and predominantly identified within CD4⁺ T cells. Together, these findings reveal a transcriptionally balanced and favorable immunological profile associated with non-progressive HIV infection and inform the design of immune-based strategies toward a functional HIV cure.IMPORTANCEUnderstanding molecular traits associated with natural control in LTNPs is critical for advancing HIV remission and cure strategies. Using single-cell RNA sequencing, we found that LTNPs had more naive T cells and fewer CD8⁺ effector-GNLY cells than typical progressors, along with lower activation, cytotoxicity, inflammation, and IFN-α scores across effector-state T-cell subsets. Differential expression and GO analyses showed predominant downregulation of migration, translation, and antiviral pathways, while preserving early activation markers. Co-expression network analysis revealed higher innate/immune-regulatory module activity and lower B-cell and cytotoxicity modules in LTNPs. HIV-1 RNA⁺ cells were detected less frequently in LTNPs and mainly detected in CD4⁺ T cells. These findings highlight balanced immune programs in LTNPs, which may inform strategies toward a functional HIV cure.