Distinct Transcriptomic Profiles in ART-Treated People with HIV Are Associated with NF-κB-regulated Gene Expression...

Despite effective antiretroviral therapy (ART), people with HIV (PWH) continue to experience elevated morbidity, potentially driven by persistent immune dysregulation. This study aimed to define transcriptomic heterogeneity in peripheral CD4+ T cells and identify immune signatures associated with clinical stratification in ART-treated PWH.

We analyzed transcriptomic and immunologic (plasma cytokine) data from a well-characterized cohort of ART-suppressed PWH to identify biologically meaningful subgroups.

Bulk RNA sequencing was performed on peripheral CD4+ T cells from 154 ART-treated PWH. Plasma levels of immune mediators were also quantified. We applied Pairwise Controlled Manifold Approximation (PaCMAP), a novel dimensionality reduction technique, to identify transcriptomic clusters and assessed their associations with clinical and immunological parameters, including CD4:CD8 ratio and cell-associated HIV DNA/RNA.

PaCMAP identified three distinct transcriptomic clusters among PWH. These clusters were enriched for differential expression of genes regulated by NF-κB, suggesting a role for chronic immune activation and inflammation. While clustering was not associated with HIV reservoir size, there was a modest association with CD4:CD8 ratio, a key marker of immune recovery. Additionally, plasma levels of IL-1β, TNF-α, and G-CSF differed across clusters, supporting a link between plasma cytokines and CD4+ T cell transcriptomic diversity.

Our findings define transcriptomic subgroups in ART-treated PWH that are characterized by NF-κB-driven gene expression and distinct inflammatory cytokine profiles. These immune signatures may serve as biomarkers for immunological stratification and provide insight into persistent immune dysfunction despite viral suppression.