Distinct Transcriptomic Profiles in ART-Treated People with HIV Are Associated with NF-κB–regulated Gene Expression and Inflammatory Cytokine Signatures

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