Persistent Activation of Monocytes/Macrophages and Cell Senescence in SIV-Infected Macaques on ART

Despite effective viral suppression with antiretroviral therapy (ART), people living with HIV (PLWH) experience persistent inflammation, immune dysfunction, and premature onset of cardiovascular and aging-related comorbidities. To define the underlying mechanisms, we performed longitudinal transcriptomic profiling in peripheral blood mononuclear cells (PBMCs) from a cohort of simian immunodeficiency virus (SIV)-infected rhesus macaques spanning four key stages: pre-infection, acute infection, short-term ART, and long-term ART. Bulk RNA sequencing revealed dynamic immune remodeling across infection and treatment. Acute SIV infection induced robust antiviral and inflammatory programs, with upregulation of interferon-stimulated genes (ISGs), IL-27, JAK/STAT, and NF-?B signaling, coupled with suppression of T- and B-cell activation pathways. Short-term ART effectively reversed these transcriptional perturbations, restoring adaptive immune gene expression and reducing innate antiviral responses to near-baseline levels. In contrast, chronic SIV infection on long-term ART maintained viral suppression but was characterized by reactivation of innate immune pathways, including TLR2/TLR4/MYD88, NF-?B, and inflammasome (NLRP3/NLRP12, caspase-1) signaling, along with sustained macrophage activation, platelet/coagulation signaling, and senescence-associated secretory phenotype. Protein analyses confirmed persistent CASPASE-1 and NF-?B activation in spleen tissue. Pathologic evaluation of a carotid artery from an SIV-infected, long-term ART–treated macaque revealed macrophage-rich plaques with p21? senescent cells with intraluminal thrombus formation, recapitulating key features of HIV-associated atherogenesis. Together, these findings demonstrate that while ART normalizes acute infection–induced immune dysregulation, chronic SIV infection sustains a chronic, macrophage- and TLR-driven inflammatory state linked to vascular injury and aging process regardless of long-term suppression of viremia. Targeting inflammasome, NF-?B, and senescence pathways may mitigate non-AIDS comorbidities in PLWH. Overall design: We randomly selected 4 animals from a previous cohort that had longitudinal PBMC samples collected at four key time-points: pre-SIV infection (day 0), 6 weeks post-SIV infection (acute SIV infection), after 2 months of short-term ART, and after one year (12 months and 20 months) of long-term ART, for RNA-seq analyses. This cohort effectively models the major stages of HIV infection in humans: 1) pre-infection, 2) acute HIV infection, 3) HIV infection on short-term ART treatment, and 4) chronic HIV infection on long-term ART treatment as seen in PLWH. Of note, the plasma samples from two of the animals in group 4 chronic HIV infection on long-term ART treatment were collected at two time points (12 months and 20 months), hence adding to 6 samples in that group. To comprehensively profile the dynamic transcriptomic changes in the PBMCs collected before and after SIV infection, with or without ART treatment, we conducted the bulk RNA-seq and performed six pairwise comparisons: 1) acute SIV-infection vs. baseline, 2) acute SIV-infection on short-term ART vs. acute SIV-infection, 3) acute SIV-infection on short-term ART vs baseline, 4) chronic SIV-infection on long-term ART vs acute SIV-infection, 5) chronic SIV-infection on long-term ART vs baseline, and 6) chronic SIV-infection on long-term ART vs chronic SIV-infection on short-term ART.