Long-Term Elite Controllers of HIV-1 Infection Exhibit a Deep Perturbation of Monocyte Homeostasis

Elite controllers (ECs) represent a unique subset of people living with HIV (PLWHs), who can suppress viral replication without requiring antiretroviral therapy (ART). However, despite this viral control, ECs exhibit increased incidences of various comorbid conditions and heightened systemic inflammation, which has been linked to monocyte activation. In this study, we performed an in-depth phenotypic analysis of monocytes in a cohort of long-term ECs (LTECs) and compared them to non-controller patients with ART-mediated control of HIV replication and to non-controller patients with uncontrolled viral replication. A total of 67 participants were included: 22 LTECs, 15 non-controllers on ART (onART), 10 non-controllers without ART (offART), and 20 uninfected controls (UCs) as a reference group. Monocyte phenotypes were analyzed using spectral flow cytometry with a 13-marker panel. The data were analyzed using two approaches: (a) FCS Express software v.7 to define different subsets of monocytes and assess the levels of expression of eight different monocyte functional markers and (b) R software v.4.1.1 for unsupervised multidimensional analysis, including batch correction, dimensionality reduction, and clustering analysis. Monocyte phenotypic profiling was conducted using three different approaches: (1) assessment of monocyte subsets (classical, intermediate, and non-classical monocytes); (2) evaluation of the levels of expression of eight monocyte functional markers, and (3) characterization of monocyte clusters defined through the dimensionality reduction of flow cytometry data (56 different clusters). The monocyte phenotype of the onART group closely resembled that of the UC group. In contrast, LTECs exhibited important alterations in the monocyte phenotype compared to that of the UCs, including (a) an increased proportion of intermediate monocytes and a decreased proportion of classical monocytes (p < 0.01), (b) altered expressions of functional markers across monocyte subsets (p < 0.05), and (c) alterations in sixteen different monocyte clusters (twelve decreased and four increased, p < 0.05). Many of these alterations were also observed when comparing the LTEC and onART groups. Our findings suggest that monocyte-driven mechanisms may contribute to HIV control in LTECs; however, some of these alterations could also promote systemic inflammation and immune activation. These observations provide a compelling rationale for considering therapeutic interventions in this unique population of PLWHs.