Background
Despite early antiretroviral treatment (ART) initiation, persistent immunological alterations have been described in individuals treated during acute HIV infection (AHI). We performed longitudinal phenotypic and transcriptional profiling of peripheral blood mononuclear cells (PBMCs) after AHI to better understand the impact of early ART on cellular immune responses.
Methods
We conducted 26-color flow cytometry on matched PBMC samples (n=39) during AHI (T0, n=36), after a median of 0.76 years on suppressive ART (UD, n=36), and after a median of 1.99 years on ART (UD+1, n=26). Age-matched HIV-uninfected controls (HCs, n=21) were also included. Cells were clustered using FlowSOM. Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) was performed on a subset of participants at T0 (n=7), UD+1 (n=7), and HCs (n=7), using unsupervised weighted-nearest neighbor (WNN) clustering based on RNA and protein data to accurately define cell identities.
Results
Flow cytometric analysis revealed 30 PBMC metaclusters of CD4 T cells, CD8 T cells, γδ T cells, MAIT cells, NK cells, B cells, and monocytes. During AHI (T0), there was a proportional expansion of highly activated T cells and plasmablasts and contraction of naïve cells. Despite early ART initiation, the CD8 T cell proportion remained elevated during viral suppression, compared to HCs, with persistent activation and relative enrichment of CD8 TEMRA cells. CITE-seq confirmed the expansion of CD8 T cells with an exhausted and effector memory profile. Additionally, the proportion of non-classical monocytes exhibited a decrease during AHI that did not normalize with ART. Principal component analysis demonstrated that terminal differentiation of T cells and residual immune activation defined individuals treated during AHI compared to HCs. Flow cytometry particularly showed profound alterations in γδ T cells, including the rapid relative accumulation of γδ TEMRA T cells and persistent upregulation of activation markers. Differential gene expression analysis of γδ T cells revealed upregulation of genes involved in ER stress-induced apoptosis, T cell activation/transmigration, and IFN-γ secretion in early treated individuals (UD+1) compared to HCs.
Conclusions
Early ART initiation during acute HIV infection (AHI) does not fully prevent phenotypic and transcriptional changes in PBMCs. These immunological alterations might be linked to ongoing antiviral responses or persistent inflammation, highlighting the need for further research.