Extracellular vesicles carrying HIV-1 Nef induce long-term hyperreactivity of myeloid cells [ATAC-Seq]

A possible explanation for chronic inflammation in HIV-infected individuals treated with anti-retroviral therapy is hyperreactivity of myeloid cells due to a phenomenon called ‘trained immunity’. Here, we demonstrate that human monocyte-derived macrophages originating from monocytes initially treated with extracellular vesicles containing HIV-1 protein Nef (exNef), but differentiating in the absence of exNef, released increased levels of pro-inflammatory cytokines after lipopolysaccharide stimulation. This effect was associated with epigenetic changes related to inflammation and cholesterol metabolism pathways, upregulation of the lipid rafts, and was blocked by methyl-beta-cyclodextrin, statin, and by an inhibitor of the lipid raft-associated receptor IGF1R. Bone marrow-derived macrophages from exNef-injected mice, as well as from mice transplanted with bone marrow from exNef-injected animals, produced elevated levels of TNFalpha upon stimulation. These phenomena are consistent with exNef-induced trained immunity that may contribute to persistent inflammation and associated co-morbidities in HIV-infected individuals with undetectable HIV load. All analyzed samples are from primary human monocytes treated in vitro with EVs carrying (experimental samples) or not carrying (control samples) HIV-1 Nef. Cells were then differentiated into MDM for 6 days without EVs. MDM wre either used for ATAC-seq analysis, or stimulated with LPS and used for RNA-seq analysis. Replicates are included for some RNA-seq samples, no replicates for ATAC-seq samples.