Macrophage heterogeneity influences cellular response to HIV infection and latency modulation

HIV reservoirs persist in macrophages in people with HIV despite antiretroviral therapy, representing a barrier to cure. Factors that govern the establishment and reversal of HIV latency in different macrophage types remain poorly understood. An in vitro HIV latency model was used to investigate infection in human monocyte-derived macrophages (MDM), alveolar-like MDM (AlvMDM), and monocyte-derived microglia (MDMi). HIV infection and latency reactivation were similar between MDM and AlvMDM, while MDMi showed low susceptibility to HIV infection and minimal latent infection. Polarization of MDM and AlvMDM with M2-, but not M1-, inducing cytokines enhanced HIV reactivation, while TLR stimulation inhibited HIV reactivation in latently infected AlvMDM, but not MDM. Single-cell RNA-seq analysis identified nonproductively infected macrophages expressing HIV RNA transcripts, consistent with latently infected cells. Latently infected MDM and AlvMDM exhibited upregulated expression of genes encoding cell surface receptors, including MERTK and the immune checkpoint molecule CD137, respectively. Purification of nonproductively infected AlvMDM with high CD137 expression enriched for cells with higher HIV DNA content. Substantial differences were observed between macrophage types in both the extent and nature of transcriptional changes in response to latent and productive infection, with HIV infection having a greater impact on AlvMDM as compared to MDM. These findings highlight significant differences between macrophage types regarding their susceptibility to latency modulation and response to HIV infection. Further, we identify unique transcriptional changes in latently infected, monocyte-derived macrophages which differ by macrophage type. These findings have implications for the development of strategies to target latently infected tissue macrophages for HIV elimination.