Transcriptomic signatures of immune suppression and cellular dysfunction distinguish latent from transcriptionally active HIV-1 infection in dendritic cells

Dendritic cells (DCs) are essential for antiviral immunity but are also susceptible to HIV-1 infection. Although sensing and restriction pathways in DCs are well described, the mechanisms underlying latent infection and its functional consequences remain unclear. Here, we performed transcriptomic profiling of monocyte-derived DCs harboring transcriptionally active (Active-HIV) or latent HIV-1 (Latent-HIV) proviruses using a dual-reporter virus. Gene set enrichment analysis revealed suppression of metabolic and stress-modulatory programs in Active-HIV compared to unexposed DCs. In contrast, Latent-HIV showed broad downregulation of pathways, including interferon and innate responses and metabolic programs, indicating a hyporesponsive and dampened antiviral state despite the absence of differentially expressed genes (DEGs). DEG analysis of Active-HIV versus Latent-HIV showed that active transcription associates with cellular stress, cytoskeletal remodeling, and RNA-processing. Functional analyses further demonstrated activation of RNA processes, suppression of antigen-presentation pathways, and altered membrane and cytoskeletal signaling in Active-HIV. These pathways suggest that transcriptionally active HIV-1 leverages cellular machinery to support replication, creating a metabolically strained yet immunologically engaged state that disrupts antigen presentation. Conversely, latently infected DCs display a hyporesponsive state consistent with proviral silencing. This dichotomy reveals distinct mechanisms of DC dysfunction that may facilitate HIV-1 persistence and immune evasion. Overall design: Primary monocyte-derived dendritic cells were infected with a VSV-G pseudotyped dual-reporter HIV-1 for five days. Transcriptionally active HIV-1-infected cells (MKO2+GFP+) and latently infected cells (MKO2+GFP-) were isolated by FACS. HIV-1-uninfected and -unexposed cells were included as controls.