HIV infection reprogrammes CD4+ T cells for quiescence and entry into proviral latency

Abstract

Human immunodeficiency virus (HIV) persists in infected individuals despite effective antiretroviral therapy due to the rapid establishment of latent reservoirs, mainly composed of quiescent memory CD4+ T cells. The mechanisms governing latent reservoir formation remain poorly understood. Here, using single-cell RNA-seq and functional studies in human primary CD4+ T cell models, we show that HIV infection with reporter constructs and laboratory and patient-derived strains triggers transcriptomic remodelling, activating the p53 pathway and a quiescence programme mediated by Krüppel-like factor 2 (KLF2), a key quiescence regulator. Loss- and gain-of-function studies, including unbiased shRNA screens and confirmatory studies in CD4+ T cells from HIV+ donors, demonstrate that HIV infection drives KLF2 and p53 signalling, which downregulate MYC and proliferation pathways, resulting in proviral transcriptional silencing. This enhances latent reservoir formation in T cells, ensuring viral persistence. These findings present a mechanism for forming the latent HIV reservoir and broaden the repertoire of strategies through which viruses control host cells to their advantage. HIV infection triggers transcriptomic remodelling and a quiescence programme via KLF2 and the p53 pathway leading to proviral silencing.