Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence

Understanding how HIV-1-infected cells proliferate and persist is key to HIV-1 eradication, but the heteroge-neity and rarity of HIV-1-infected cells hamper mechanistic interrogations. Here, we used single-cell DOGMA-seq to simultaneously capture transcription factor accessibility, transcriptome, surface proteins, HIV-1 DNA, and HIV-1 RNA in memory CD4+ T cells from six people living with HIV-1 during viremia and after suppressive antiretroviral therapy. We identified increased transcription factor accessibility in latent HIV-1-infected cells (RORC) and transcriptionally active HIV-1-infected cells (interferon regulatory transcription factor [IRF] and activator protein 1 [AP-1]). A proliferation program (IKZF3, IL21, BIRC5, and MKI67 co-expression) promoted the survival of transcriptionally active HIV-1-infected cells. Both latent and transcriptionally active HIV-1 -in-fected cells had increased IKZF3 (Aiolos) expression. Distinct epigenetic programs drove the heterogeneous cellular states of HIV-1-infected cells: IRF:activation, Eomes:cytotoxic effector differentiation, AP-1:migra-tion, and cell death. Our study revealed the single-cell epigenetic, transcriptional, and protein states of latent and transcriptionally active HIV-1-infected cells and cellular programs promoting HIV-1 persistence.

Automated summary

Understanding the proliferation and persistence of HIV-1-infected cells is crucial for eradicating HIV-1. By examining the transcription factor accessibility, transcriptome, surface proteins, HIV-1 DNA, and HIV-1 RNA of single CD4+ memory T cells, we identified specific transcription factor accessibility in latent and transcriptionally active HIV-1-infected cells. Additionally, a proliferation program was found to promote the survival of transcriptionally active HIV-1-infected cells. Different epigenetic programs were also involved in driving the heterogeneous cellular states of HIV-1-infected cells, including activation, cytotoxic effector differentiation, migration, and cell death.