Non-Canonical Epigenetic Regulation of HIV Infection in Macrophage

Persistently infected macrophages serve as a long-term HIV reservoir and barrier to viral eradication, and also contribute to neurological complications in patients despite antiretroviral therapy (ART). To better understand the regulation of HIV in macrophages, we compared HIV infected human monocyte derived macrophages (MDM) to acutely infected primary CD4 T cells and Jurkat cell lines latently infected with HIV (JLAT). HIV genomes in MDM were actively transcribed despite enrichment with heterochromatin-associated H3K9me3 across the complete HIV genome in combination with elevated activation marks of H3K9ac and H3K27ac at the LTR. In contrast, JLAT showed conventional bivalent H3K4me3/H3K27me3 while CD4 showed an intermediate epigenotype. 5'-methylcytosine (5mC) was enriched across the HIV genome in latently infected JLAT cells, while 5'-hydroxymethylcytosine (5hmc) was enriched in CD4 and MDM. HIV infection induced multinucleation of MDMs along with DNA damage associate p53 phosphorylation, as well as loss of TET2 and the nuclear redistribution of 5-hydoxymethylation. RNA-seq analysis demonstrated that MDMs have a distinct transcriptional response to HIV persistent infection, including activation of CCL7, LAG3, and interferon signaling. Taken together, our findings suggest that HIV induces a unique macrophage nuclear and transcriptional profile, and viral genomes are maintained in a non-canonical bivalent epigenetic state. Overall design: RNA-seq of HIV-infected MDM and CD4 cells.