In vivo detection of antisense HIV-1 transcripts in untreated and ART-treated individuals

Natural antisense transcripts (AST) are expressed in eukaryotes, prokaryotes, and viruses and can possess regulatory functions at the transcriptional and/or post-transcriptional levels. In vitro studies have shown that HIV-1 AST promote viral latency through epigenetic silencing of the proviral 5′ long terminal repeat. However, expression of AST in vivo has not been convincingly demonstrated. Here, we used single RNA template amplification and sequencing to demonstrate expression of AST in unstimulated PBMC collected from people with HIV-1 (PWH). Our results show that expression levels of AST could be higher during ART compared with untreated individuals and that clones of infected cells persisting under ART continue to express HIV AST. This study is the first to verify HIV-1 AST expression in vivo with sequencing, documenting AST presence without cellular activation and suggest its natural occurrence in PWH. These findings advance our understanding of HIV-1 persistence and underscore the need for larger studies to determine if targeting AST in viral reservoirs could lead to new approaches for the design of strategies towards achieving HIV remission without ART.