The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist

Abstract

The shock-and-kill strategy reactivates HIV-1 latent reservoir for immune clearance. Einkauf et al. found that some HIV-1-infected cells that persist and proliferate have transcriptionally active HIV-1 in permissive chromatin. Silent proviruses in repressive chromatin resist reactivation. Understanding HIV-1-chromatin interactions and how transcriptionally active HIV-1-infected cells survive is a pressing need.

Figure 1.. The impact of chromatin environment on HIV-1 expression, persistence, and clonal expansion dynamics

(A) PRIP-seq: parallel HIV-1 RNA, integration site, and proviral DNA analysis. Cells are plated at limiting dilution such that there is only one infected cell in a group of cells. HIV-1 RNA is separated from genomic DNA using HIV-1-specific biotinylated probes, reverse transcribed with the same probes, amplified, and measured by droplet digital PCR. Genomic DNA from cells in each well is amplified using phi29-mediated multiple displacement whole-genome amplification using universal primers and then used for HIV-1 integration site sequencing and HIV-1 proviral genome sequencing in separate aliquots. (B) The chromatin environment that determines gene expression is orchestrated by multiple levels of epigenetic regulators. The chromatin environment can be examined by chromatin conformation (by HiC), chromatin accessibility (by ATAC-seq), active versus repressive chromatin marks (by ChIP-seq), and DNA CpG methylation profiles (by bisulfite sequencing). (C) Host determinants of HIV-1 transcription and persistence in vivo. Despite ART, a substantial proportion (>25%) of HIV-1-infected cells harboring intact HIV-1 are transcriptionally active. The level of HIV-1 transcription is associated with the chromatin environment. Most transcriptionally active HIV-1-infected cells are eliminated by the immune selection pressure. However, some transcriptionally active HIV-1-infected cells harboring intact HIV-1 that reside in permissive chromatin can survive, persist, and proliferate despite long-term ART. Silent HIV-1 proviruses that reside in repressive chromatin resist latency reversal. Latency reversing agents may increase HIV-1 expression from already transcriptionally active HIV-1-infected cells but may not reactivate transcriptionally silent HIV-1-infected cells.