Single-cell transcriptional landscapes reveal HIV-1–driven aberrant host gene transcription as a potential therapeutic target

Abstract

<jats:p>Understanding HIV-1–host interactions can identify the cellular environment supporting HIV-1 reactivation and mechanisms of clonal expansion. We developed HIV-1 SortSeq to isolate rare HIV-1–infected cells from virally suppressed, HIV-1–infected individuals upon early latency reversal. Single-cell transcriptome analysis of HIV-1 SortSeq<jats:sup>+</jats:sup> cells revealed enrichment of nonsense-mediated RNA decay and viral transcription pathways. HIV-1 SortSeq<jats:sup>+</jats:sup> cells up-regulated cellular factors that can support HIV-1 transcription (<jats:italic>IMPDH1</jats:italic> and <jats:italic>JAK1</jats:italic>) or promote cellular survival (<jats:italic>IL2</jats:italic> and <jats:italic>IKBKB</jats:italic>). HIV-1–host RNA landscape analysis at the integration site revealed that HIV-1 drives high aberrant host gene transcription downstream, but not upstream, of the integration site through HIV-1–to–host aberrant splicing, in which HIV-1 RNA splices into the host RNA and aberrantly drives host RNA transcription. HIV-1–induced aberrant transcription was driven by the HIV-1 promoter as shown by CRISPR-dCas9–mediated HIV-1–specific activation and could be suppressed by CRISPR-dCas9–mediated inhibition of HIV-1 5′ long terminal repeat. Overall, we identified cellular factors supporting HIV-1 reactivation and HIV-1–driven aberrant host gene transcription as potential therapeutic targets to disrupt HIV-1 persistence.</jats:p>

Antigen-driven clonal selection shapes the persistence of HIV-1 infected CD4+T cellsin vivo

“…Strikingly, all four proviruses in BACH2 were in the same orientation relative to host gene transcription and upstream of the BACH2 translation start site, similar to 55 BACH2 integrants identified previously. Moreover, despite defects including deletions and/or inversions ( Figure 3A,), these proviruses retained the 5' LTR and splicing donor sequences required to generate LTR-driven chimeric transcripts (48,49). Similarly, the two proviruses in STAT5B were in the same orientation as STAT5B in intron 1, upstream of the translation start site, as with 42 of 57 proviruses previously described.…”

Filgotinib suppresses HIV-1–driven gene transcription by inhibiting HIV-1 splicing and T cell activation

“…We used a cell line model (HIV-1-infected Jurkat clone 8B10) in which HIV-1-dsGFP reporter is integrated into the intron of a proliferation-related proto-oncogene, VAV1 (71). Integration into VAV1 is associated with clonal expansion of the HIV-1-infected cells in HIV-1-infected individuals (72) and in lentivirus-transduced CAR T cells (73), suggesting that integration into VAV1 is a clinically relevant mechanism driving integration site-dependent proliferation in vivo.…”

“…Filgotinib suppresses HIV-1-driven aberrant host gene transcription. The hallmark of HIV-1-driven aberrant host gene transcription at the integration site is HIV-1-to-host RNA splicing and high levels of host gene transcription downstream but not upstream of the HIV-1 integration site (71). In this event, the host gene transcription is controlled by HIV-1 promoter activity, not host immune homeostasis.…”

“…In this event, the host gene transcription is controlled by HIV-1 promoter activity, not host immune homeostasis. When HIV-1 proviruses are integrated into proliferation-related genes, HIV-1-driven aberrant host gene transcription leads to excessive and unchecked proliferation of gene expression as a mechanism for HIV-1 integration site-dependent proliferation (71). We hypothesized that inhibition of HIV-1 transcription or splicing by HIV-1-suppressing agents can disrupt HIV-1-driven aberrant host gene transcription.…”

“…Despite the essential role of RNA splicing (32,108,109) in HIV-1 life cycle and pathogenesis, little is known about how targeting HIV-1 RNA splicing can be applied as a therapeutic strategy in the context of HIV-1 persistence (110). Studies have shown that HIV-1 splicing and HIV-1-induced aberrant splicing are associated with HIV-1 persistence (71,111,112), which makes RNA splicing an important potential therapeutic target. In contrast to traditional differential gene expression analysis, which identifies a list of upand downregulated genes, we broadened transcriptome analysis into qualitative visualization of the RNA transcription landscape.…”