HIV-1-mediated insertional activation of STAT5B and BACH2 trigger viral reservoir in T regulatory cells

Abstract

HIV-1 insertions targeting BACH2 or MLK2 are enriched and persist for decades in hematopoietic cells from patients under combination antiretroviral therapy. However, it is unclear how these insertions provide such selective advantage to infected cell clones. Here, we show that in 30/87 (34%) patients under combination antiretroviral therapy, BACH2, and STAT5B are activated by insertions triggering the formation of mRNAs that contain viral sequences fused by splicing to their first protein-coding exon. These chimeric mRNAs, predicted to express full-length proteins, are enriched in T regulatory and T central memory cells, but not in other T lymphocyte subsets or monocytes. Overexpression of BACH2 or STAT5B in primary T regulatory cells increases their proliferation and survival without compromising their function. Hence, we provide evidence that HIV-1-mediated insertional activation of BACH2 and STAT5B favor the persistence of a viral reservoir in T regulatory cells in patients under combination antiretroviral therapy.

Proviral sequencing suggests the majority of the HIV reservoir is expressed over time but significant decay is obscured by clonal expansion

“…This suggests that cell division contributed to the increase in intact proviruses, though we cannot rule out the contribution of a limited amount of viral replication without sequencing the integration sites. Evidence supporting a role for clonal expansion in proviral persistence has been mounting, including that infected effector memory (EM) T cells increase as KI67 positive cells become more prominent 41 and that monotypic virus increases over time on ART, as shown in our paper and others 32,[35][36][37][38]41,50,63 . Several studies have also shown identical sequences over time -consistent with clonal expansion of the "true" reservoir 32-38,41,50,63 36,64 .…”

“…We speculate that positive selection would be favored when a defective provirus inserts into an intron next to an oncogene exon, and LTR transcription occurs with minimal HIV protein expression. Splicing between a strong HIV donor site and an oncogene acceptor site could result in higher expression of an oncogene as recently described 63 . Our work advances the findings of Cesana by showing that unopposed strong donor splice sequences correlate with proviral expansion.…”

The Impact of Cellular Proliferation on the HIV-1 Reservoir

“…Their last finding was the most surprising of all. They demonstrated HIV could splice to downstream host genes including STAT5B [75], and in vitro experiments showed a preference for HIV-host chimeric transcripts spliced from SD4 [70].…”

“…Many HIV genomes from patients on ART have been found integrated into genes implicated in human cancer, most frequently BACH2, MDC1 [76,114,115], MKL2 [7,122], and in genes associated with cell growth and mitosis, including STAT5B, PARP8, DDX6, PKP4, and MAP4 [7,75,76,114,115]. One study found all of the integrations in BACH2 and MKL2 were in the sense orientation [115,122] and mapped to introns upstream of the transcription start site (TSS) [122].…”

HIV-1 promoter is gradually silenced when integrated into BACH2

“…An increase of BACH2 transcripts in 361 regulatory and effector T-cells were observed when HIV-1 was integrated in BACH2 (Cesana, 362 et al 2017). Enhanced expression of the wild-type BACH2 in regulatory T-cells leads to 363 increased proliferation capacity without affecting the cells' phenotype (Cesana, et al 2017).…”