Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape

Abstract

SUMMARY Despite antiretroviral therapy, HIV-1 persists in memory CD4+ T cells creating a barrier to cure. The majority of HIV-1 proviruses are defective and considered clinically irrelevant. Using cells from HIV-1-infected individuals and reconstructed patient-derived defective proviruses, we show that defective proviruses can be transcribed into RNAs that are spliced and translated. Proviruses with defective major splice donors (MSDs) can activate novel splice sites to produce HIV-1 transcripts and cells with these proviruses can be recognized by HIV-1-specific cytotoxic T lymphocytes (CTLs). Further, cells with proviruses containing lethal mutations upstream of CTL epitopes can also be recognized by CTLs potentially through aberrant translation. Thus, CTLs may change the landscape of HIV-1 proviruses by preferential targeting cells with specific types of defective proviruses. Additionally, the expression of defective proviruses will need to be considered in the measurement of HIV-1 latency reversal.

Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells

“…We observed a significant decrease in levels of HIV DNA in the anti-CD3/CD28 plus HIV-specific CD8 + T cell clones (Figure proviruses, resulting in selection for proviruses with epitope deletions. These data are in line with previous reports that provide indirect evidence implicating CD8 + T cells in shaping the defective proviral landscape in vivo (29). Thus, we conclude that, under conditions of ex vivo latency reversal, HIV-specific CD8 + T cells can eliminate a subset of defective HIV proviruses, while intactinducible reservoirs resist CD8 + T cell-mediated killing.…”

“…Of note, we have recently demonstrated that a subset of defective proviruses is able to express viral antigens, resulting in recognition by HIV-specific CD8 + T cells (29). The magnitudes of the CD8 + T cell plus LRA-mediated reductions in HIV DNA observed in the current study, along with the lack of decreases in intact-inducible proviruses as measured by QVOA, were highly suggestive of preferential elimination of cells harboring defective proviruses.…”

“…Our second hypothesis is based on recent demonstrations that approximately 57% of cells harboring intact-inducible provirus are derived from expanded CD4 + T cell clones (20,21), as well as our own evidence that CD8 + T cell pressures shape this proviral landscape in individuals on ART (29). Based on these lines of evidence, we propose that reservoir-harboring cells may have been selected for those with some intrinsic resistance to CD8 + T cell-mediated killing.…”

“…The elimination of cells harboring defective HIV proviruses is needed to account for the magnitudes of these reductions, given that these outnumber intact proviruses by approximately 20 to 1 (52). This ties into our recent demonstration that antigen expression can be induced from a subset of defective HIV proviruses, allowing for recognition by CD8 + T cells (29). Note, however, that a considerable proportion of defective proviruses are not capable of expressing a given antigen, imposing limits on the degrees to which CD8 + T cells can reduce HIV DNA.…”

“…QVOAs rely on limiting dilutions of replicates of stimulated CD4 + T cells to calculate maximal likelihood estimates of infectious units per million cells (IUPM) (2,23,28). Furthermore, QVOAs strictly measure replication-competent virus, while HIV DNA, p24 antigen, or viral RNA assays may be confounded by the presence of defective proviruses (29,30). Upon treating ex vivo CD4 + T cells with combinations of CD8 + T cells and LRAs, we observed consistent reductions in levels of HIV DNA that, surprisingly, were not accompanied by reductions in infectious viral reservoirs as mea- Figure 2, A and C).…”