The Distribution of HIV DNA and RNA in Cell Subsets Differs in Gut and Blood of HIV-Positive Patients on ART: Implications for Viral Persistence

Abstract

Even with optimal antiretroviral therapy, human immunodeficiency virus (HIV) persists in plasma, blood cells, and tissues. To develop new therapies, it is essential to know what cell types harbor residual HIV. We measured levels of HIV DNA, RNA, and RNA/DNA ratios in sorted subsets of CD4+ T cells (CCR7+, transitional memory, and effector memory) and non-CD4+ T leukocytes from blood, ileum, and rectum of 8 ART-suppressed HIV-positive subjects. Levels of HIV DNA/million cells in CCR7+ and effector memory cells were higher in the ileum than blood. When normalized by cell frequencies, most HIV DNA and RNA in the blood were found in CCR7+ cells, whereas in both gut sites, most HIV DNA and RNA were found in effector memory cells. HIV DNA and RNA were observed in non-CD4+ T leukocytes at low levels, particularly in gut tissues. Compared to the blood, the ileum had higher levels of HIV DNA and RNA in both CD4+ T cells and non-CD4+ T leukocytes, whereas the rectum had higher HIV DNA levels in both cell types but lower RNA levels in CD4+ T cells. Future studies should determine whether different mechanisms allow HIV to persist in these distinct reservoirs, and the degree to which different therapies can affect each reservoir.

Measuring the latent reservoir in vivo

“…Therapy largely corrects this shift and results in redistribution of mostly CD45RO + memory T cells from the lymphoid tissue back to the circulation (5,88). The dense concentration of lymphoid cells promotes the cell-to-cell spread of HIV in anatomical compartments (89); consequently, the distribution of T cell subsets and the proportion of CD4 + lymphocytes that are latently infected may be higher in tissues than in the circulation (90,91). Thus, measurements of the latent reservoir from blood represent a population that must be cleared to achieve a cure, but this population is a small and unrepresentative portion of the total reservoir.…”

Pharmacologic HIV-1 Nef blockade promotes CD8 T cell–mediated elimination of latently HIV-1–infected cells in vitro

“…Furthermore, viral RNA is detectable in the plasma and cells by ultrasensitive assays despite ongoing therapy (46)(47)(48)(49) and multiply spliced HIV-1 viral msRNA such as that coding for Nef is readily detectable in the plasma of HIV-1-infected individuals with undetectable plasma viral load (12,50), suggesting that HIV-1 latency is not a state of complete transcriptional quiescence. Additionally, intensification of standard triple HAART therapy with the integrase inhibitor raltegtravir was shown to increase episomal DNA in fully suppressed individuals, indicative of ongoing HIV-1 transcription in the setting of HAART (51).…”

Exploring HIV latency using transcription profiling

“…Although much HIV latency research utilises in vitro models or cells from peripheral blood, prior work has highlighted differences between the gut and blood in the phenotype of infected T and non-T cells 12,13 . Furthermore, gut and blood compartments differ in levels of T cell activation and its relationship with HIV transcription 12 .…”