Tissue‐specific differences in HIV DNA levels and mechanisms that govern HIV transcription in blood, gut, genital tract and liver in ART‐treated women

Abstract

Introduction: Sex-specific differences affect multiple aspects of HIV infection, yet few studies have quantified HIV levels in tissues from women. Since an HIV functional cure will likely require a major reduction of infected cells from most tissues, we measured total and intact HIV DNA and the HIV transcription profile in blood, gut, genital tract and liver from HIV-positive antiretroviral therapy (ART)-treated women. Methods: Peripheral blood mononuclear cells (PBMC) and biopsies from the gastrointestinal (ileum, colon, rectosigmoid +/liver) and genital (ectocervix, endocervix and endometrium) tracts were collected from 6 ART-treated (HIV RNA < 200 copies/mL) women. HIV DNA (total and intact) and levels of read-through, initiated (total), 5'elongated, polyadenylated and multiply spliced HIV transcripts were measured by droplet digital PCR. Immunophenotyping of cells was performed using Cytometry by time of flight (CyTOF). Results: We detected total HIV DNA in all tissues and intact HIV DNA in blood, ileum, colon, rectosigmoid and ectocervix. Initiated HIV transcripts per provirus were higher in PBMC and endometrium than in ileum, colon, rectosigmoid, ectocervix or endocervix, and higher in the rectum than either ileum or colon. 5'Elongated HIV transcripts per provirus were comparable in PBMC and endometrium, but higher than in gut or cervical samples. Polyadenylated and multiply spliced HIV transcripts were detected in PBMC (6/6 and 3/6 individuals respectively), but rarely in the tissues. Conclusions: These results suggest tissue-specific differences in the mechanisms that govern HIV expression, with lower HIV transcription in most tissues than blood. Therapies aimed at disrupting latency, such as latency-reversing or latency-silencing agents, will be required to penetrate into multiple tissues and target different blocks to HIV transcription.

HIV DNA persists in hepatocytes in people with HIV-hepatitis B co-infection on antiretroviral therapy

“…First, it is possible that all productively infected or transcriptionally active cells could have been cleared from the liver during ART, although this would be surprising, given that cell-associated HIV RNA was clearly detected in CD4+ T cells in blood on ART in this and many previous studies. 46 , 89 , 90 , 91 , 92 , 93 , 94 , 95 , 96 Second, the sensitivity of detection of HIV RNA in liver was greatly reduced compared to blood given the total cell numbers from liver biopsies were limited and we were also using whole liver biopsies, not sorted CD4+ T cells. Third, it is possible that the HIV DNA we detected in liver on ART was all defective and therefore transcription may not have been possible.…”

“…In vitro , HIV can directly infect hepatocytes, 13 , 16 , 19 , 20 , 21 , 22 , 23 Kupffer cells, 7 , 8 , 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 liver sinusoidal endothelial cells, 16 , 17 hepatic stellate cells, 18 and ex vivo , HIV DNA and/or RNA have been detected in liver biopsies from PWH off ART. 31 , 39 , 40 , 41 , 42 In studies of PWH on ART or non-human primates infected with either simian immunodeficiency virus (SIV) or a hybrid virus of SIV with an HIV envelope (SHIV) on ART who underwent autopsy, detection of HIV DNA or HIV RNA using quantitative (q)PCR or using in situ hybridisation has been reported in the liver at low but detectable levels in multiple studies, 43 , 44 , 45 , 46 however the location of infection within the liver has not been examined. Given that CD4+ T cells can be recruited to the liver during inflammation, 47 , 48 , 49 and that the liver is rich with blood in liver sinusoids, 50 detection of HIV DNA could potentially represent latently or productively infected CD4+ T cells and not true infection of liver cells.…”

Role of macrophages in HIV pathogenesis and cure: NIH perspectives

“…The role of cells of myeloid lineage as persistent reservoirs is an understudied area and needs further research. Mechanisms underlying viral persistence and latency vary among different tissues and therefore different approaches will be needed for the elimination of HIV from different sites 57–59 . Several initiatives and grant funding opportunities jointly supported by multiple NIH institutes, such as Basic Research on HIV Persistence (PAR‐14‐247), have supported research to better understand the mechanisms of HIV persistence, the dynamics of rebound, and mechanisms of viral suppression in the absence of ART, including studies of Elite Controllers and Post‐Treatment Controllers.…”

“…Mechanisms underlying viral persistence and latency vary among different tissues and therefore different approaches will be needed for the elimination of HIV from different sites. [57][58][59] Several ini- ART within 48hr of birth can achieve HIV remission. 60 Findings from such studies will provide novel insights and critical knowledge about HIV reservoir dynamics, composition of the reservoir, optimal timing of ART, and potential for ART-free remission that will inform the development of strategies to achieve long-term viral remission in children living with HIV.…”

“…61 Mechanisms underlying viral persistence varies between different tissues and therefore different approaches will be needed for the elimination of HIV from different sites. [57][58][59] The NIDDK's interest in research on HIV persistence is focused on understanding the processes leading to the establishment and persistence of important latent HIV reservoirs in multiple anatomical sites relevant to its mission, including the gut, adipose tissue, kidney, liver, and male genital tract 61 as well as in monocytes, macrophages, and other cell types residing within those tissues. Indeed, monocytes/macrophages may harbor a large portion of the gut reservoir.…”