High levels of genetically intact HIV in HLA-DR+ memory T cells indicates their value for reservoir studies

Abstract

Objective: The contribution of HLA-DR+ memory CD4+ T cells to the HIV reservoir during prolonged antiretroviral therapy is unclear as these cells are commonly excluded when assessing for replication-competent HIV. To address this issue, we examined the distribution of genetically intact HIV DNA within HLA-DR− and HLA-DR+ memory CD4+ T cells and the RNA transcriptional profile of these cells during antiretroviral therapy. Design/methods: Full-length DNA sequencing was used to examine the HIV DNA landscape within HLA-DR+ and HLA-DR− memory CD4+ T cells. RNA quantification and sequencing was used to interrogate the relationship between HLA-DR status and HIV RNA transcription. Results: HLA-DR+ CD4+ T cells contained a high frequency of genetically intact HIV genomes, contributing over half of the genetically intact viral sequences to the reservoir. Expansions of genetically identical sequences were identified in all T-cell subsets, indicating that cellular proliferation maintains genetically intact and defective viral DNA during therapy. Intracellular HIV RNA levels in HLA-DR+ and HLA-DR− T cells were not statistically different by either long terminal repeat quantitative PCR quantification or single-genome RNA sequencing of the p6-RT region. Conclusion: The high proportion of intact viral DNA sequences in the proliferative HLA-DR+ subset suggests they are critical in maintaining HIV infection during effective therapy. As such, these cells should be included in any immune intervention targeting HIV during effective therapy.

The multifaceted nature of HIV latency

“…The transition from an activated state to quiescence may offer a narrow window of opportunity that per-Although the HIV reservoir is usually defined as a pool of cells harboring replication-competent (and therefore intact) genomes, several lines of evidence indicate that defective proviruses, even if not capable of replication, have the ability to produce viral transcripts and viral proteins (45,46). Albeit indirectly, these defective genomes likely contribute to sustained inflammation and T cell activation even after prolonged ART (47,48), which may in turn contribute to HIV persistence by promoting the proliferation of infected T cells (49,50).…”

Relationship between CD4 T cell turnover, cellular differentiation and HIV persistence during ART

“…There are several limitations of our study that deserve comment. Since all of our analyses related to HLA-DR- CD4 subpopulations, events that occur during transient activation of cells in vivo (such as enhanced HIV transcription) were not recorded [ 69 , 70 ]. All of our observations were also restricted to circulating cells.…”

Phenotypic analysis of the unstimulated in vivo HIV CD4 T cell reservoir

“…The analysis of proviral sequences, on the other hand, has revealed differences in the frequencies of genome-intact provirus in different sorted subsets. For instance, sequencing of near full-length HIV provirus has identified Th1 and Tem, particularly those that are HLADR+, as subsets preferentially harboring intact viral genomes ( Hiener et al, 2017 ; Horsburgh et al, 2020 ; Lee et al, 2017 ). Viral sequencing has also revealed many intact proviruses within clonally expanded populations, particularly within the Tem and Th1 subsets, and those expressing Ox40 or CD161 ( De Scheerder et al, 2019 ; Hiener et al, 2017 ; Kuo et al, 2018 ; Lee et al, 2017 ; Li et al, 2019 ).…”