CXCR4-Using HIV Strains Predominate in Naive and Central Memory CD4 ⁺ T Cells in People Living with HIV on Antiretroviral Therapy: Implications for How Latency Is Established and Maintained

Abstract

HIV can persist in people living with HIV (PLWH) on antiretroviral therapy (ART) in multiple CD4+ T cell subsets, including naive cells, central memory (CM) cells, transitional (TM) cells, and effector memory (EM) cells. Since these cells express different levels of the viral coreceptors CXCR4 and CCR5 on their surface, we sought to determine whether the HIV envelope protein (Env) was genotypically and phenotypically different between CD4+ T cell subsets isolated from PLWH on suppressive ART (n = 8). Single genome amplification for the HIV env gene was performed on genomic DNA extracts from different CD4+ T cell subsets. We detected CXCR4-using (X4) strains in five of the eight participants studied, and in these participants, the prevalence of X4 strains was higher in naive CD4+ T cells than in the memory subsets. Conversely, R5 strains were mostly found in the TM and EM populations. Identical sets of env sequences, consistent with clonal expansion of some infected cells, were more frequent in EM cells. These expanded identical sequences could also be detected in multiple CD4+ T cell subsets, suggesting that infected cells can undergo T cell differentiation. These identical sequences largely encoded intact and functional Env proteins. Our results are consistent with a model in which X4 HIV strains infect and potentially establish latency in naive and CM CD4+ T cells through direct infection, in addition to maintenance of the reservoir through differentiation and proliferation of infected cells. IMPORTANCE In people living with HIV (PLWH) on suppressive ART, latent HIV can be found in a diverse range of CD4+ T cells, including quiescent naive and central memory cells that are typically difficult to infect in vitro. It is currently unclear how latency is established in these cells in vivo. We show that in CD4+ T cells from PLWH on suppressive ART, the use of the coreceptor CXCR4 was prevalent among viruses amplified from naive and central memory CD4+ T cells. Furthermore, we found that expanded numbers of identical viral sequences were most common in the effector memory population, and these identical sequences were also found in multiple different CD4+ T cell subsets. Our results help to shed light on how a range of CD4+ T cell subsets come to harbor HIV DNA, which is one of the major barriers to eradicating the virus from PLWH.

Naive infection predicts reservoir diversity and is a formidable hurdle to HIV eradication

“…Although studying 2 uniform populations of HIV-infected individuals may have resulted in stronger levels of significance when comparing the level of clonality and naive infection, our approach provided additional insights revealing a continuum of reservoir size, and coreceptor tropism. We clearly found that those individuals with larger and predominant CXCR4-tropic reservoirs had more naive infection, consistent with a prior study ( 42 ), and more diverse reservoirs. This finding is reasonable because CXCR4-tropic viruses can directly infect naive T cells.…”

The Biology of the HIV-1 Latent Reservoir and Implications for Cure Strategies

“…HIV-1 persists in all subsets of memory CD4 + T cells, including the classic memory subsets (memory stem cells, central memory cells, transitional memory cells, and effector memory cells), and a variety of functional subsets (particularly T follicular helper cells, T regulatory cells, T helper 1 (Th1) cells, and Th17 cells). Although memory cells harbor the bulk of HIV proviral DNA during ART, naive cells can also contribute to HIV persistence (Roche et al, 2019;Venanzi Rullo et al, 2019). Cells that have intrinsic self-renewing capacity might prove to be the most recalcitrant source of virus during long-term ART.…”

Longitudinal analysis of subtype C envelope tropism for memory CD4+ T cell subsets over the first 3 years of untreated HIV-1 infection

“…When we analysed the percentage of infected cells per subset, we found EM cells were preferentially infected compared to other subsets. This preferential infection of EM cells is likely mediated through the higher expression of CCR5 on these cells [32,33,56]. However, while our data suggests that infection of different memory CD4 + T cell subsets is reliant on the level of CCR5 expression, we cannot rule out other factors known to contribute to viral tropism including enhanced CD4 usage or fusogenicity [57].…”