CD161 ⁺ CD4 ⁺ T Cells Harbor Clonally Expanded Replication-Competent HIV-1 in Antiretroviral Therapy-Suppressed Individuals

Abstract

The presence of an extremely stable latent reservoir of HIV-1 is the major obstacle to eradication, despite effective antiretroviral therapy (ART). Recent studies have shown that clonal expansion of latently infected cells without viral reactivation is an important phenomenon that maintains the long-term stability of the reservoir, yet its underlying mechanism remains unclear. Here we report that a subset of CD4+ T cells, characterized by CD161 expression on the surface, is highly permissive for HIV-1 infection. These cells possess a significantly higher survival and proliferative capacity than their CD161-negative counterparts. More importantly, we found that these cells harbor HIV-1 DNA and replication-competent latent viruses at a significantly higher frequency. By using massive single-genome proviral sequencing from ART-suppressed individuals, we confirm that CD161+ CD4+ T cells contain remarkably more identical proviral sequences, indicating clonal expansion of the viral genome in these cells. Taking the results together, our study identifies infected CD161+ CD4+ T cells to be a critical force driving the clonal expansion of the HIV-1 latent reservoir, providing a novel mechanism for the long-term stability of HIV-1 latency. IMPORTANCE The latent reservoir continues to be the major obstacle to curing HIV-1 infection. The clonal expansion of latently infected cells adds another layer maintaining the long-term stability of the reservoir, but its mechanism remains unclear. Here, we report that CD161+ CD4+ T cells serve as an important compartment of the HIV-1 latent reservoir and contain a significant amount of clonally expanded proviruses. In our study, we describe a feasible strategy that may reduce the size of the latent reservoir to a certain extent by counterbalancing the repopulation and dissemination of latently infected cells.

Longitudinal Analysis of Peripheral and Colonic CD161+ CD4+ T Cell Dysfunction in Acute HIV-1 Infection and Effects of Early Treatment Initiation

“…Collectively, these observations point towards the ability to be directly infected with HIV-1, and suggest a possible mechanism behind the depletion of CD161 + CD4 + T cells in the peripheral blood and colonic mucosa during AHI. This is supported by the inverse association between VL and the frequency of CD161 + CD4 + T cells in both peripheral blood and colonic mucosa in the present study, as well as previous studies, indicating their high susceptibility to HIV-1 infection in vitro [ 10 , 11 ]. However, in the ECHO cohort, pre-infection frequency of CD161 + CD4 + T cells in the peripheral blood were higher in participants that remained uninfected during the course of the study, compared to those that became HIV-infected.…”

“…CCR6 + CD4 + T cells are highly permissive to HIV-1 infection, and are depleted from peripheral blood during chronic HIV-1 infection (CHI) [ 9 ]. CD161 + CD4 + T cells are also depleted from peripheral blood during CHI, and are susceptible to infection by both CCR5 and C-X-C chemokine receptor (CXCR) 4-tropic viruses [ 10 , 11 ]. Furthermore, CD161 + CD4 + T cells are enriched in the healthy female genital tract, but are depleted in this tissue during CHI [ 12 ].…”

“…Furthermore, CD161 + CD4 + T cells are enriched in the healthy female genital tract, but are depleted in this tissue during CHI [ 12 ]. Recently, CD161 + CD4 + T cells were shown to harbor replication-competent HIV-1 clones in the peripheral blood [ 11 ], thus contributing to the latent viral reservoir. In SIV models, the depletion of peripheral CD161 + CD4 + T cells was linked to disease progression in rhesus macaques, while no depletion was observed in the natural SIV host, sooty mangabeys [ 13 ].…”

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

“…Next, we applied PP-SLIDE to characterize latent cells from HIV-infected individuals, using a CyTOF panel ( Supplementary file 1 ) that is directed at markers of the major subsets and differentiation states of CD4+ T cells and includes receptors and intracellular proteins associated with latency ( Banga et al, 2016 ; Buzon et al, 2014 ; Chomont et al, 2009 ; Descours et al, 2017 ; Fromentin et al, 2016 ; Hogan et al, 2018 ; Iglesias-Ussel et al, 2013 ; Khoury et al, 2016 ; Li et al, 2019 ; Serra-Peinado et al, 2019 ; Sun et al, 2015 ). Since reactivation events are rare and reducing background was key, we conjugated different anti-Gag antibodies to three different metal lanthanides and only considered cells displaying a Gag signal in all three channels as true events.…”

“…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 ). These and many other studies ( Cohn et al, 2020 ; Liu et al, 2020 ) have solidified the view that clonal expansion plays a major role in maintaining the long-lived HIV reservoir.…”