Natural Killer Cell Receptors and Ligands Are Associated With Markers of HIV-1 Persistence in Chronically Infected ART Suppressed Patients.

Geoffrey T Ivison,John W Mellors,Elena Vendrame,Mary Carrington,Deborah K Mcmahon,Ronald J Bosch,Catherine A Blish,Giovanny J Martínez-Colón,Rosemary Vergara,Maureen P Martin,Nancy Q Zhao,Susan Holmes,Joshua C Cyktor,Joseph Eron,Sean C Bendall,R Brad Jones,Rajesh T Gandhi,Thanmayi Ranganath

doi:10.3389/fcimb.2022.757846

Abstract

The latent HIV-1 reservoir represents a major barrier to achieving a long-term antiretroviral therapy (ART)-free remission or cure for HIV-1. Natural Killer (NK) cells are innate immune cells that play a critical role in controlling viral infections and have been shown to be involved in preventing HIV-1 infection and, in those who are infected, delaying time to progression to AIDS. However, their role in limiting HIV-1 persistence on long term ART is still uncharacterized. To identify associations between markers of HIV-1 persistence and the NK cell receptor-ligand repertoire, we used twin mass cytometry panels to characterize the peripheral blood NK receptor-ligand repertoire in individuals with long-term antiretroviral suppression enrolled in the AIDS Clinical Trial Group A5321 study. At the time of testing, participants had been on ART for a median of 7 years, with virological suppression <50 copies/mL since at most 48 weeks on ART. We found that the NK cell receptor and ligand repertoires did not change across three longitudinal samples over one year—a median of 25 weeks and 50 weeks after the initial sampling. To determine the features of the receptor-ligand repertoire that associate with markers of HIV-1 persistence, we performed a LASSO normalized regression. This analysis revealed that the NK cell ligands CD58, HLA-B, and CRACC, as well as the killer cell immunoglobulin-like receptors (KIRs) KIR2DL1, KIR2DL3, and KIR2DS4 were robustly predictive of markers of HIV-1 persistence, as measured by total HIV-1 cell-associated DNA, HIV-1 cell-associated RNA, and single copy HIV-RNA assays. To characterize the roles of cell populations defined by multiple markers, we augmented the LASSO analysis with FlowSOM clustering. This analysis found that a less mature NK cell phenotype (CD16+CD56dimCD57-LILRB1-NKG2C-) was associated with lower HIV-1 cell associated DNA. Finally, we found that surface expression of HLA-Bw6 measured by CyTOF was associated with lower HIV-1 persistence. Genetic analysis revealed that this was driven by lower HIV-1 persistence in HLA-Bw4/6 heterozygotes. These findings suggest that there may be a role for NK cells in controlling HIV-1 persistence in individuals on long-term ART, which must be corroborated by future studies.

Highlights

For over two decades, it has been possible for patients to achieve undetectable HIV-1 viral loads, using modern anti-retroviral therapies (ART) (Perelson et al, 1997)
CADNA and cell-associated HIV-1 RNA (CA-RNA) values per million CD4+ T- cells were calculated by dividing the total HIV-1 DNA or RNA copies/ million peripheral blood mononuclear cells (PBMCs) [normalized for CCR5 copies measured by quantitative PCR (qPCR) as published (Hong et al, 2016)] by the CD4+ T-cell percentage (x 0.01) reported from the same specimen date or from a CD4+ T-cell percentage imputed using linear interpolation from specimen dates before and after the Cell-associated HIV-1 DNA (CA-DNA) or CARNA results
Regimens at time of ART initiation were non-nucleoside reverse transcriptase inhibitor (NNRTI)-based in 42%, protease inhibitor (PI)- based in 34% and integrase strand transfer inhibitor (InSTI)-based in 18%

Summary

Introduction

It has been possible for patients to achieve undetectable HIV-1 viral loads, using modern anti-retroviral therapies (ART) (Perelson et al, 1997). Numerous studies since have demonstrated that patients who are able to strictly adhere to their ART regimens and maintain viral suppression represent negligible risk for sexual transmission of HIV-1 (LeMessurier et al, 2018). While this represents a tremendous victory for public health, it is not yet a complete success. Rapid post-exposure prophylaxis is able to limit the establishment of this latent reservoir (Sultan et al, 2014; Bamford et al, 2017; Iloanusi et al, 2019), once established it becomes extremely tenacious with an estimated half-life of between 4-13 years with consistent ART treatment (Siliciano et al, 2003; Gandhi et al, 2017). Eliminating the latent HIV-1 reservoir remains the major barrier to achieving an HIV-1 long-term remission or cure

Methods

Results

Conclusion