Scientists claim HIV-1 regularly mutates to avoid attack by natural killer (NK) cells. A team identified inhibitory killer immunoglobulin-like receptor (KIR)-associated polymorphisms in the HIV-1 sequences of chronically infected patients, which enhance the binding of inhibitory KIRs to HIV-1-infected CD4+ T cells and reduce the antiviral activity of KIR-positive NK cells.
The results suggest KIR-positive NK cells can place immunological pressure on HIV-1, which the virus has to evade by selecting for sequence polymorphisms. The team, led by researchers at the Ragon Institute of Massachusetts General Hospital (MGH), MIT, and Harvard, report their findings in Nature. The paper is titled “HIV-1 adaptation to NK-cell-mediated immune pressure.”
Research has also shown that NK cells can suppress HIV replication in cultured tissues. Studies also suggest that infected patients with certain KIR variants on their NK cells are better able to control HIV viral levels. What is not yet known is whether KIR variants allow NK cells to control HIV replication through direct recognition of infected cells or through an indirect mechanism.
To investigate this further, the Ragon Institute researchers looked for mutations in HIV proteins recognized by KIRs, in a population of 91 individuals with chronic, untreated HIV-1 infection. They identified 22 positions in the HIV-1 genome at which amino acid polymorphisms were significantly associated with the presence of a specific KIR gene.
One particular region was selected for further analysis because it encodes an overlapping segment spanning one end of the Vpu gene and the other end of Env gene, and the polymorphisms were present at significantly higher frequencies in individuals possessing at least one copy of the KIR2DL2 gene than in patients without this KIR variant.
To determine the functional consequences of these KIR2DL2-associated polymorphisms in Vpu and Env, the researchers constructed HIV-1 viral variants that encoded either the Vpu and Env-spanning polymorphism present in the KIR2DL2+ individuals (Vpu-EnvV/V) or the equivalent sequence (Vpu-EnvWT/WT) found in KIR2DL2- individuals.
There was no difference in terms of the ability of either strain to replicate in CD4+ T cells in vitro. CD4+ T cells infected with the two strains were next co-cultured with autologous NK cells derived from KIR2DL2+ or KIR2DL2- HIV-1-negative individuals. While both viruses replicated well in the presence of KIR2DL2- NK cells, the Vpu-EnvWT/WT virus was markedly inhibited by NK cells derived from KIR2DL2+ but not KIR2DL2- subjects.
“Thus, the Vpu–EnvV/V virus, which contains polymorphisms that were strongly associated with the presence of KIR2DL2 on the population level, was not inhibited by KIR2DL2+ NK cells in vitro, whereas the wild-type variant that was rarely observed in KIR2DL2+ individuals was strongly inhibited by KIR2DL2+ NK cells, consistent with the selection of Vpu–EnvV/V viruses in KIR2DL2+ individuals,” the authors note.
Further studies evaluating the activation of NK cells in vitro after stimulation with autologous CD4+ cells infected with either the Vpu-EnvWT/WT virus, or the Vpu-EnvV/V virus, suggested a mechanistic model by which the inhibitory NK cell receptor KIR2DL2 does not bind to cells infected with HIV-1 strains containing the Vpu-EnvWT/WT sequence but can bind to cells infected with Vpu-EnvV/V.
This binding then provides a strong inhibitory signal that protects the virus from lysis by NK cells. The actual binding of KIR2DL2 to CD4+ cells infected with the Vpu-EnvV/V strain was confirmed using a KIR2DL2-IgG fusion construct. Significantly, binding of a fusion construct of KIR2DL3 (an allele at the same locus as KIR2DL2) was not affected by the KIR2DL2-associated polymorphism.
Two additional amino-acid polymorphisms were associated with the presence of the KIR2DL2 gene in the same study population. Equivalent studies with viruses engineered to carry these polymorphisms yielded similar results in terms of differential recognition of HIV-1-infected cells by KIR2DL2+ NK cells.
“Taken together, these data demonstrate that HIV-1 may evolve in KIR2DL2+ individuals to enrich particular amino-acid polymorphisms in an effort to escape recognition by KIR2DL2+ NK cells,” the authors conclude. “The selection of particular amino-acid residues that result in enhanced binding of inhibitory KIRs to infected cells represents a novel approach by which HIV-1 can evade NK-cell-mediated immunity.”
The researchers says scientists will need to uncover the mechanisms that allow NK cells to recognize HIV-infected cells and learn how to manipulate the cells for therapy or prevention. “Recent animal studies have suggested that NK cells may develop immunologic memory responses, and if that ability is found in human cells, inducing such a response through vaccination is an exciting possibility we’d like to explore.”