Killer cell immunoglobulin-like receptor 3DL1 variation modifies HLA-B*57 protection against HIV-1

Abstract

HLA-B*57 control of HIV involves enhanced CD8+ T cell responses against infected cells, but extensive heterogeneity exists in the level of HIV control among B*57+ individuals. Using whole-genome sequencing of untreated B*57+ HIV-1-infected controllers and noncontrollers, we identified a single variant (rs643347A/G) encoding an isoleucine-to-valine substitution at position 47 (I47V) of the inhibitory killer cell immunoglobulin-like receptor KIR3DL1 as the only significant modifier of B*57 protection. The association was replicated in an independent cohort and across multiple outcomes. The modifying effect of I47V was confined to B*57:01 and was not observed for the closely related B*57:03. Positions 2, 47, and 54 tracked one another nearly perfectly, and 2 KIR3DL1 allotypes differing only at these 3 positions showed significant differences in binding B*57:01 tetramers, whereas the protective allotype showed lower binding. Thus, variation in an immune NK cell receptor that binds B*57:01 modifies its protection. These data highlight the exquisite specificity of KIR-HLA interactions in human health and disease.

Keywords: AIDS/HIV; Innate immunity; MHC class 1; NK cells.

Figure 1. Influence of KIR3DL1 aa 47 on HIV control in HLA-B*57⁺ individuals.

Only individuals with 2 expressed KIR3DL1 alleles were included in the analysis. Individuals with KIR3DS1, KIR3DL1*004 (1 or 2 copies), and KIR3DL1^+/– (i.e., KIR3DL1/S1 missing on 1 haplotype) were excluded. Statistical analysis was performed using logistic regression. CTR, HIV controllers (n = 188); NC, noncontrollers (n = 136). The numbers above the bars denote the number of individuals in each group.

Figure 2. Effect of individual KIR3DL1 alleles on longitudinal HIV viremia in subjects with B*57 subtypes.

A mixed linear-effects model adjusting for all HLA-A, -B, and -C alleles and post-enrollment timing of measurements was used to estimate the effect of each KIR3DL1 allele for groups including individuals with (A) B*57:01 only and (B) B*57:03 only. 47I alleles are shown in red, and 47V alleles are shown in blue. The horizontal bars represent a 95% CI. The size of the black dots was scaled according to the frequency of each allele. Alleles with estimates that did not cross the line, which represents no change in VL (0), are significant. (C) Extracellular domain aa alignment of the KIR3DL1 alleles tested in A and B (http://www.ebi.ac.uk/ipd/kir/). Red = D0, green = D1, blue = D2. Positions 2, 47, and 54 are highlighted in yellow.

Figure 3. HLA-B*57:01/LF9 tetramer binding to KIR3DL1 variants.

293T cells were transfected with FLAG-tagged KIR3DL1*001, KIR3DL1*015, or mutants and stained with HLA-B*57:01/LF9 or HLA-B*08:01/FLR tetramers (350 ng each). (A) MFI of HLA-B*57:01/LF9 binding to FLAG-positive sections from a representative experiment (performed in triplicate). ****P < 0.0001, by ANOVA with Tukey’s multiple comparisons test. Data represent the mean ± SEM. (B) The MFI of tetramer staining on FLAG-positive sections was normalized to HLA-B*57:01/LF9 binding to KIR3DL1*001 across 4 independent transfection experiments. Data represent the mean ± SEM.