Differential Immunodominance Hierarchy of CD8+ T-Cell Responses in HLA-B*27:05- and -B*27:02-Mediated Control of HIV-1 Infection

Abstract

The well-characterized association between HLA-B*27:05 and protection against HIV disease progression has been linked to immunodominant HLA-B*27:05-restricted CD8⁺ T-cell responses toward the conserved Gag KK10 (residues 263 to 272) and polymerase (Pol) KY9 (residues 901 to 909) epitopes. We studied the impact of the 3 amino acid differences between HLA-B*27:05 and the closely related HLA-B*27:02 on the HIV-specific CD8⁺ T-cell response hierarchy and on immune control of HIV. Genetic epidemiological data indicate that both HLA-B*27:02 and HLA-B*27:05 are associated with slower disease progression and lower viral loads. The effect of HLA-B*27:02 appeared to be consistently stronger than that of HLA-B*27:05. In contrast to HLA-B*27:05, the immunodominant HIV-specific HLA-B*27:02-restricted CD8⁺ T-cell response is to a Nef epitope (residues 142 to 150 [VW9]), with Pol KY9 subdominant and Gag KK10 further subdominant. This selection was driven by structural differences in the F pocket, mediated by a polymorphism between these two HLA alleles at position 81. Analysis of autologous virus sequences showed that in HLA-B*27:02-positive subjects, all three of these CD8⁺ T-cell responses impose selection pressure on the virus, whereas in HLA-B*27:05-positive subjects, there is no Nef VW9-mediated selection pressure. These studies demonstrate that HLA-B*27:02 mediates protection against HIV disease progression that is at least as strong as or stronger than that mediated by HLA-B*27:05. In combination with the protective Gag KK10 and Pol KY9 CD8⁺ T-cell responses that dominate HIV-specific CD8⁺ T-cell activity in HLA-B*27:05-positive subjects, a Nef VW9-specific response is additionally present and immunodominant in HLA-B*27:02-positive subjects, mediated through a polymorphism at residue 81 in the F pocket, that contributes to selection pressure against HIV.IMPORTANCE CD8⁺ T cells play a central role in successful control of HIV infection and have the potential also to mediate the eradication of viral reservoirs of infection. The principal means by which protective HLA class I molecules, such as HLA-B*27:05 and HLA-B*57:01, slow HIV disease progression is believed to be via the particular HIV-specific CD8⁺ T cell responses restricted by those alleles. We focus here on HLA-B*27:05, one of the best-characterized protective HLA molecules, and the closely related HLA-B*27:02, which differs by only 3 amino acids and which has not been well studied in relation to control of HIV infection. We show that HLA-B*27:02 is also protective against HIV disease progression, but the CD8⁺ T-cell immunodominance hierarchy of HLA-B*27:02 differs strikingly from that of HLA-B*27:05. These findings indicate that the immunodominant HLA-B*27:02-restricted Nef response adds to protection mediated by the Gag and Pol specificities that dominate anti-HIV CD8⁺ T-cell activity in HLA-B*27:05-positive subjects.

Keywords: CD8+ T cell; HIV Gag; HIV Nef; HLA; HLA-B*27; human immunodeficiency virus.

FIG 1

HLA-B*27:02 is associated with protection against HIV disease progression. HLA differences by log rank test are shown as follows: fraction of HLA-B*27:02-positive (n = 12) and HLA-B*27-negative (n = 721) subjects remaining AIDS free (absolute CD4 < 200/μl) (A) and fraction of HLA-B*27:02-positive (n = 13) and HLA-B*27:05-positive (n = 64) subjects remaining AIDS free by the 1987 CDC definition for AIDS.

FIG 2

Characterization of HLA-B*27:02-restricted cytotoxic T-lymphocyte (CTL) responses. (A) IFN-γ ELISpot assay recognition of a panel of 410 overlapping peptides spanning the B clade proteome. The amino acid sequences of overlapping peptide and confirmed optimal epitope and HLA restriction are shown. Gag KK10 is KRWIILGLNLK, Pol KY9 is KRKGGIGGY, and Nef VW9 is VRYPLTFGW. (B) Confirmative fluorescence-activated cell sorter (FACS) staining of a HLA-B*27:02-positive subject R120 with an HLA-mismatched tetramer on the left and the HLA-B*27:02-restricted VRYPLTFGW (VW9) on the right.

FIG 3

Differential recognition of HLA-B*27-restricted epitopes. (A) Epitope responses from one representative HLA-B*27:05-positive subject (top) and one HLA-B*27:02-positive subject (bottom). CD8 is shown on the x axis and tetramer-PE on the y axis. (B) (Left) Percentage of HLA-B*2702-positive subjects (n = 7) and HLA-B*2705-positive subjects (n = 19) making responses to the indicated epitopes. **, P < 0.001, Fisher's exact test. (Right) Differential recognition of HLA-B*27 epitopes is related to peptide-MHC binding avidity. Peptide-MHC binding avidity is measured as the Kd (equilibrium dissociation constant) and shown as log10 (1/Ka), where Ka is the equilibrium constant for dissociation of an acid. Shaded are the three epitopes Gag KK10 (KRWIILGLNLK), Pol KY9 (KRKGGIGGY), and Nef VW9 (VRYPLTFGW).

FIG 4

Structural modeling of the impact of HLA-*27:05/HLA-B*27:02 polymorphisms on F-pocket amino acid compatibility. The crystal structure of HLA-B*27:05 in complex with the KK10 peptide (17, 18) was used to model how the polymorphisms in HLA-B*2702 might impact C-terminal anchoring of peptide epitopes. Wincoot was used to generate a model with the following mutations in the HLA-B*27:05 F pocket: D77N, T81I, and L81A. The peptide was modeled with a Trp or a Lys at position 10. (A) The KK10 peptide is shown in red, with Lys-10 depicted by red sticks. Left images show the HLA-HLA-B*2705 F pocket in gray, with Asp-77, Thr-80, and Leu-81 depicted by gray sticks. The dotted line represents a van der Waals contact between Lys-10 and Leu-81. Right images show the modeled HLA-B*2702 F pocket in cyan, with Asn-77, Ile-80, and Ala-81 depicted by cyan sticks. A red cross represents the loss of interactions between Lys-10 and Ala-81 in HLA-B*27:02. (B) KK10 peptide modeled with Trp at position 10 is shown in blue, with Trp-10 depicted by blue sticks. Left panels show the HLA-B*2705 F pocket in gray, with Asp-77, Thr-80, and Leu-81 depicted by gray sticks. A red circle shows the steric clash that would occur between Trp-10 and Leu-81. Right images show the modeled HLA-B*2702 F pocket in cyan, with Asn-77, Ile-80, and Ala-81 depicted by cyan sticks. Black dotted lines represent a van der Waals contact, and red dotted lines represent hydrogen bonds.