High-avidity, high-IFNγ-producing CD8 T-cell responses following immune selection during HIV-1 infection

Abstract

HIV-1 mutations, which reduce or abolish CTL responses against virus-infected cells, are frequently selected in acute and chronic HIV infection. Among population HIV-1 sequences, immune selection is evident as human leukocyte antigen (HLA) allele-associated substitutions of amino acids within or near CD8 T-cell epitopes. In these cases, the non-adapted epitope is susceptible to immune recognition until an escape mutation renders the epitope less immunogenic. However, several population-based studies have independently identified HLA-associated viral changes, which lead to the formation of a new T-cell epitope, suggesting that the immune responses that these variants or 'neo-epitopes' elicit provide an evolutionary advantage to the virus rather than the host. Here, we examined the functional characteristics of eight CD8 T-cell responses that result from viral adaptation in 125 HLA-genotyped individuals with chronic HIV-1 infection. Neo-epitopes included well-characterized immunodominant epitopes restricted by common HLA alleles, and in most cases the T-cell responses against the neo-epitope showed significantly greater functional avidity and higher IFNγ production than T cells for non-adapted epitopes, but were not more cytotoxic. Neo-epitope formation and emergence of cognate T-cell response coincident with a rise in viral load was then observed in vivo in an acutely infected individual. These findings show that HIV-1 adaptation not only abrogates the immune recognition of early targeted epitopes, but may also increase immune recognition to other epitopes, which elicit immunodominant but non-protective T-cell responses. These data have implications for immunodominance associated with polyvalent vaccines based on the diversity of chronic HIV-1 sequences.

Figure 1

Comparison of IFNγ responses elicited by non-adapted and adapted peptides from individuals with detectable HIV viremia in the study. Each data point represents the average SFU of triplicate wells after subtraction of background.

Figure 2

Comparative functional avidity of IFNγ responses against non-adapted and adapted epitopes associated with “classical escape” from (a) HLA-B*0801-restricted responses against FLKEKGGL and (b) HLA-B57-restricted response against STTVKAACWW. In both examples, responses are abrogated by the HLA-associated substitution. In contrast, CTL responses against neo-epitopes have higher functional avidity than their non-adapted epitopes (c–f). Representative plots of peptide stimulated IFNγ responses to HLA- C*0702-restricted KRQ(D/E)ILDLWVY (c), −B*4402-restricted QEEHE(R/K)THSNW (d), −B*0702-restricted TPGPG(I/V)RYPL (e), and −A*0201-restricted SLYNTV(V/A)TL. Peptide concentrations (X-axis) from 2μg/ml followed by 1:2 dilution, and thereafter 1:10 dilutions dependant on cell availability. Non-adapted epitopes are shown as triangles and neo-epitopes (adapted epitopes) are squares in all plots.

Figure 3

Patterns of immunoreactivity associated with neo-epitopes in which IFNγ responses display equivalent or marginally enhanced IFN-γ responses to the HLA-adapted variant epitope, in contrast to “classical escape” in which there is typically abrogation of IFNγ responses to escape variants.

Figure 4

Single IFNγ producing cells are marginally increased in adapted cultures compared with non-adapted cultures while single IL-2 producing cells are significantly increased in central memory cells from both adapted and non-adapted peptide-stimulated T cell cultures (p<0.05 mixed models analysis). The frequency of cytokine producing cells is plotted for central memory (CM) and effector memory (EM) populations from adapted and non-adapted cultures. Single IFNγ producing cells from non-adapted, and adapted cultures, dual IFNγ/IL-2 producing cells from non-adapted and adapted cultures and single IL-2 producing cells from non-adapted and adapted cultures are shown.

Figure 5

Evolution of the HLA-B*1503-restricted CD8 T cell response against WKFDSRLAF and following adaptation, against WRFDSRLAF in a single individual following sexual transmission of HIV-1. K to R substitution within the epitope occurs by day 266 in the autologous viral sequence. Antiretroviral therapy commenced 393 post-transmission and all HIV-1 specific CD8 T-cell responses were not detected (<50 SFU) thereafter.

Figure 6

Breadth (a) and Magnitude (b) of all tested HIV protein-specific responses in a single individual following sexual transmission of HIV-1. (a) The number of IFNγ responses detected at each time point against epitopes in Gag, Pol, Env, Nef and Nef variants are shown. HIV RNA levels at each time point in relation to number of responses are also shown. (b) The Magnitude of IFNγ responses (SFU) against Gag, Pol, Env, Nef and Nef variants.