Certain HLA alleles appear to be preferentially utilized to mount HIV-1-specific optimal epitope responses during vaccination (). Vaccine-induced responses restricted by A03, A03/11, B14, B27, B35, B44/49, and B57/58 were all significantly overrepresented (p<0.0016). Similar findings were previously reported for an ALVAC-HIV vaccine within individuals possessing a B27 or B57 HLA allele [13
]. Notably, all individuals with HLA-B27 (present in 10% of our population), B14 (present in 13%), B57/58 (present in 10%), and 7/9 (78%) with B35 (present in 23%) possessed vaccine-induced T-cell responses restricted by these alleles, while other HLA alleles were infrequently utilized to restrict vaccine-induced responses. In particular, only 4/18 (22%) of HLA-A02 (present in 45%) vaccinees mounted an A02-restricted response, in agreement with other studies showing little contribution of HLA-A02 during primary infection or vaccination [14
]. B07 (1/9; 11%) and B08 (0/8; 0%) were also infrequent or non-contributors to vaccine-induced T-cell responses. The over representation of responses restricted by B27, B57/B58, and B35 are of particular interest due to previously published data which correlated these alleles with differences in rate of progression to AIDS [15
]. B27 and B57/58 HLA types have been shown to be protective alleles, while a subset of B35 HLA types (Px), in contrast, have been shown as risk alleles.
ELISpot response frequency and epitopes restricted by HLA alleles in vaccinated individuals
Our data and others have shown in addition to specific HLA alleles preferentially utilized to mount vaccine-induced responses, specific HIV-1 epitopes were targeted () [16
]. All HLA-B27+ vaccinees mounted a B27-restricted Gag p24 response against KRWIILGLNK (KK10) in conjunction with a Pol response against FKRKGGIGGY (FY10). The latter epitope is likely KRKGGIGGY (KY9), which was a recently reported B27-restricted epitope found in chronic infection [17
]. Similarly, all HLA-B57+ vaccinees mounted a B57-restricted Gag p24 response against TSTLQEQIGW (TW10) [12
]. The preferential selection of certain epitopes may be because they have significantly higher affinity for their HLA alleles, as assessed by HLA binding assays (). The HLA-B35-restricted responses were split between the Px and PY alleles, which differ in their binding motif anchor residues. Both motifs bind peptides with a proline at position two, but peptides bound by PY alleles have a tyrosine at the C-terminus position, whereas peptides bound by Px alleles have other C-terminal residues. All B35Px vaccinees recognized the B35-restricted Env DPNPQEVVL (DL9) epitope in conjunction with the B35-restricted Pol IPLTEEAEL (IL9) epitope. Conversely, 71% of B35PY vaccinees recognized the B35-restricted Pol NPDIVIYQY (NY9) epitope (). Interestingly, B35+ participants receiving the VRC vaccine only mounted four responses to Gag and 28 responses to other HIV proteins regardless of HLA restriction. In addition, among 21 B35+ MRK-Gag vaccinees, only one mounted a B35-restricted response. These data suggest that in the absence of highly mutable Env and Pol epitopes (present within the VRC vaccine) HLA class I alleles other than B35 are utilized to mount a response.
Epitope affinity, TCR avidity, and HLA surface expression play a role in determining CD8+ T-cell immunodominance
Other data from our group suggest that epitopes targeted early in infection determine disease progression [8
]. However, that study did not address why specific epitopes/HLA were immunodominant in both early infection and vaccination. It has been postulated that high-avidity T-cell responses dominate in early infection [18
]. In this study we found vaccine-induced B27 KK10-specific T cells to be of low avidity. Of note, vaccine-induced B27 KK10-specific T cells were of lower avidity than KK10-specific T cells from HIV-1 infected individuals. In contrast B35-specific T cells were of higher avidity than those restricted by other alleles (p=0.0017; ; see Supplemental Table 3
for complete list). This suggests that B35 may be preferentially utilized after vaccination, because T cells restricted by this allele are of higher avidity than T cells restricted by other alleles.
However, it remained unclear why T cells restricted by B27 dominate in early infection and after vaccination despite their low avidity. We hypothesized that this may be due to higher cell surface density of B27 molecules. To address this we quantitatively measured cell surface expression of HLA-B27 in relation to HLA-A24 and HLA-A11 alleles () and found that HLA-B27 is expressed at a 45% higher level on the cell surface than other HLA alleles tested. Thus, T cells restricted by HLA alleles which are expressed at high levels at the cell surface can dominate even if they have low avidity TCRs. Unfortunately it was not possible to assess the surface expression of a larger set of HLA alleles including HLA-B57 due to the unavailability of specific IgG antibodies.
In addition to TCR avidity, epitope affinity, and HLA surface expression, factors such as intracellular abundance and stability of epitopes and proteosome/tapasin-dependence may also play a role in determining immunodominance [19
], although these were outside the scope of this study.
In conclusion, our data suggest that upon vaccination of healthy seronegative individuals certain HLA alleles are preferentially utilized to mount HIV-1-specific T cell responses (B27, B57, B35, B14), whereas other alleles are rarely utilized (A02, B07). Furthermore, the epitopes targeted by these alleles are highly predictable and appear to be selected based on affinity for their cognate HLA. Finally we show data suggesting that B35Px DL9/IL9-specific T cells likely dominate after vaccination because they possess high avidity TCRs, whereas B27-restricted T cells likely dominate because of the higher cell surface expression of HLA-B27. Our data suggest that immunodominance and immune focusing play a substantial role in vaccine-induced responses. This has obvious consequences for vaccine design since it appears that responses can be predicted based on HLA genotype and immunogen sequence.