CD8+ TCR Bias and Immunodominance in HIV-1 Infection

Henrik N. Kløverpris, Reuben McGregor, James E. McLaren, Kristin Ladell, Mikkel Harndahl, Anette Stryhn, Jonathan M. Carlson, Catherine Koofhethile, Bram Gerritsen, Can Keşmir, Fabian Chen, Lynn Riddell, Graz Luzzi, Alasdair Leslie, Bruce D. Walker, Thumbi Ndung’u, Søren Buus, David A. Price and Philip J. Goulder
J Immunol June 1, 2015, 194 (11) 5329-5345; DOI: https://doi.org/10.4049/jimmunol.1400854

Abstract

Immunodominance describes a phenomenon whereby the immune system consistently targets only a fraction of the available Ag pool derived from a given pathogen. In the case of CD8+ T cells, these constrained epitope-targeting patterns are linked to HLA class I expression and determine disease progression. Despite the biological importance of these predetermined response hierarchies, little is known about the factors that control immunodominance in vivo. In this study, we conducted an extensive analysis of CD8+ T cell responses restricted by a single HLA class I molecule to evaluate the mechanisms that contribute to epitope-targeting frequency and antiviral efficacy in HIV-1 infection. A clear immunodominance hierarchy was observed across 20 epitopes restricted by HLA-B*42:01, which is highly prevalent in populations of African origin. Moreover, in line with previous studies, Gag-specific responses and targeting breadth were associated with lower viral load set-points. However, peptide–HLA-B*42:01 binding affinity and stability were not significantly linked with targeting frequencies. Instead, immunodominance correlated with epitope-specific usage of public TCRs, defined as amino acid residue–identical TRB sequences that occur in multiple individuals. Collectively, these results provide important insights into a potential link between shared TCR recruitment, immunodominance, and antiviral efficacy in a major human infection.

Introduction

CD8+ T cells play a central role in the immune response to viruses (1). However, clear-cut differences exist between distinct specificities in terms of antiviral efficacy (2, 3). Moreover, epitope-targeting patterns are often predetermined within a hierarchy of immunodominance across restriction elements (4–12). These biologically imposed limitations can therefore dictate the outcome of certain viral infections.

In the case of HIV-1, disease progression is strongly affected by the expression of particular HLA alleles (13, 14). Although several mechanisms have been proposed to explain this association (13), one key factor is the relative ability of epitope-specific CD8+ T cell populations to kill HIV-infected cells. For example, Gag-specific responses typically contain HIV-1 more effectively in vivo (15–19) and in vitro (20, 21) compared with those that target other viral proteins. In addition, protective HLA class I molecules, such as HLA-B*27 and HLA-B*57 (22–24), restrict immunodominant Gag-specific responses that select viral escape variants with impaired replicative capacity (22, 25–27).

A number of factors can influence immunodominance (2, 4, 6, 11). Ag presentation itself is the culmination of several upstream events, such as the kinetics of protein expression, the abundance of protein delivered into the cytoplasm, intracytoplasmic proteosomal cleavage, translocation by TAP, peptide loading onto MHC, ERAP1/2 trimming, and transport to the cell surface (28). Peptide–MHC binding affinity and stability determine the subsequent availability of Ag over time, whereas TCR avidity and the frequency of naive precursors govern the size of the potentially responsive T cell pool (7, 9, 10, 12). The phenomenon of immunodomination, whereby certain responses are subordinated in the presence of particular high-frequency responses (29), also plays a role. Nonetheless, despite the complexity of these multifaceted processes, the end result is a largely predictable pattern of immunodominance for any given virus.

Emerging studies highlight a key role for the TCR repertoire as an independent determinant of antiviral efficacy in multiple systems (30–35). Although the process of V(D)J rearrangement can theoretically generate 1015–20 distinct TCRs (36), extreme biases exist during recombination, thymic selection, naive T cell recruitment, and subsequent clonal expansion (6, 10, 36–38). These biases can ultimately generate identical or “public” epitope-specific TCRs in multiple individuals (38). However, the role of TCR bias in relation to immunodominance remains ill-defined, with murine studies yielding apparently contradictory data (39, 40).

To assess the potential influence of TCR publicity on CD8+ T cell immunodominance and antiviral efficacy in a human viral infection, we conducted an extensive analysis of HLA-B*42:01–restricted responses directed against an array of different epitopes derived from HIV-1. The prevalence of HLA-B*42:01 in most populations of African origin, combined with the substantial repertoire of associated viral peptides, enabled a large-scale study controlled for the restriction element across multiple individuals with chronic HIV-1 infection. Consequently, we were able to detect statistically meaningful correlations between these parameters.

Materials and Methods

Study subjects

The study cohort comprised 2093 female adults with chronic, antiretroviral therapy–naive C-clade HIV-1 infection, recruited from five cohorts: Durban, South Africa (14, 17, 25, 41); Gaborone, Botswana (42); Bloemfontein, South Africa (43); Kimberley, South Africa (44); and Thames Valley, U.K. (45). A total of 246 HLA-B*42:01+ individuals with documented proviral DNA sequences, CD4+ T cell counts, plasma viral loads, and four-digit HLA-genotyping data was identified within the entire cohort, from which 181 were screened with overlapping peptides (OLPs) to map HIV-specific CD8+ T cell responses in IFN-γ ELISPOT assays. Informed consent was obtained from all participants. The following Institutional Review Boards approved the study: University of KwaZulu-Natal; University of the Free State, South Africa; Health Research Development Committee, Botswana Ministry of Health, Botswana; Office of Human Research Administration, Harvard School of Public Health; and University of Oxford.

IFN-γ ELISPOT

Virus-specific CD8+ T cell responses across the whole HIV-1 proteome were determined for 1009 C-clade–infected subjects via direct ex vivo IFN-γ ELISPOT analysis. Ags comprised 410 OLPs based on the C-clade consensus (2001) arranged in a matrix system with 11–12 peptides/pool. Responses to matrix pools were deconvoluted by subsequent testing with the individual 18-mer peptides contained in each pool (15). Associations between HLA-B*42:01 expression and OLP targeting were calculated from a total of 181 HLA-B*42:01+ individuals. Percent targeting frequency (immunodominance rank) calculations for HLA-B*42:01–restricted epitopes required the exclusion of 27 individuals coexpressing HLA-B*07:02/39:10/42:02/81:01 to eliminate alternative presentation by other B7 superfamily members (46). Viral load set-point calculations versus targeting of HLA-B*42:01–restricted OLPs were based exclusively on data from the Durban cohort (n = 126) to minimize the influence of external factors.

HLA class I typing

Four-digit HLA-A/B/C genotyping was performed using real-time reverse sequence-specific oligonucleotide kits (Dynal), as described previously (47).

Epitope mapping and HLA restriction

Epitope mapping and recognition assays were performed as described previously (16, 45). Single allele–matched B lymphoblastoid cell lines (BLCLs) were used to determine HLA restriction (16, 48).

Tetramers

Tetrameric peptide–HLA complexes were generated and used as described previously (16, 49). Samples were acquired using an LSR II flow cytometer (BD Biosciences) and analyzed with FlowJo version 8.8.6 (TreeStar). Events were gated serially on singlets, lymphocytes, live cells, and CD3+ T cells prior to analysis in bivariate tetramer versus CD8 plots.

Proviral DNA sequencing

Sequences from Gag (n = 1857), Pol (n = 1052), and Nef (n = 1327) were generated by extraction of genomic DNA from PBMCs and amplification via nested PCRs, as described previously (17, 44, 47). Purified products were sequenced using the Big Dye Terminator Ready Reaction (Life Technologies) (41, 50). Vif, Rev, and Env sequences were available from 255 subjects (51).

Peptide–HLA binding and stability assays

Peptide–HLA stability was measured as described previously (52). Peptide–HLA binding affinity was measured via AlphaScreen technology (PerkinElmer) (53).

TCR clonotyping

Clonotypic analysis of Ag-specific CD8+ T cell populations restricted by HLA-B*42:01 was performed as described previously (54). Briefly, viable HIV-specific tetramer+ CD8+ T cell populations (n = 48) were sorted by flow cytometry at >98% purity directly into RNAlater. A median of 2120 cells (25th percentile = 1068 cells, 75th percentile = 4340 cells) was sorted per population, with a median response magnitude of 0.60% (25th percentile = 0.3%, 75th percentile = 1.4%). The number of sorted cells correlated with response magnitude (r = +0.8, p < 0.0001). Unbiased amplification of all expressed TRB gene products was conducted using a template-switch anchored RT-PCR with a 3′ C region primer. Amplicons were subcloned, sampled, sequenced (n = 3592), and analyzed as described previously (55). IMGT nomenclature is used in this report (56).

Statistical analysis

Associations between HLA-B*42:01 expression, HIV-1 polymorphisms, and 18-mer peptide (OLP) responses were determined as described previously (44, 57). The Dunn multiple-comparisons test was used to compare median viral loads between OLP responders and nonresponders, the number of OLP responses between different HIV-1 proteins (breadth), and the number of different TCR clonotypes between responses. The two-tailed Mann–Whitney U test was used to compare viral loads and CD4+ T cell counts between individuals carrying wild-type sequences or escape polymorphisms within the Gag-RM9 epitope. All p values were calculated using GraphPad Prism version 6.0c (GraphPad). Differences in Gag-RM9 sequence polymorphisms between HLA-B*42:01+ and HLA-B*42:01− subjects were calculated using the Fisher exact test. Correlations between percent targeting frequency (IFN-γ OLP ELISPOT responders) and either peptide–HLA binding affinities (IC50 KD value) or peptide–HLA binding half-lives (hours) were calculated using the Spearman rank test. Clonotypic data were normalized as described previously (58–60). Briefly, all samples were rarefied down to the lowest estimated coverage (88%) prior to calculations of TCR sharing. This process was repeated 10,000 times, and mean publicity scores were used for statistical analysis.

Results

HLA-B*42:01–restricted responses conform to a strict immunodominance hierarchy

Initially, we used IFN-γ ELISPOT assays to screen 1009 antiretroviral therapy–naive C-clade–infected female individuals, 181 (18%) of whom carried the HLA-B*42:01 allele, for responses to a panel of 410 OLPs (15, 16, 61) spanning the entire HIV-1 proteome (Table I). This panel comprised seven HLA-B*42:01–restricted epitopes already listed in the Los Alamos Immunology Database (http://www.hiv.lanl.gov) (62). In addition, we identified 13 novel epitopes via statistical associations between recognition of a particular 18-mer OLP and the expression of HLA-B*42:01 (q < 0.05). This set of 20 HLA-B*42:01–restricted HIV-1 epitopes was used for further analysis.

View this table:
Table I. HLA-B*42:01 associations with IFN-γ OLP responses (n = 1009)

Next, we ranked the response hierarchy among these 20 epitopes based on targeting frequency (immunodominance rank). A total of 154 HLA-B*42:01+ individuals was included in this analysis, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression. Targeting frequency correlated with response magnitude (r = +0.96, p < 0.0001; Supplemental Fig. 1) and conformed to a clear pattern of immunodominance (Fig. 1A).

FIGURE 1.
FIGURE 1.

Identification of immunodominant and subdominant HLA-B*42:01–restricted epitopes. (A) Targeting frequencies for “protein–18-mer peptide-optimal epitope name” OLPs in HLA-B*42:01+ individuals, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression (n = 154). Responses were determined via IFN-γ ELISPOT assays. (B) Correlation between HLA-B*42:01 status and targeting of OLP-275 (KVVPRRKAKIIKDYGKQM) in IFN-γ ELISPOT assays. Significance was determined using the Fisher exact test. (C) Identification of the optimal HLA-B*42:01–restricted epitope Int-IM9 (IIKDYGKQM) via peptide truncations in IFN-γ ELISPOT assays. (D) Confirmation of HLA-B*42:01 as the restriction element for Int-IM9 via peptide pulsing of BLCLs partially HLA matched to donor R014 (A*30:01/33:01, B*42:01/57:03, Cw17:01/18:01). Autologous or mismatched BLCLs were used as positive and negative controls, respectively. (E) Unequivocal confirmation of HLA-B*42:01 as the restriction element for Int-IM9 via cognate tetramer staining of responding PBMCs. Similar data are shown for three other novel epitopes: Gag-RM9 (RPGGKKHYM), Vif-HI10 (HPKVSSEVHI), and Env-IF9 (IPRRIRQGF). An HLA-mismatched tetramer was used as the negative control.

To validate the novel HLA-B*42:01–restricted CD8+ T cell epitopes, we first mapped Int-IM9 (IIKDYGKQM) as the optimal peptide within OLP Int-275 (KVVPRRKAKIIKDYGKQM), which was targeted at a frequency of 53% (Fig. 1B–D). Of note, Int-IM9 is the first example of a B7 superfamily–restricted epitope that does not contain proline at position 2, which acts as the primary anchor residue. We then used HLA-B*42:01 tetramers (16, 63) to rapidly and unequivocally identify an additional three optimal epitopes from OLP Gag-3 (Gag-RM9, RPGGKKHYM), OLP Vif-407 (Vif-HI10, HPKVSSEVHI), and OLP Env-401 (Env-IF9, IPRRIRQGF) (Fig. 1E, Table I). Finally, we demonstrated that 10 of the novel epitopes listed in Table I bound strongly to HLA-B*42:01 (KD, 2–82 nM; binding half-life, 1.1–22.4 h) (Supplemental Table I).

The identification of 20 HLA-B*42:01–restricted epitopes with predictable targeting patterns provided a unique opportunity to probe the biological impact and mechanistic basis of immunodominance patterns in HIV-1 infection.

Gag-specific responses are associated with lower viral load set-points

To establish the efficacy of each HLA-B*42:01–restricted response, we compared viral load set-points in HLA-B*42:01+ responders and nonresponders (Fig. 2). Five of the six Gag-specific responses showed a trend toward lower median viral loads, which was statistically significant for the Gag-RM9 epitope after multiple-comparisons analysis (p = 0.002). In contrast, three of the six responses directed against accessory/regulatory proteins (two Nef-specific and one Vif-specific) showed a trend toward higher median viral loads, although no significant associations were observed after correction for multiple comparisons. Discordant associations with viral load set-point were also observed for response breadth (Fig. 3). In particular, only the number of Gag-specific responses was linked to immune control in the context of HLA-B*42:01 restriction, confirming previous analyses across the entire cohort (15). Thus, epitope-specific differences discriminate HLA-B*42:01–restricted responses with respect to immune control of HIV-1 replication.

FIGURE 2.
FIGURE 2.

Subdominant HLA-B*42:01–restricted Gag-specific responses are associated with lower viral loads. Viral load set-points were compared across OLP-specific CD8+ T cell responses targeting Gag (A), Pol (B), Nef (C), or Vpr/Vif/Env (D) in HLA-B*42:01+ responders and nonresponders, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression (n = 126). Horizontal lines indicate median values. All p values < 0.1, by the Dunn multiple-comparisons test, are shown.

FIGURE 3.
FIGURE 3.

Discordant viral load associations with HLA-B*42:01–restricted protein-specific responses. Viral load set-points were compared across groups making 0, 1, 2, and >2 protein-specific responses directed against Gag (A), Pol (B), Nef (C), or Vpr/Vif/Env (D) in the cohort of HLA-B*42:01+ individuals, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression (n = 126). Horizontal lines indicate median values. All p values < 0.05, by the Dunn multiple-comparisons test, are shown.

Gag-specific selection pressure is associated with loss of antiviral efficacy

The ability of certain CD8+ T cell responses to exert antiviral selection pressure has previously been associated with immune efficacy (15–17, 44). To examine this phenomenon across HLA-B*42:01–restricted specificities, we initially focused on the Gag-RM9 response, which exhibited the strongest association with viremic control (Fig. 2A). Escape mutations were selected in 92% of HLA-B*42:01+ subjects compared with only 54% of HLA-B*42:01− individuals (p = 2 × 10−35) (Fig. 4A). These polymorphisms were associated with higher viral load set-points (median HIV RNA copies/ml plasma = 3,860 versus 18,550, p = 0.003) (Fig. 4B) and lower CD4+ T cell counts (median CD4+ T cells/μl = 467 versus 328, p = 0.03) (Fig. 4C) in HLA-B*42:01+ individuals. Given the absence of such associations in HLA-B*42:01− subjects, it is likely that these effects operate via evasion of the Gag-RM9 response. Moreover, a beneficial effect on viral load set-point in Gag-RM9 responders carrying the wild-type epitope was observed across 60 HLA-B*42:01+ individuals for whom IFN-γ ELISPOT and viral sequence data were available from the same time point (median HIV RNA copies/ml plasma = 387 versus 2470, p = 0.04) (Fig. 4D). These findings suggest that the Gag-RM9 response contributes to viremic control most effectively in the absence of viral escape, but also to some extent in the presence of mutations that compromise CD8+ T cell recognition (Fig. 4E).

FIGURE 4.
FIGURE 4.

HIV-1 sequence polymorphisms in Gag-RM9 are CD8+ T cell escape mutations associated with loss of immune control. (A) HLA-B*42:01+ (red) and HLA-B*42:01− (green) associations with mutations in Gag-RM9 (departure from wild-type). Significance was determined using the Fisher exact test. Viral load set-points (B) and CD4+ T cell counts (C) in HLA-B*42:01+ (red) and HLA-B*42:01− (green) individuals carrying either wild-type Gag-RM9 (RPGGKKHYM) or any mutation in this epitope. The x-axis shows the number of sequences analyzed in each case. (D) Viral load set-points in 60 HLA-B*42:01+ individuals carrying either wild-type Gag-RM9 or any mutation in this epitope stratified for responder or nonresponder status. (E) Impact of the commonly selected H28R, M30R, and M30K variants on CD8+ T cell recognition in IFN-γ ELISPOT assays. Data from subject R019 (A*02:01/30:01, B*35:01/42:01, Cw*16:01/17:01) are shown. (F) HLA-B*42:01 binding affinities and half-lives (stability) for the peptides shown in (E). In (B)–(D), horizontal lines indicate median values presented by 25th percentile boxes and ranges (SD); significance was determined using the Mann–Whitney U test.

In further analyses, we examined the relationship between viral sequences across the whole HIV-1 genome and HLA-B*42:01 expression in a total of 1867 individuals. Four polymorphisms in the Gag-RM9 epitope were selected by HLA-B*42:01 (H28R, H28S, M30R, and M30K) (Table II). These mutations resulted in reduced CD8+ T cell recognition (Fig. 4E), at least in part through decreased peptide–HLA-B*42:01 binding (Fig. 4F). In total, we identified 20 polymorphic sites located in 9 of the 20 HLA-B*42:01–restricted epitopes (q < 0.05), including the novel Gag-GF9 epitope (Table II). Of the 10 top-ranking immunodominant HLA-B*42:01–restricted responses, all six targeting epitopes in Gag, Pol, or Vpr showed evidence of selection pressure on the virus. In contrast, only one of the four responses targeting epitopes in Nef or Vif showed evidence of selection pressure. These data provide further evidence of variable antiviral efficacy across the 20 HLA-B*42:01–restricted responses, most notably those targeting immunodominant epitopes.

View this table:
Table II. HLA-B*42:01–associated HIV-1 polymorphisms

TCR bias in the HLA-B*42:01–restricted repertoire

The presence of public TCR clonotypes, defined on the basis of TRB amino acid sequence identity across multiple individuals responding to the same epitope (36, 38, 64), has previously been linked with CD8+ T cell efficacy in SIV (33, 34), HIV (30, 65), and CMV (35) infection. To examine this phenomenon in the setting of HLA-B*42:01–restricted responses to HIV-1, we sorted viable tetramer+ CD8+ T cell populations (n = 48) specific for six of the seven most frequently targeted epitopes (Gag-TL9, Int-IM9, Vpr-FL9, Nef-TL10, Vif-HI10, and Int-LI9) (Supplemental Fig. 2) and sequenced a total of 3592 constituent TCR clones across eight donors/specificity (Tables III, IV, V, VI, VII, and VIII). Clonotypic data for the Gag-RM9 response were only available from one subject (Supplemental Table II) and could not be included in further analyses.

View this table:
Table III. Clonal analysis of HLA-B*42:01–restricted TL9-specific CD8+ T cell populations
View this table:
Table IV. Clonal analysis of HLA-B*42:01–restricted IM9-specific CD8+ T cell populations
View this table:
Table V. Clonal analysis of HLA-B*42:01–restricted FL9-specific CD8+ T cell populations
View this table:
Table VI. Clonal analysis of HLA-B*42:01–restricted LI9-specific CD8+ T cell populations
View this table:
Table VII. Clonal analysis of HLA-B*42:01-restricted HI10–specific CD8+ T cell populations
View this table:
Table VIII. Clonal analysis of HLA-B*42:01–restricted TL10-specific CD8+ T cell populations

For the top two ranking immunodominant responses, Gag-TL9 (Table III) and Int-IM9 (Table IV), public TCRs were identified in six of eight and four of eight subjects, respectively. The most prevalent examples in terms of recurrence were TRBV12-3/4/CASSFSKNTEAF/TRBJ1-1 (Gag-TL9) and TRBV9/CASSVDKGGTDTQY/TRBJ2-3 (Int-IM9), each of which were shared by four of eight individuals. Public clonotypes were also identified for Vpr-FL9, ranked third in the immunodominance hierarchy (Table V). Each specificity was characterized by diverse, but distinct, patterns of TRBV usage (Fig. 5A). Moreover, within each specificity, almost all public clonotypes used the same TRBV gene (Fig. 5B). For example, the four Int-IM9–specific public clonotypes all expressed TRBV9 (Table IV), suggesting “hard-wired” germline-encoded Ag recognition.

FIGURE 5.
FIGURE 5.

Clonality and TCR bias in HLA-B*42:01–restricted epitope-specific responses. (A) TRBV usage is depicted for six HLA-B*42:01–restricted epitope-specific responses. The number of individuals analyzed is indicated in each case. (B) Percentage of responders to Gag-TL9, Int-IM9, or Vpr-FL9 stratified for the presence of public TCRs. Significance was determined using the Fisher exact test. (C) Number of different TCR clonotypes detected in each of the six epitope-specific responses. All p values < 0.1, by the Dunn multiple-comparisons test, are shown. (D) Correlation between clonality and response magnitude. Significance was determined using the Spearman rank test.

Overall, we identified 11 different public clonotypes, all of which were confined exclusively to the top three ranked immunodominant specificities (Gag-TL9, Int-IM9, and Vpr-FL9) (Tables III–V). In contrast, no public clonotypes were present within the Nef-TL10, Vif-HI10, and Int-LI9 specificities, ranked fifth to seventh in the immunodominance hierarchy (Tables VI–VIII). These observations suggest that clonotypic publicity is a feature of immunodominant HIV-specific CD8+ T cell responses restricted by HLA-B*42:01. The Vpr-FL9–specific CD8+ T cell populations were the most polyclonal (Fig. 5C), but no correlation was found between clonality and response magnitude (p = 0.2) (Fig. 5D). Almost identical results were obtained after normalization procedures that account for differences in sampling depth between individuals (data not shown).

Public clonotypes are involved in immunodominant CD8+ T cell responses

A stable peptide–MHC interaction is a prerequisite for immunogenicity, but other factors also contribute (12). Based on our observations above, we hypothesized that TCR bias may play a role in immunodominance. Accordingly, we compared measures of public TCR occurrence with epitope targeting across all HLA-B*42:01+ individuals (n = 154) (Fig. 6A). Strong correlations were observed for immunodominance rank (r = −0.94, p < 0.0001) (Fig. 6B) and targeting frequency (r = +0.92, p = 0.03) (Fig. 6C), both of which held whether we compared the frequency of individuals sharing any public TCR or the frequency of individuals sharing the most common public TCR. The latter correlation was even more marked after normalization for sampling depth (r = +0.94, p = 0.005; data not shown). Although we deliberately analyzed an identical number of CD8+ T cell populations from an identical number of individuals for each specificity (n = 8), this result is important because it indicates that the detected association is not an artifact of differential sequence coverage. An additional correlation was observed for response magnitude (Fig. 6D). Moreover, exclusively private responses were significantly less dominant than responses incorporating public TCRs (p = 0.04) (Fig. 6E).

FIGURE 6.
FIGURE 6.

Epitope-targeting frequency correlates with shared TCR recruitment. (A) Targeting frequencies for six optimal epitopes in HLA-B*42:01+ individuals, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression (n = 154). (B) Immunodominance rank, shown as most targeted ranked 1, versus the percentage of individuals sharing any public TCR. Significance was determined using the Spearman rank test. (C) Targeting frequencies for the same six epitopes versus the percentage of individuals sharing the most frequent public TCR. Significance was determined using the Spearman rank test. (D) Response magnitude, including responders and nonresponders (mean), versus the percentage of individuals sharing the most frequent public TCR. Significance was determined using the Spearman rank test. (E) Targeting frequencies for all six epitopes stratified for the presence or absence of public TCRs. Significance was determined using the Mann–Whitney U test.

Type 1 bias, defined by TRBV sharing alone, was not directly linked to immunodominance (p = 0.2; data not shown). Similarly, there was no association between type IV bias, defined by near-identical (disparity < 2 aa) CDR3 sequences (36), and targeting frequency (p = 0.7; data not shown). It is also notable that response magnitude did not correlate with the frequency of public TCRs (p = 0.74; data not shown). Thus, public TCR recruitment is linked to increased targeting frequency independently of nonidentical bias and response magnitude.

Peptide–HLA-B*42:01 binding contributes minimally to immunodominance

To assess the relative impact of TCR bias with respect to other factors that shape immunodominance (6, 16, 66), we examined peptide–HLA-B*42:01 binding affinity and stability (52, 53) for 16 of the epitopes described in this study (Supplemental Table I). The two immunodominant epitopes, Gag-TL9 and Int-IM9, bound HLA-B*42:01 with affinities of KD = 82 and 19 nM, respectively, and corresponding half-lives of 3.6 and 13.5 h (Fig. 7A, 7B). Across all epitopes, however, no significant correlations were detected between these binding parameters and immunodominance (Fig. 7C, 7D). Nonetheless, peptide–HLA-B*42:01 binding half-life correlated positively with targeting frequency when Gag-TL9 was excluded from the analysis (r = +0.53, p = 0.04; data not shown). Neither binding affinity nor stability correlated with response magnitude (p = 0.42 and p = 0.32, respectively; data not shown). Thus, peptide binding alone cannot explain the observed patterns of immunodominance in this system.

FIGURE 7.
FIGURE 7.

Peptide–HLA-B*42:01 binding affinities and half-lives for 16 optimal epitopes. HLA-B*42:01 binding affinities (A) and half-lives (B) for the Gag-TL9 (TPQDLNTML) and Int-IM9 (IIKDYGKQM) peptides. Peptide binding affinities (C) and half-lives (D) for the optimal epitopes versus targeting frequencies for the 16 corresponding OLPs in HLA-B*42:01+ individuals, stratified for lack of HLA-B*07:02/39:10/42:02/81:01 coexpression (n = 154). Significance was determined using the Spearman rank test.

Discussion

In this study, we conducted an extensive analysis of CD8+ T cell responses restricted by a single HLA class I molecule to evaluate the mechanisms that contribute to immunodominance and antiviral efficacy in HIV-1 infection. Epitope-targeting frequencies conformed to a clear hierarchy across 20 different HLA-B*42:01–restricted specificities, within which the presence and multiplicity of responses directed against Gag were consistently associated with lower viral load set-points. Immunodominance patterns correlated with epitope-specific public TCR usage, but no clear role was identified for peptide–HLA-B*42:01 binding affinity or stability in the observed response profile. Collectively, these results suggest that the available TCR repertoire can influence immunodominance patterns and CD8+ T cell efficacy in chronic HIV-1 infection.

Initially, we used OLPs spanning the entire viral proteome to screen a large cohort of individuals with chronic C-clade infection for HIV-specific CD8+ T cell responses. This comprehensive and unbiased strategy allowed the identification of novel and previously defined HLA-B*42:01–restricted epitopes that adhered to a strict pattern of immunodominance, thereby enabling more detailed downstream analyses. It is notable that the accurate quantification of certain responses can be compromised by this approach, especially when the optimal epitope resides in the central part of the corresponding OLP (18, 67). Nonetheless, we found a strong correlation between optimal peptide-specific and OLP-defined responses (r = +0.85, p < 0.0001; data not shown). Although this finding justifies the use of OLP screening, it remains conceivable that minor discrepancies could negatively influence the observed correlation between response magnitude and targeting frequency.

Subsequent analyses revealed a significant association between HLA-B*42:01–restricted Gag-specific CD8+ T cell responses and lower viral load set-points, consistent with the notion that protein-targeting patterns influence immune efficacy. Mechanistically, this may be a function of the rapid processing kinetics and relative abundance of Gag-derived epitopes on the cell surface, enabling the elimination of infected targets prior to the production of viral progeny (57, 68, 69). In addition, Gag targeting may be beneficial due to the fitness costs incurred by viral escape mutations within highly conserved, functionally constrained regions of the viral proteome (25–27, 70, 71). However, not all escape mutations reduce viral replicative capacity, as exemplified by the Gag-RM9 variants associated with higher viral loads in our study. This observation is consistent with a recent analysis of the M30R polymorphism, which was shown to increase viral replicative capacity and precipitate disease progression in association with HLA-B*42:01 (72).

The detected association between TCR publicity and immunodominance is particularly striking given the vast recombinatorial diversity that shapes the available repertoire in each individual (36, 38, 64, 65). Across a total of 48 ex vivo datasets, however, TCR bias was apparent at multiple levels. In particular, each epitope-specific CD8+ T cell population displayed distinct patterns of TRBV usage. Moreover, the extent of TCR sharing varied as a function of epitope specificity. In line with previous studies, clonal diversity per se did not correlate with immunodominance (73). However, the most frequently targeted epitopes mobilized cognate repertoires characterized by the presence of high-frequency public TCRs. It is established that public TCRs arise in the naive repertoire as a function of convergent recombination, whereby production frequency is dictated on a probabilistic basis by the number of rearrangements, nucleotide additions, and amino acid codons that can generate a particular sequence (64, 74). The subsequent recruitment of these TCRs into the epitope-specific memory repertoire is governed by Ag avidity and clonal proliferation (10, 55). Accordingly, our observations suggest that commonly targeted epitopes are structurally compatible with frequently generated TCRs, at least in the context of HLA-B*4201. In this scenario, public TCRs populate a recurrence “hot spot” in the naive repertoire, enabling immunodominant epitopes to initiate and maintain CD8+ T cell responses in multiple individuals. Consistent with this proposition, naive precursor frequencies are known to influence immunodominance patterns (6, 7, 9, 75, 76). However, the extent to which frequently produced TCRs contribute to the overall precursor pool for any given epitope remains to be determined.

It is noteworthy that the public TCRs detected for each of the three immunodominant specificities were largely constrained by a distinct TRBV segment. This suggests a determinative role for the germline-encoded CDR1 and CDR2 loops. One possibility is that specific residues encoded by these TRBV genes interact with HLA-B*42:01, potentially influencing thymic selection to skew naive CD8+ T cell frequencies toward particular specificities (77). Alternatively, germline-encoded recognition of the bound peptide may contribute to immunodominance patterns (78). Immunodominant epitope-specific TCRs constructed almost entirely from germline DNA have been described previously and may represent an evolutionarily conserved mechanism to combat ancient pathogens that have coevolved with the human race (37, 64, 79, 80). Although this is unlikely to apply directly in the case of HIV-1, it is intriguing to speculate that structural homology with such epitopes may inadvertently underlie the immunodominance patterns described in this report.

In contrast to the association between immunodominance and TCR bias controlled within the framework of a single HLA class I molecule, peptide binding to HLA-B*42:01 contributed little to the observed epitope-targeting frequencies in this study. However, it is important to note that other factors, such as Ag-processing efficiency (81, 82), kinetics (57, 69, 83), and protein abundance (84, 85), play a key role alongside a requirement for sufficient peptide–MHC binding (9, 86). Further studies will therefore be necessary to assess the contribution of TCR recruitment in relation to these well-defined determinants of immunodominance.

In summary, we present clear evidence linking epitope-targeting frequencies to TCR bias. Although the extent to which this phenomenon applies across other systems remains to be defined, our data suggest that Ag-specific repertoire studies will be important for a full understanding of both natural and vaccine-induced immune responses against intracellular pathogens.

Disclosures

The authors have no financial conflicts of interest.

Footnotes

  • This work was supported by the Wellcome Trust (to D.A.P. and P.J.G.) and National Institutes of Health Grant R01 AI46995. H.N.K. is funded by the Danish Agency for Science, Technology and Innovation via Grant 12-132295, The Lundbeck Foundation via Grant R151-2013-14624, and The MAERSK Foundation for Medical Improvement. D.A.P. is a Wellcome Trust Senior Investigator.

  • The online version of this article contains supplemental material.

  • Abbreviations used in this article:

    BLCL
    B lymphoblastoid cell line
    OLP
    overlapping peptide.

  • Received April 3, 2014.
  • Accepted February 25, 2015.

References

  1. ↵
    1. Zinkernagel R. M.
    1996. Immunology taught by viruses. Science 271: 173–178.
    OpenUrlAbstract
  2. ↵
    1. Yewdell J. W.
    2006. Confronting complexity: real-world immunodominance in antiviral CD8+ T cell responses. Immunity 25: 533–543.
    OpenUrlCrossRefPubMed
  3. ↵
    1. Appay V.,
    2. D. C. Douek,
    3. D. A. Price
    . 2008. CD8+ T cell efficacy in vaccination and disease. Nat. Med. 14: 623–628.
    OpenUrlCrossRefPubMed
  4. ↵
    1. Boulanger D. S.,
    2. R. Oliveira,
    3. L. Ayers,
    4. S. H. Prior,
    5. E. James,
    6. A. P. Williams,
    7. T. Elliott
    . 2010. Absence of tapasin alters immunodominance against a lymphocytic choriomeningitis virus polytope. J. Immunol. 184: 73–83.
    OpenUrlAbstract/FREE Full Text
    1. Crotzer V. L.,
    2. R. E. Christian,
    3. J. M. Brooks,
    4. J. Shabanowitz,
    5. R. E. Settlage,
    6. J. A. Marto,
    7. F. M. White,
    8. A. B. Rickinson,
    9. D. F. Hunt,
    10. V. H. Engelhard
    . 2000. Immunodominance among EBV-derived epitopes restricted by HLA-B27 does not correlate with epitope abundance in EBV-transformed B-lymphoblastoid cell lines. J. Immunol. 164: 6120–6129.
    OpenUrlAbstract/FREE Full Text
  6. ↵
    1. Jenkins M. K.,
    2. H. H. Chu,
    3. J. B. McLachlan,
    4. J. J. Moon
    . 2010. On the composition of the preimmune repertoire of T cells specific for peptide-major histocompatibility complex ligands. Annu. Rev. Immunol. 28: 275–294.
    OpenUrlCrossRefPubMed
  7. ↵
    1. Jenkins M. K.,
    2. J. J. Moon
    . 2012. The role of naive T cell precursor frequency and recruitment in dictating immune response magnitude. J. Immunol. 188: 4135–4140.
    OpenUrlAbstract/FREE Full Text
    1. Koelle D. M.,
    2. Z. Liu,
    3. C. L. McClurkan,
    4. R. C. Cevallos,
    5. J. Vieira,
    6. N. A. Hosken,
    7. C. A. Meseda,
    8. D. C. Snow,
    9. A. Wald,
    10. L. Corey
    . 2003. Immunodominance among herpes simplex virus-specific CD8 T cells expressing a tissue-specific homing receptor. Proc. Natl. Acad. Sci. USA 100: 12899–12904.
    OpenUrlAbstract/FREE Full Text
  9. ↵
    1. Kotturi M. F.,
    2. I. Scott,
    3. T. Wolfe,
    4. B. Peters,
    5. J. Sidney,
    6. H. Cheroutre,
    7. M. G. von Herrath,
    8. M. J. Buchmeier,
    9. H. Grey,
    10. A. Sette
    . 2008. Naive precursor frequencies and MHC binding rather than the degree of epitope diversity shape CD8+ T cell immunodominance. J. Immunol. 181: 2124–2133.
    OpenUrlAbstract/FREE Full Text
  10. ↵
    1. La Gruta N. L.,
    2. W. T. Rothwell,
    3. T. Cukalac,
    4. N. G. Swan,
    5. S. A. Valkenburg,
    6. K. Kedzierska,
    7. P. G. Thomas,
    8. P. C. Doherty,
    9. S. J. Turner
    . 2010. Primary CTL response magnitude in mice is determined by the extent of naive T cell recruitment and subsequent clonal expansion. J. Clin. Invest. 120: 1885–1894.
    OpenUrlCrossRefPubMed
  11. ↵
    1. Siddiqui S.,
    2. S. Basta
    . 2011. CD8+ T cell immunodominance in lymphocytic choriomeningitis virus infection is modified in the presence of toll-like receptor agonists. J. Virol. 85: 13224–13233.
    OpenUrlAbstract/FREE Full Text
  12. ↵
    1. Trautmann L.,
    2. M. Rimbert,
    3. K. Echasserieau,
    4. X. Saulquin,
    5. B. Neveu,
    6. J. Dechanet,
    7. V. Cerundolo,
    8. M. Bonneville
    . 2005. Selection of T cell clones expressing high-affinity public TCRs within human cytomegalovirus-specific CD8 T cell responses. J. Immunol. 175: 6123–6132.
    OpenUrlAbstract/FREE Full Text
  13. ↵
    1. Goulder P. J.,
    2. B. D. Walker
    . 2012. HIV and HLA class I: an evolving relationship. Immunity 37: 426–440.
    OpenUrlCrossRefPubMed
  14. ↵
    1. Kiepiela P.,
    2. A. J. Leslie,
    3. I. Honeyborne,
    4. D. Ramduth,
    5. C. Thobakgale,
    6. S. Chetty,
    7. P. Rathnavalu,
    8. C. Moore,
    9. K. J. Pfafferott,
    10. L. Hilton,
    11. et al
    . 2004. Dominant influence of HLA-B in mediating the potential co-evolution of HIV and HLA. Nature 432: 769–775.
    OpenUrlCrossRefPubMed
  15. ↵
    1. Kiepiela P.,
    2. K. Ngumbela,
    3. C. Thobakgale,
    4. D. Ramduth,
    5. I. Honeyborne,
    6. E. Moodley,
    7. S. Reddy,
    8. C. de Pierres,
    9. Z. Mncube,
    10. N. Mkhwanazi,
    11. et al
    . 2007. CD8+ T-cell responses to different HIV proteins have discordant associations with viral load. Nat. Med. 13: 46–53.
    OpenUrlCrossRefPubMed
  16. ↵
    1. Kloverpris H. N.,
    2. A. Stryhn,
    3. M. Harndahl,
    4. M. van der Stok,
    5. R. P. Payne,
    6. P. C. Matthews,
    7. F. Chen,
    8. L. Riddell,
    9. B. D. Walker,
    10. T. Ndung’u,
    11. et al
    . 2012. HLA-B*57 micropolymorphism shapes HLA allele-specific epitope immunogenicity, selection pressure, and HIV immune control. J. Virol. 86: 919–929.
    OpenUrlAbstract/FREE Full Text
  17. ↵
    1. Matthews P. C.,
    2. A. Prendergast,
    3. A. Leslie,
    4. H. Crawford,
    5. R. Payne,
    6. C. Rousseau,
    7. M. Rolland,
    8. I. Honeyborne,
    9. J. Carlson,
    10. C. Kadie,
    11. et al
    . 2008. Central role of reverting mutations in HLA associations with human immunodeficiency virus set point. J. Virol. 82: 8548–8559.
    OpenUrlAbstract/FREE Full Text
  18. ↵
    1. Mothe B.,
    2. A. Llano,
    3. J. Ibarrondo,
    4. M. Daniels,
    5. C. Miranda,
    6. J. Zamarreño,
    7. V. Bach,
    8. R. Zuniga,
    9. S. Pérez-Álvarez,
    10. C. T. Berger,
    11. et al
    . 2011. Definition of the viral targets of protective HIV-1-specific T cell responses. J. Transl. Med. 9: 208.
    OpenUrlCrossRefPubMed
  19. ↵
    1. Matthews P. C.,
    2. M. Koyanagi,
    3. H. N. Kløverpris,
    4. M. Harndahl,
    5. A. Stryhn,
    6. T. Akahoshi,
    7. H. Gatanaga,
    8. S. Oka,
    9. C. Juarez Molina,
    10. H. Valenzuela Ponce,
    11. et al
    . 2012. Differential clade-specific HLA-B*3501 association with HIV-1 disease outcome is linked to immunogenicity of a single Gag epitope. J. Virol. 86: 12643–12654.
    OpenUrlAbstract/FREE Full Text
  20. ↵
    1. Chen H.,
    2. A. Piechocka-Trocha,
    3. T. Miura,
    4. M. A. Brockman,
    5. B. D. Julg,
    6. B. M. Baker,
    7. A. C. Rothchild,
    8. B. L. Block,
    9. A. Schneidewind,
    10. T. Koibuchi,
    11. et al
    . 2009. Differential neutralization of human immunodeficiency virus (HIV) replication in autologous CD4 T cells by HIV-specific cytotoxic T lymphocytes. J. Virol. 83: 3138–3149.
    OpenUrlAbstract/FREE Full Text
  21. ↵
    1. Sáez-Cirión A.,
    2. M. Sinet,
    3. S. Y. Shin,
    4. A. Urrutia,
    5. P. Versmisse,
    6. C. Lacabaratz,
    7. F. Boufassa,
    8. V. Avettand-Fènoël,
    9. C. Rouzioux,
    10. J. F. Delfraissy,
    11. et al,
    12. ANRS EP36 HIV Controllers Study Group
    . 2009. Heterogeneity in HIV suppression by CD8 T cells from HIV controllers: association with Gag-specific CD8 T cell responses. J. Immunol. 182: 7828–7837.
    OpenUrlAbstract/FREE Full Text
  22. ↵
    1. Leslie A. J.,
    2. K. J. Pfafferott,
    3. P. Chetty,
    4. R. Draenert,
    5. M. M. Addo,
    6. M. Feeney,
    7. Y. Tang,
    8. E. C. Holmes,
    9. T. Allen,
    10. J. G. Prado,
    11. et al
    . 2004. HIV evolution: CTL escape mutation and reversion after transmission. Nat. Med. 10: 282–289.
    OpenUrlCrossRefPubMed
    1. O’Brien S. J.,
    2. X. Gao,
    3. M. Carrington
    . 2001. HLA and AIDS: a cautionary tale. Trends Mol. Med. 7: 379–381.
    OpenUrlCrossRefPubMed
  24. ↵
    1. Altfeld M.,
    2. M. M. Addo,
    3. E. S. Rosenberg,
    4. F. M. Hecht,
    5. P. K. Lee,
    6. M. Vogel,
    7. X. G. Yu,
    8. R. Draenert,
    9. M. N. Johnston,
    10. D. Strick,
    11. et al
    . 2003. Influence of HLA-B57 on clinical presentation and viral control during acute HIV-1 infection. AIDS 17: 2581–2591.
    OpenUrlCrossRefPubMed
  25. ↵
    1. Crawford H.,
    2. J. G. Prado,
    3. A. Leslie,
    4. S. Hué,
    5. I. Honeyborne,
    6. S. Reddy,
    7. M. van der Stok,
    8. Z. Mncube,
    9. C. Brander,
    10. C. Rousseau,
    11. et al
    . 2007. Compensatory mutation partially restores fitness and delays reversion of escape mutation within the immunodominant HLA-B*5703-restricted Gag epitope in chronic human immunodeficiency virus type 1 infection. J. Virol. 81: 8346–8351.
    OpenUrlAbstract/FREE Full Text
    1. Martinez-Picado J.,
    2. J. G. Prado,
    3. E. E. Fry,
    4. K. Pfafferott,
    5. A. Leslie,
    6. S. Chetty,
    7. C. Thobakgale,
    8. I. Honeyborne,
    9. H. Crawford,
    10. P. Matthews,
    11. et al
    . 2006. Fitness cost of escape mutations in p24 Gag in association with control of human immunodeficiency virus type 1. J. Virol. 80: 3617–3623.
    OpenUrlAbstract/FREE Full Text
  27. ↵
    1. Schneidewind A.,
    2. M. A. Brockman,
    3. R. Yang,
    4. R. I. Adam,
    5. B. Li,
    6. S. Le Gall,
    7. C. R. Rinaldo,
    8. S. L. Craggs,
    9. R. L. Allgaier,
    10. K. A. Power,
    11. et al
    . 2007. Escape from the dominant HLA-B27-restricted cytotoxic T-lymphocyte response in Gag is associated with a dramatic reduction in human immunodeficiency virus type 1 replication. J. Virol. 81: 12382–12393.
    OpenUrlAbstract/FREE Full Text
  28. ↵
    1. Peaper D. R.,
    2. P. Cresswell
    . 2008. Regulation of MHC class I assembly and peptide binding. Annu. Rev. Cell Dev. Biol. 24: 343–368.
    OpenUrlCrossRefPubMed
  29. ↵
    1. Altfeld M.,
    2. E. T. Kalife,
    3. Y. Qi,
    4. H. Streeck,
    5. M. Lichterfeld,
    6. M. N. Johnston,
    7. N. Burgett,
    8. M. E. Swartz,
    9. A. Yang,
    10. G. Alter,
    11. et al
    . 2006. HLA alleles associated with delayed progression to AIDS contribute strongly to the initial CD8+ T cell response against HIV-1. PLoS Med. 3: e403. Available at: http://journals.plos.org/plosmedicine/article?id=10.1371/journal.pmed.0030403.
    OpenUrlCrossRefPubMed
  30. ↵
    1. Iglesias M. C.,
    2. J. R. Almeida,
    3. S. Fastenackels,
    4. D. J. van Bockel,
    5. M. Hashimoto,
    6. V. Venturi,
    7. E. Gostick,
    8. A. Urrutia,
    9. L. Wooldridge,
    10. M. Clement,
    11. et al
    . 2011. Escape from highly effective public CD8+ T-cell clonotypes by HIV. Blood 118: 2138–2149.
    OpenUrlAbstract/FREE Full Text
    1. Ladell K.,
    2. M. Hashimoto,
    3. M. C. Iglesias,
    4. P. G. Wilmann,
    5. J. E. McLaren,
    6. S. Gras,
    7. T. Chikata,
    8. N. Kuse,
    9. S. Fastenackels,
    10. E. Gostick,
    11. et al
    . 2013. A molecular basis for the control of preimmune escape variants by HIV-specific CD8+ T cells. Immunity 38: 425–436.
    OpenUrlCrossRefPubMed
    1. Messaoudi I.,
    2. J. A. Guevara Patiño,
    3. R. Dyall,
    4. J. LeMaoult,
    5. J. Nikolich-Zugich
    . 2002. Direct link between MHC polymorphism, T cell avidity, and diversity in immune defense. Science 298: 1797–1800.
    OpenUrlAbstract/FREE Full Text
  33. ↵
    1. Price D. A.,
    2. T. E. Asher,
    3. N. A. Wilson,
    4. M. C. Nason,
    5. J. M. Brenchley,
    6. I. S. Metzler,
    7. V. Venturi,
    8. E. Gostick,
    9. P. K. Chattopadhyay,
    10. M. Roederer,
    11. et al
    . 2009. Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection. J. Exp. Med. 206: 923–936.
    OpenUrlAbstract/FREE Full Text
  34. ↵
    1. Price D. A.,
    2. S. M. West,
    3. M. R. Betts,
    4. L. E. Ruff,
    5. J. M. Brenchley,
    6. D. R. Ambrozak,
    7. Y. Edghill-Smith,
    8. M. J. Kuroda,
    9. D. Bogdan,
    10. K. Kunstman,
    11. et al
    . 2004. T cell receptor recognition motifs govern immune escape patterns in acute SIV infection. Immunity 21: 793–803.
    OpenUrlCrossRefPubMed
  35. ↵
    Wang, G. C., P. Dash, J. A. McCullers, P. C. Doherty, and P. G. Thomas. 2012. T cell receptor αβ diversity inversely correlates with pathogen-specific antibody levels in human cytomegalovirus infection. Sci. Transl. Med. 4: 128ra42.
  36. ↵
    1. Miles J. J.,
    2. D. C. Douek,
    3. D. A. Price
    . 2011. Bias in the αβ T-cell repertoire: implications for disease pathogenesis and vaccination. Immunol. Cell Biol. 89: 375–387.
    OpenUrlCrossRefPubMed
  37. ↵
    1. Miles J. J.,
    2. A. M. Bulek,
    3. D. K. Cole,
    4. E. Gostick,
    5. A. J. A. Schauenburg,
    6. G. Dolton,
    7. V. Venturi,
    8. M. P. Davenport,
    9. M. P. Tan,
    10. S. R. Burrows,
    11. et al
    . 2010. Genetic and structural basis for selection of a ubiquitous T cell receptor deployed in Epstein-Barr virus infection. PLoS Pathog. 6: e1001198. Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1001198.
    OpenUrlCrossRefPubMed
  38. ↵
    1. Turner S. J.,
    2. P. C. Doherty,
    3. J. McCluskey,
    4. J. Rossjohn
    . 2006. Structural determinants of T-cell receptor bias in immunity. Nat. Rev. Immunol. 6: 883–894.
    OpenUrlCrossRefPubMed
  39. ↵
    1. Billam P.,
    2. K. L. Bonaparte,
    3. J. Liu,
    4. T. J. Ruckwardt,
    5. M. Chen,
    6. A. B. Ryder,
    7. R. Wang,
    8. P. Dash,
    9. P. G. Thomas,
    10. B. S. Graham
    . 2011. T cell receptor clonotype influences epitope hierarchy in the CD8+ T cell response to respiratory syncytial virus infection. J. Biol. Chem. 286: 4829–4841.
    OpenUrlAbstract/FREE Full Text
  40. ↵
    1. Kedzierska K.,
    2. C. Guillonneau,
    3. S. Gras,
    4. L. A. Hatton,
    5. R. Webby,
    6. A. W. Purcell,
    7. J. Rossjohn,
    8. P. C. Doherty,
    9. S. J. Turner
    . 2008. Complete modification of TCR specificity and repertoire selection does not perturb a CD8+ T cell immunodominance hierarchy. Proc. Natl. Acad. Sci. USA 105: 19408–19413.
    OpenUrlAbstract/FREE Full Text
  41. ↵
    1. Feeney M. E.,
    2. Y. Tang,
    3. K. A. Roosevelt,
    4. A. J. Leslie,
    5. K. McIntosh,
    6. N. Karthas,
    7. B. D. Walker,
    8. P. J. Goulder
    . 2004. Immune escape precedes breakthrough human immunodeficiency virus type 1 viremia and broadening of the cytotoxic T-lymphocyte response in an HLA-B27-positive long-term-nonprogressing child. J. Virol. 78: 8927–8930.
    OpenUrlAbstract/FREE Full Text
  42. ↵
    1. Shapiro R. L.,
    2. M. D. Hughes,
    3. A. Ogwu,
    4. D. Kitch,
    5. S. Lockman,
    6. C. Moffat,
    7. J. Makhema,
    8. S. Moyo,
    9. I. Thior,
    10. K. McIntosh,
    11. et al
    . 2010. Antiretroviral regimens in pregnancy and breast-feeding in Botswana. N. Engl. J. Med. 362: 2282–2294.
    OpenUrlCrossRefPubMed
  43. ↵
    1. Huang K.-H. G.,
    2. D. Goedhals,
    3. J. M. Carlson,
    4. M. A. Brockman,
    5. S. Mishra,
    6. Z. L. Brumme,
    7. S. Hickling,
    8. C. S. W. Tang,
    9. T. Miura,
    10. C. Seebregts,
    11. et al
    . 2011. Progression to AIDS in South Africa is associated with both reverting and compensatory viral mutations. PLoS ONE 6: e19018. Available at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0019018.
    OpenUrlCrossRefPubMed
  44. ↵
    Carlson, J. M., J. Listgarten, N. Pfeifer, V. Tan, C. Kadie, B. D. Walker, T. Ndung'u, R. Shapiro, J. Frater, Z. L. Brumme, et al. 2012. Widespread impact of HLA restriction on immune control and escape pathways in HIV-1. J. Virol. 86: 5230–5243.
  45. ↵
    1. Payne R. P.,
    2. H. Kløverpris,
    3. J. B. Sacha,
    4. Z. Brumme,
    5. C. Brumme,
    6. S. Buus,
    7. S. Sims,
    8. S. Hickling,
    9. L. Riddell,
    10. F. Chen,
    11. et al
    . 2010. Efficacious early antiviral activity of HIV Gag- and Pol-specific HLA-B*2705-restricted CD8+ T cells. J. Virol. 84: 10543–10557.
    OpenUrlAbstract/FREE Full Text
  46. ↵
    1. Leslie A.,
    2. D. A. Price,
    3. P. Mkhize,
    4. K. Bishop,
    5. A. Rathod,
    6. C. Day,
    7. H. Crawford,
    8. I. Honeyborne,
    9. T. E. Asher,
    10. G. Luzzi,
    11. et al
    . 2006. Differential selection pressure exerted on HIV by CTL targeting identical epitopes but restricted by distinct HLA alleles from the same HLA supertype. J. Immunol. 177: 4699–4708.
    OpenUrlAbstract/FREE Full Text
  47. ↵
    1. Honeyborne I.,
    2. A. Prendergast,
    3. F. Pereyra,
    4. A. Leslie,
    5. H. Crawford,
    6. R. Payne,
    7. S. Reddy,
    8. K. Bishop,
    9. E. Moodley,
    10. K. Nair,
    11. et al
    . 2007. Control of human immunodeficiency virus type 1 is associated with HLA-B*13 and targeting of multiple gag-specific CD8+ T-cell epitopes. J. Virol. 81: 3667–3672.
    OpenUrlAbstract/FREE Full Text
  48. ↵
    1. Goulder P. J.,
    2. M. M. Addo,
    3. M. A. Altfeld,
    4. E. S. Rosenberg,
    5. Y. Tang,
    6. U. Govender,
    7. N. Mngqundaniso,
    8. K. Annamalai,
    9. T. U. Vogel,
    10. M. Hammond,
    11. et al
    . 2001. Rapid definition of five novel HLA-A*3002-restricted human immunodeficiency virus-specific cytotoxic T-lymphocyte epitopes by elispot and intracellular cytokine staining assays. J. Virol. 75: 1339–1347.
    OpenUrlAbstract/FREE Full Text
  49. ↵
    1. Altman J. D.,
    2. P. A. Moss,
    3. P. J. Goulder,
    4. D. H. Barouch,
    5. M. G. McHeyzer-Williams,
    6. J. I. Bell,
    7. A. J. McMichael,
    8. M. M. Davis
    . 1996. Phenotypic analysis of antigen-specific T lymphocytes. Science 274: 94–96.
    OpenUrlAbstract/FREE Full Text
  50. ↵
    1. Leslie A.,
    2. D. Kavanagh,
    3. I. Honeyborne,
    4. K. Pfafferott,
    5. C. Edwards,
    6. T. Pillay,
    7. L. Hilton,
    8. C. Thobakgale,
    9. D. Ramduth,
    10. R. Draenert,
    11. et al
    . 2005. Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J. Exp. Med. 201: 891–902.
    OpenUrlAbstract/FREE Full Text
  51. ↵
    1. Rousseau C. M.,
    2. B. A. Birditt,
    3. A. R. McKay,
    4. J. N. Stoddard,
    5. T. C. Lee,
    6. S. McLaughlin,
    7. S. W. Moore,
    8. N. Shindo,
    9. G. H. Learn,
    10. B. T. Korber,
    11. et al
    . 2006. Large-scale amplification, cloning and sequencing of near full-length HIV-1 subtype C genomes. J. Virol. Methods 136: 118–125.
    OpenUrlCrossRefPubMed
  52. ↵
    1. Harndahl M.,
    2. M. Rasmussen,
    3. G. Roder,
    4. S. Buus
    . 2011. Real-time, high-throughput measurements of peptide-MHC-I dissociation using a scintillation proximity assay. J. Immunol. Methods 374: 5–12.
    OpenUrlCrossRefPubMed
  53. ↵
    1. Harndahl M.,
    2. S. Justesen,
    3. K. Lamberth,
    4. G. Røder,
    5. M. Nielsen,
    6. S. Buus
    . 2009. Peptide binding to HLA class I molecules: homogenous, high-throughput screening, and affinity assays. J. Biomol. Screen. 14: 173–180.
    OpenUrlAbstract/FREE Full Text
  54. ↵
    Quigley, M. F., J. R. Almeida, D. A. Price, and D. C. Douek. 2011. Unbiased molecular analysis of T cell receptor expression using template-switch anchored RT-PCR. Curr. Protoc. Immunol. Chapter 10: Unit 10.33.
  55. ↵
    1. Price D. A.,
    2. J. M. Brenchley,
    3. L. E. Ruff,
    4. M. R. Betts,
    5. B. J. Hill,
    6. M. Roederer,
    7. R. A. Koup,
    8. S. A. Migueles,
    9. E. Gostick,
    10. L. Wooldridge,
    11. et al
    . 2005. Avidity for antigen shapes clonal dominance in CD8+ T cell populations specific for persistent DNA viruses. J. Exp. Med. 202: 1349–1361.
    OpenUrlAbstract/FREE Full Text
  56. ↵
    1. Lefranc M. P.,
    2. C. Pommié,
    3. M. Ruiz,
    4. V. Giudicelli,
    5. E. Foulquier,
    6. L. Truong,
    7. V. Thouvenin-Contet,
    8. G. Lefranc
    . 2003. IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains. Dev. Comp. Immunol. 27: 55–77.
    OpenUrlCrossRefPubMed
  57. ↵
    1. Kløverpris H. N.,
    2. R. P. Payne,
    3. J. B. Sacha,
    4. J. T. Rasaiyaah,
    5. F. Chen,
    6. M. Takiguchi,
    7. O. O. Yang,
    8. G. J. Towers,
    9. P. Goulder,
    10. J. G. Prado
    . 2013. Early antigen presentation of protective HIV-1 KF11Gag and KK10Gag epitopes from incoming viral particles facilitates rapid recognition of infected cells by specific CD8+ T cells. J. Virol. 87: 2628–2638.
    OpenUrlAbstract/FREE Full Text
  58. ↵
    1. Chao A.,
    2. L. Jost
    . 2012. Coverage-based rarefaction and extrapolation: standardizing samples by completeness rather than size. Ecology 93: 2533–2547.
    OpenUrlCrossRefPubMed
    1. Costa A. I.,
    2. D. Koning,
    3. K. Ladell,
    4. J. E. McLaren,
    5. B. P. Grady,
    6. I. M. Schellens,
    7. P. van Ham,
    8. M. Nijhuis,
    9. J. A. Borghans,
    10. C. Keşmir,
    11. et al
    . 2015. Complex T-cell receptor repertoire dynamics underlie the CD8+ T-cell response to HIV-1. J. Virol. 89: 110–119.
    OpenUrlAbstract/FREE Full Text
  60. ↵
    1. Gold M. C.,
    2. J. E. McLaren,
    3. J. A. Reistetter,
    4. S. Smyk-Pearson,
    5. K. Ladell,
    6. G. M. Swarbrick,
    7. Y. Y. Yu,
    8. T. H. Hansen,
    9. O. Lund,
    10. M. Nielsen,
    11. et al
    . 2014. MR1-restricted MAIT cells display ligand discrimination and pathogen selectivity through distinct T cell receptor usage. J. Exp. Med. 211: 1601–1610.
    OpenUrlAbstract/FREE Full Text
  61. ↵
    1. Draenert R.,
    2. M. Altfeld,
    3. C. Brander,
    4. N. Basgoz,
    5. C. Corcoran,
    6. A. G. Wurcel,
    7. D. R. Stone,
    8. S. A. Kalams,
    9. A. Trocha,
    10. M. M. Addo,
    11. et al
    . 2003. Comparison of overlapping peptide sets for detection of antiviral CD8 and CD4 T cell responses. J. Immunol. Methods 275: 19–29.
    OpenUrlCrossRefPubMed
  62. ↵
    Llano, A., N. Frahm, and C. Brander. 2009. How to optimally define optimal cytotoxic T lymphocyte epitopes in HIV infection? HIV Molecular Immunology Database, Los Alamos, New Mexico.
  63. ↵
    Leisner, C., N. Loeth, K. Lamberth, S. Justesen, C. Sylvester-Hvid, E. G. Schmidt, M. Claesson, S. Buus, and A. Stryhn. 2008. One-pot, mix-and-read peptide-MHC tetramers. PLoS One 3: e1678. Available at: http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001678.
  64. ↵
    1. Venturi V.,
    2. H. Y. Chin,
    3. T. E. Asher,
    4. K. Ladell,
    5. P. Scheinberg,
    6. E. Bornstein,
    7. D. van Bockel,
    8. A. D. Kelleher,
    9. D. C. Douek,
    10. D. A. Price,
    11. M. P. Davenport
    . 2008. TCR beta-chain sharing in human CD8+ T cell responses to cytomegalovirus and EBV. J. Immunol. 181: 7853–7862.
    OpenUrlAbstract/FREE Full Text
  65. ↵
    1. Turner S. J.,
    2. N. L. La Gruta,
    3. K. Kedzierska,
    4. P. G. Thomas,
    5. P. C. Doherty
    . 2009. Functional implications of T cell receptor diversity. Curr. Opin. Immunol. 21: 286–290.
    OpenUrlCrossRefPubMed
  66. ↵
    1. Kloverpris H. N.,
    2. E. Adland,
    3. M. Koyanagi,
    4. A. Stryhn,
    5. M. Harndahl,
    6. P. C. Matthews,
    7. R. Shapiro,
    8. B. D. Walker,
    9. T. Ndung'u,
    10. C. Brander,
    11. et al
    . 2014. HIV subtype influences HLA-B*07:02-associated HIV disease outcome. AIDS Res. Hum. Retroviruses 30: 468–475.
    OpenUrlCrossRefPubMed
  67. ↵
    1. Draenert R.,
    2. C. L. Verrill,
    3. Y. Tang,
    4. T. M. Allen,
    5. A. G. Wurcel,
    6. M. Boczanowski,
    7. A. Lechner,
    8. A. Y. Kim,
    9. T. Suscovich,
    10. N. V. Brown,
    11. et al
    . 2004. Persistent recognition of autologous virus by high-avidity CD8 T cells in chronic, progressive human immunodeficiency virus type 1 infection. J. Virol. 78: 630–641.
    OpenUrlAbstract/FREE Full Text
  68. ↵
    1. Chen D. Y.,
    2. A. Balamurugan,
    3. H. L. Ng,
    4. W. G. Cumberland,
    5. O. O. Yang
    . 2012. Epitope targeting and viral inoculum are determinants of Nef-mediated immune evasion of HIV-1 from cytotoxic T lymphocytes. Blood 120: 100–111.
    OpenUrlAbstract/FREE Full Text
  69. ↵
    1. Sacha J. B.,
    2. C. Chung,
    3. E. G. Rakasz,
    4. S. P. Spencer,
    5. A. K. Jonas,
    6. A. T. Bean,
    7. W. Lee,
    8. B. J. Burwitz,
    9. J. J. Stephany,
    10. J. T. Loffredo,
    11. et al
    . 2007. Gag-specific CD8+ T lymphocytes recognize infected cells before AIDS-virus integration and viral protein expression. J. Immunol. 178: 2746–2754.
    OpenUrlAbstract/FREE Full Text
  70. ↵
    1. Crawford H.,
    2. W. Lumm,
    3. A. Leslie,
    4. M. Schaefer,
    5. D. Boeras,
    6. J. G. Prado,
    7. J. Tang,
    8. P. Farmer,
    9. T. Ndung’u,
    10. S. Lakhi,
    11. et al
    . 2009. Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients. J. Exp. Med. 206: 909–921.
    OpenUrlAbstract/FREE Full Text
  71. ↵
    1. Schneidewind A.,
    2. M. A. Brockman,
    3. J. Sidney,
    4. Y. E. Wang,
    5. H. Chen,
    6. T. J. Suscovich,
    7. B. Li,
    8. R. I. Adam,
    9. R. L. Allgaier,
    10. B. R. Mothé,
    11. et al
    . 2008. Structural and functional constraints limit options for cytotoxic T-lymphocyte escape in the immunodominant HLA-B27-restricted epitope in human immunodeficiency virus type 1 capsid. J. Virol. 82: 5594–5605.
    OpenUrlAbstract/FREE Full Text
  72. ↵
    1. Prince J. L.,
    2. D. T. Claiborne,
    3. J. M. Carlson,
    4. M. Schaefer,
    5. T. Yu,
    6. S. Lahki,
    7. H. A. Prentice,
    8. L. Yue,
    9. S. A. Vishwanathan,
    10. W. Kilembe,
    11. et al
    . 2012. Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis. PLoS Pathog. 8: e1003041. Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003041.
    OpenUrlCrossRefPubMed
  73. ↵
    1. Koning D.,
    2. A. I. Costa,
    3. I. Hoof,
    4. J. J. Miles,
    5. N. M. Nanlohy,
    6. K. Ladell,
    7. K. K. Matthews,
    8. V. Venturi,
    9. I. M. Schellens,
    10. J. A. Borghans,
    11. et al
    . 2013. CD8+ TCR repertoire formation is guided primarily by the peptide component of the antigenic complex. J. Immunol. 190: 931–939.
    OpenUrlAbstract/FREE Full Text
  74. ↵
    1. Venturi V.,
    2. D. A. Price,
    3. D. C. Douek,
    4. M. P. Davenport
    . 2008. The molecular basis for public T-cell responses? Nat. Rev. Immunol. 8: 231–238.
    OpenUrlCrossRefPubMed
  75. ↵
    1. Obar J. J.,
    2. K. M. Khanna,
    3. L. Lefrançois
    . 2008. Endogenous naive CD8+ T cell precursor frequency regulates primary and memory responses to infection. Immunity 28: 859–869.
    OpenUrlCrossRefPubMed
  76. ↵
    1. Schmidt J.,
    2. C. Neumann-Haefelin,
    3. T. Altay,
    4. E. Gostick,
    5. D. A. Price,
    6. V. Lohmann,
    7. H. E. Blum,
    8. R. Thimme
    . 2011. Immunodominance of HLA-A2-restricted hepatitis C virus-specific CD8+ T cell responses is linked to naive-precursor frequency. J. Virol. 85: 5232–5236.
    OpenUrlAbstract/FREE Full Text
  77. ↵
    1. Scott-Browne J. P.,
    2. J. White,
    3. J. W. Kappler,
    4. L. Gapin,
    5. P. Marrack
    . 2009. Germline-encoded amino acids in the αβ T-cell receptor control thymic selection. Nature 458: 1043–1046.
    OpenUrlCrossRefPubMed
  78. ↵
    1. Cole D. K.,
    2. F. Yuan,
    3. P. J. Rizkallah,
    4. J. J. Miles,
    5. E. Gostick,
    6. D. A. Price,
    7. G. F. Gao,
    8. B. K. Jakobsen,
    9. A. K. Sewell
    . 2009. Germ line-governed recognition of a cancer epitope by an immunodominant human T-cell receptor. J. Biol. Chem. 284: 27281–27289.
    OpenUrlAbstract/FREE Full Text
  79. ↵
    1. Hislop A. D.,
    2. N. E. Annels,
    3. N. H. Gudgeon,
    4. A. M. Leese,
    5. A. B. Rickinson
    . 2002. Epitope-specific evolution of human CD8+ T cell responses from primary to persistent phases of Epstein-Barr virus infection. J. Exp. Med. 195: 893–905.
    OpenUrlAbstract/FREE Full Text
  80. ↵
    1. Ishizuka J.,
    2. G. B. Stewart-Jones,
    3. A. van der Merwe,
    4. J. I. Bell,
    5. A. J. McMichael,
    6. E. Y. Jones
    . 2008. The structural dynamics and energetics of an immunodominant T cell receptor are programmed by its Vbeta domain. Immunity 28: 171–182.
    OpenUrlCrossRefPubMed
  81. ↵
    1. Zhang S. C.,
    2. E. Martin,
    3. M. Shimada,
    4. S. B. Godfrey,
    5. J. Fricke,
    6. S. Locastro,
    7. N. Y. Lai,
    8. P. Liebesny,
    9. J. M. Carlson,
    10. C. J. Brumme,
    11. et al
    . 2012. Aminopeptidase substrate preference affects HIV epitope presentation and predicts immune escape patterns in HIV-infected individuals. J. Immunol. 188: 5924–5934.
    OpenUrlAbstract/FREE Full Text
  82. ↵
    1. Kløverpris H. N.,
    2. A. Stryhn,
    3. M. Harndahl,
    4. R. Payne,
    5. G. J. Towers,
    6. F. Chen,
    7. L. Riddell,
    8. B. D. Walker,
    9. T. Ndung’u,
    10. A. Leslie,
    11. et al
    . 2013. HLA-specific intracellular epitope processing shapes an immunodominance pattern for HLA-B*57 that is distinct from HLA-B*58:01. J. Virol. 87: 10889–10894.
    OpenUrlAbstract/FREE Full Text
  83. ↵
    1. Schmidt J.,
    2. A. K. Iversen,
    3. S. Tenzer,
    4. E. Gostick,
    5. D. A. Price,
    6. V. Lohmann,
    7. U. Distler,
    8. P. Bowness,
    9. H. Schild,
    10. H. E. Blum,
    11. et al
    . 2012. Rapid antigen processing and presentation of a protective and immunodominant HLA-B*27-restricted hepatitis C virus-specific CD8+ T-cell epitope. PLoS Pathog. 8: e1003042. Available at: http://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1003042.
    OpenUrlCrossRefPubMed
  84. ↵
    1. Briggs J. A.,
    2. M. N. Simon,
    3. I. Gross,
    4. H. G. Kräusslich,
    5. S. D. Fuller,
    6. V. M. Vogt,
    7. M. C. Johnson
    . 2004. The stoichiometry of Gag protein in HIV-1. Nat. Struct. Mol. Biol. 11: 672–675.
    OpenUrlCrossRefPubMed
  85. ↵
    1. Jacks T.,
    2. M. D. Power,
    3. F. R. Masiarz,
    4. P. A. Luciw,
    5. P. J. Barr,
    6. H. E. Varmus
    . 1988. Characterization of ribosomal frameshifting in HIV-1 gag-pol expression. Nature 331: 280–283.
    OpenUrlCrossRefPubMed
  86. ↵
    1. Harndahl M.,
    2. M. Rasmussen,
    3. G. Roder,
    4. I. Dalgaard Pedersen,
    5. M. Sørensen,
    6. M. Nielsen,
    7. S. Buus
    . 2012. Peptide-MHC class I stability is a better predictor than peptide affinity of CTL immunogenicity. Eur. J. Immunol. 42: 1405–1416.
    OpenUrlCrossRefPubMed
Back to top

In this issue

Print
Download PDF
Article Alerts
Email Article
Citation Tools

Jump to section