Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design

<div><p>A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8⁺ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8⁺ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8⁺ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8⁺ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r = - 0.65, p = 0.009). Moreover, subjects possessing CD8⁺ T cells recognizing at least one conserved epitope had 1.4 log₁₀ lower set-point viremia compared to those recognizing only variable epitopes (p = 0.021). The association between viral control and the breadth of conserved CD8⁺ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p = 0.215). The associations with viral control were independent of functional avidity of CD8⁺ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8⁺ T cell responses to multiple conserved epitopes of HIV-1.</p></div

CD8⁺ T cell responses against conserved epitopes (bCSp) are associated with viral control.

<p>(A) The plasma VL set point was compared to breadth of conserved epitopes (Spearman Rank Correlation, r = −0.65, p = 0.009). The solid line represents a regression line. (B) The median plasma viral set point in individuals who mounted CD8⁺ T cell responses against at least one conserved epitope (Mann Whitney, p = 0.018). (A–B) Subjects possessing B*35Px, B*27 and B*57 alleles are represented by red circles, green triangles and inverted green triangles respectively.</p

Breadth of HIV-1-specific CD8⁺ T cell responses to conserved Gag epitopes correlate with lower viremia.

<p>VL set point was compared to breadth of CD8⁺ T cell responses. (A and B) Correlation between breadth of CD8⁺ T cell responses against conserved Gag or variable Gag epitopes (clade-B) with plasma VL set point (Spearman Rank Correlation, r = −0.65, p = 0.009 and r = −0.32, p = 0.250 respectively). (A–B) The solid line represents a regression line. (C) The median plasma VL set point in individuals who mounted CD8⁺ T cell responses against at least one conserved (bCSp) Gag epitope (Mann Whitney, p = 0.019). (A–C) Subject possessing B*35Px, B*27 and B*57 allele are represented by red circles, green triangles and inverted green triangles respectively.</p

Targeting conserved epitope (bCSp) was independent of possession of favorable alleles.

<p>(A) The median CS of epitopes by HLA group: favorable alleles (subjects possessing B*27 and B*57 alleles), unfavorable alleles (subjects possessing B*35Px alleles: B*35Px: B*35∶02, B*35∶03, B*35∶04, and B*53∶01) and neutral alleles (subjects not possessing B*27, B*57 or B*35Px alleles) (Kruskal-Wallis, p = 0.215). Horizontal lines indicate median value. (B) The median plasma VL set point in individuals (subjects not recognizing at least one conserved epitopes were excluded on this analysis) recognizing at least one conserved epitope by possession of favorable allele (Mann Whitney, p = 0.662). (C) The median plasma VL set point in individuals (not possessing favorable alleles, subjects possessing favorable alleles were excluded) who elicited CD8⁺ T cell responses against at least one conserved epitope (Mann Whitney, p = 0.067). (B–C) Subjects possessing B*35Px, B*27 and B*57 alleles are represented by red circles, green triangles and inverted green triangles respectively.</p

Method of determining CS influences significance of T cell association with and viral control.

<p>(A) The plasma VL set point was compared to breadth of conserved epitopes based on mCSp (Spearman Rank Correlation, r = −0.40, p = 0.139). (B, C) The plasma VL set point was compared to breadth of conserved epitopes based on bCSe (Spearman Rank Correlation, r = −0.52, p = 0.048) and mCSe (Spearman Rank Correlation, r = −0.52, p = 0.043) respectively. Subject possessing B*35Px, B*27 and B*57 allele are represented by red circles, green triangles and inverted green triangles respectively.</p

CD8⁺ T cell functional avidity and control of viral replication.

<p>(A) Correlation between functional avidity and CS of CD8⁺ T cell epitopes. (B) The functional avidity of CD8⁺ T cells by CS (clade-B) grouping (Kruskal-Wallis, p = 0.681). Horizontal lines indicate median values. (C–E) Correlation between average (C), maximum (D) and immunodominant (E) functional avidity of CD8⁺ T cells in each subject with average plasma viral set point (Spearman Rank Correlation, r = −0.07, p = 0.800; r = −0.18, p = 0.516 and r = −0.44, p = 0.105 respectively). (C–E) The solid line represents a regression line. Subject possessing B*35Px, B*27 and B*57 allele are represented by red circles, green triangles and inverted green triangles respectively.</p

Assessment of VL set point of subjects with primary HIV-1 infection.

a<p>DPI, days post infection.</p>b<p>SPVL#, number of longitudinal viral load data used to identify viral load set point.</p

Variable epitopes are preferentially recognized in early HIV-1-infection.

<p>A total of 123 epitopes identified in 23 subjects with early HIV-1-infection were analyzed according to their CS. (A) Epitopes were plotted against their CS. The HLA genotype of each subject is also shown. CS of each epitope was calculated as the frequency of an exact epitope match in aligned clade-B sequences (bCSp). Each symbol represents an epitope recognized by HIV-specific CD8⁺ T cells in an individual. Symbols are colored to denote the HLA restriction of the epitope. (B) The percentage of total magnitude of IFN-γ responses directed against epitopes by CS grouping (Friedman, p<0.001). (C) The percentage of total breadth of CD8⁺ T cell responses directed against epitopes by CS grouping (Friedman, p<0.0001). (B–C) The % of the total magnitude and breadth of CD8⁺ T cell responses targeting “Variable”, “Relatively Conserved” and “Conserved” epitopes. Individual subjects are denoted by a specific color. Horizontal lines indicate median values; statistical significance was assessed by matched test for 2 groups (Wilcoxon matched-pairs signed rank test) or multiple groups (Friedman test).</p