Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage - PubMed (original) (raw)
Characterization of HIV-specific CD4+ T cell responses against peptides selected with broad population and pathogen coverage
Marcus Buggert et al. PLoS One. 2012.
Abstract
CD4+ T cells orchestrate immunity against viral infections, but their importance in HIV infection remains controversial. Nevertheless, comprehensive studies have associated increase in breadth and functional characteristics of HIV-specific CD4+ T cells with decreased viral load. A major challenge for the identification of HIV-specific CD4+ T cells targeting broadly reactive epitopes in populations with diverse ethnic background stems from the vast genomic variation of HIV and the diversity of the host cellular immune system. Here, we describe a novel epitope selection strategy, PopCover, that aims to resolve this challenge, and identify a set of potential HLA class II-restricted HIV epitopes that in concert will provide optimal viral and host coverage. Using this selection strategy, we identified 64 putative epitopes (peptides) located in the Gag, Nef, Env, Pol and Tat protein regions of HIV. In total, 73% of the predicted peptides were found to induce HIV-specific CD4+ T cell responses. The Gag and Nef peptides induced most responses. The vast majority of the peptides (93%) had predicted restriction to the patient's HLA alleles. Interestingly, the viral load in viremic patients was inversely correlated to the number of targeted Gag peptides. In addition, the predicted Gag peptides were found to induce broader polyfunctional CD4+ T cell responses compared to the commonly used Gag-p55 peptide pool. These results demonstrate the power of the PopCover method for the identification of broadly recognized HLA class II-restricted epitopes. All together, selection strategies, such as PopCover, might with success be used for the evaluation of antigen-specific CD4+ T cell responses and design of future vaccines.
Conflict of interest statement
Competing Interests: The authors have declared that no competing interests exist.
Figures
Figure 1. Selection of Nef-specific epitopes using the PopCover algorithm.
Fifteen Tat 15-mer peptides were selected from the pool of 20,962 predicted HLA class II binders. Each row in the figure represents one peptide, and each column represents an HLA class II molecule. The value in each cell gives the cumulative number of times a given allele was predicted to bind any of the selected peptides. The first selected peptide covered only 11 over the 45 HLA alleles, however, when combined with the other peptides in the pool, the HLA coverage increased to 96% (43 out of 45). When taking the allelic frequency into account, this corresponded to a population-coverage of 99.8%. The coverage of the HIV genomes was similar. The first selected peptide (FPVRPQVPLRPMTYR) is present in 253 of the 396 genomes (64%) included in the analysis. With the other peptides in the pool, this coverage is increased to 99.0%.
Figure 2. Immunodominance of predicted Gag- and Nef-specific CD4+ T cell responses.
(A) Overall immunogenic analysis illustrating the individual peptides that generated a CD4+ T cell response. The vertical axis represents the total number of individuals that recognised each peptide, while the horizontal axis illustrates the individual peptide numbers within each HIV region. (B) Distribution of the number of recognised peptides per individual. (C) Percentage of peptides from different HIV proteins that induced a CD4+ T cell response. (D) Fraction of tested peptides from different HIV protein regions that generated CD4+ T cell responses per individual. The statistical analysis was performed with a one-way ANOVA and a non-parametric Kruskal Wallis test with Dunn’s multiple comparison test to compare all of the pairs of columns; *P<0.05, **P<0.01 and ***P<0.001. The data are derived from 38 independent experiments (mean and SEM).
Figure 3. Association between the breadth of Gag-specific CD4+ T cells and HIV viremia.
Correlation between CD4+ T cells targeting multiple Gag peptides and viral load in viremic subjects using the Spearman non-parametric test. Similar correlation and significance was obtained excluding subject THS-15, who had low-grade viremia and documented poor treatment adherence.
Figure 4. Functional discrepancies of CD4+ T cells targeting predicted peptides of different HIV protein regions.
(A) Representative flow cytometric plots showing the pattern of CD4+ T cell TNF secretion along with IFNγ, IL-2, MIP-1β and IL-21 upon Gag-p55 stimulation. (B) Pie charts representing the fraction of functions upregulated by the various HIV protein-specific CD4+ T cells; from one (yellow) up to five functions (black) are illustrated by the colour-scale. Permutation tests were performed to compare the differences between the pie charts. (C) Frequency comparison of the functions of Nef-specific (blue), Gag-specific (red) and Gag-p55-specific (orange) CD4+ T cells for each of the 31 functional combinations. Bars represent the means of a functional combination, and upper whiskers show SEM. Significant differences between the bars for Gag-p55 and Gag or Nef are represented by +, which indicates P<0.05 using Student’s t-test.
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