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Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection.

Ferrari G, Korber B, Goonetilleke N, Liu MK, Turnbull EL, Salazar-Gonzalez JF, Hawkins N, Self S, Watson S, Betts MR, Gay C, McGhee K, Pellegrino P, Williams I, Tomaras GD, Haynes BF, Gray CM, Borrow P, Roederer M, McMichael AJ, Weinhold KJ - PLoS Pathog. (2011)

Bottom Line: Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants.However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection.Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America. gflmp@duke.edu

ABSTRACT
In the present study, we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection, and examined whether multifunctionality is required for selection of virus escape mutations. Seven anti-retroviral therapy-naïve subjects were studied in detail between 1 and 87 weeks following onset of symptoms of acute HIV-1 infection. Synthetic peptides representing the autologous transmitted/founder HIV-1 sequences were used in multiparameter flow cytometry assays to determine the functionality of HIV-1-specific CD8+ T memory cells. In all seven patients, the earliest T cell responses were predominantly oligofunctional, although the relative contribution of multifunctional cell responses increased significantly with time from infection. Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants. However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection. Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.

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Analysis of individual functions and polyfunctional subsets.The analysis of the responses at the earliest (panels A and B) and highest recorded (panels C and D) time points are shown. The pie charts represent the relative contribution to the total response of cells exhibiting each functional parameter or combination of functional parameters. The color code for each parameter (pie slice) is reported below the x-axis of the graph. In the graph, each triangle represents the early (e-ME), late (l-ME), and non-mutating (nME) epitope-specific CD8+ T cell response detected at each time point by ICS. The color code for each group of epitopes is reported at the bottom of the figure. The grey bars represent the inter-quartile distribution of the relative frequency of each functional parameter. The dots under the x-axis represent the positive responses for each parameter. (A and C) Total MIP-1β+ responses are compared to the total responses detected as any combination of the other parameters excluding MIP-1β. (B and D) Analysis of the single or combined contribution of degranulation (CD107), IFN-γ and MIP-1β production is represented by the dots under the x-axis.
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ppat-1001273-g006: Analysis of individual functions and polyfunctional subsets.The analysis of the responses at the earliest (panels A and B) and highest recorded (panels C and D) time points are shown. The pie charts represent the relative contribution to the total response of cells exhibiting each functional parameter or combination of functional parameters. The color code for each parameter (pie slice) is reported below the x-axis of the graph. In the graph, each triangle represents the early (e-ME), late (l-ME), and non-mutating (nME) epitope-specific CD8+ T cell response detected at each time point by ICS. The color code for each group of epitopes is reported at the bottom of the figure. The grey bars represent the inter-quartile distribution of the relative frequency of each functional parameter. The dots under the x-axis represent the positive responses for each parameter. (A and C) Total MIP-1β+ responses are compared to the total responses detected as any combination of the other parameters excluding MIP-1β. (B and D) Analysis of the single or combined contribution of degranulation (CD107), IFN-γ and MIP-1β production is represented by the dots under the x-axis.

Mentions: As analysis of the functional families at the individual patient level revealed an association of total responses and ability to select for escape mutations, we investigated whether this association may reside at the level of any single or combination of the five functional parameters. We noticed that CD8+IL2+ T cells did not contribute to any of the three groups of epitope-specific responses and that the majority of CD8+TNF-α+ were also CD8+IFN-γ+ T cells, therefore, we analyzed the remaining response subsets without regard to production of IL2 and TNF-α. We observed that the earliest recorded frequency of the CD8+ T cells producing MIP-1β+ alone and in any combination with any other parameter was also significantly associated with the appearance of escape responses within subjects (Table 2, p = 0.006). A complication in interpreting the role of MIP-1β+CD8+ T cells on immune pressure is that their frequency is highly correlated with the total ICS memory fraction at the earliest time point, making it difficult to resolve which parameter, the total response or MIP-1β+, is driving the pace of immune escape. The median relative contribution of total CD8+MIP-1β+ T cells was >80% to all ME-specific responses at early time points, as shown in Figure 6A, and declined with time for the l-ME and nME groups as shown in Figure 6C. We further analyzed whether degranulation or IFN-γ production were also associated with the significant predominant contribution of CD8+MIP-1β+ cells to responses to e-ME. As shown in Figure 6B and 6D, among the possible CD8+MIP-1β+ subsets with more than one function we could identify that both CD8+MIP-1β+CD107+ and CD8+MIP-1β+CD107+IFN-γ+ subsets contributed to the e-ME-specific responses but also made a similar contribution to the l-ME and nME responses. Moreover, segregate analysis of both total CD8+IFN-γ+ (p = 0.99) and total CD8+IFN-γ+ MIP-1β+ (p = 0.27) subsets did not reveal any significant association with the appearance of escape mutants. Thus, we observed that the MIP-1β-producing CD8+T cells represent the dominant proportion of cells detectable in the early stage of infection prior to virus escape, and that this was strongly associated with immune pressure resulting in selection of the early escape mutants.


Relationship between functional profile of HIV-1 specific CD8 T cells and epitope variability with the selection of escape mutants in acute HIV-1 infection.

Ferrari G, Korber B, Goonetilleke N, Liu MK, Turnbull EL, Salazar-Gonzalez JF, Hawkins N, Self S, Watson S, Betts MR, Gay C, McGhee K, Pellegrino P, Williams I, Tomaras GD, Haynes BF, Gray CM, Borrow P, Roederer M, McMichael AJ, Weinhold KJ - PLoS Pathog. (2011)

Analysis of individual functions and polyfunctional subsets.The analysis of the responses at the earliest (panels A and B) and highest recorded (panels C and D) time points are shown. The pie charts represent the relative contribution to the total response of cells exhibiting each functional parameter or combination of functional parameters. The color code for each parameter (pie slice) is reported below the x-axis of the graph. In the graph, each triangle represents the early (e-ME), late (l-ME), and non-mutating (nME) epitope-specific CD8+ T cell response detected at each time point by ICS. The color code for each group of epitopes is reported at the bottom of the figure. The grey bars represent the inter-quartile distribution of the relative frequency of each functional parameter. The dots under the x-axis represent the positive responses for each parameter. (A and C) Total MIP-1β+ responses are compared to the total responses detected as any combination of the other parameters excluding MIP-1β. (B and D) Analysis of the single or combined contribution of degranulation (CD107), IFN-γ and MIP-1β production is represented by the dots under the x-axis.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3037354&req=5

ppat-1001273-g006: Analysis of individual functions and polyfunctional subsets.The analysis of the responses at the earliest (panels A and B) and highest recorded (panels C and D) time points are shown. The pie charts represent the relative contribution to the total response of cells exhibiting each functional parameter or combination of functional parameters. The color code for each parameter (pie slice) is reported below the x-axis of the graph. In the graph, each triangle represents the early (e-ME), late (l-ME), and non-mutating (nME) epitope-specific CD8+ T cell response detected at each time point by ICS. The color code for each group of epitopes is reported at the bottom of the figure. The grey bars represent the inter-quartile distribution of the relative frequency of each functional parameter. The dots under the x-axis represent the positive responses for each parameter. (A and C) Total MIP-1β+ responses are compared to the total responses detected as any combination of the other parameters excluding MIP-1β. (B and D) Analysis of the single or combined contribution of degranulation (CD107), IFN-γ and MIP-1β production is represented by the dots under the x-axis.
Mentions: As analysis of the functional families at the individual patient level revealed an association of total responses and ability to select for escape mutations, we investigated whether this association may reside at the level of any single or combination of the five functional parameters. We noticed that CD8+IL2+ T cells did not contribute to any of the three groups of epitope-specific responses and that the majority of CD8+TNF-α+ were also CD8+IFN-γ+ T cells, therefore, we analyzed the remaining response subsets without regard to production of IL2 and TNF-α. We observed that the earliest recorded frequency of the CD8+ T cells producing MIP-1β+ alone and in any combination with any other parameter was also significantly associated with the appearance of escape responses within subjects (Table 2, p = 0.006). A complication in interpreting the role of MIP-1β+CD8+ T cells on immune pressure is that their frequency is highly correlated with the total ICS memory fraction at the earliest time point, making it difficult to resolve which parameter, the total response or MIP-1β+, is driving the pace of immune escape. The median relative contribution of total CD8+MIP-1β+ T cells was >80% to all ME-specific responses at early time points, as shown in Figure 6A, and declined with time for the l-ME and nME groups as shown in Figure 6C. We further analyzed whether degranulation or IFN-γ production were also associated with the significant predominant contribution of CD8+MIP-1β+ cells to responses to e-ME. As shown in Figure 6B and 6D, among the possible CD8+MIP-1β+ subsets with more than one function we could identify that both CD8+MIP-1β+CD107+ and CD8+MIP-1β+CD107+IFN-γ+ subsets contributed to the e-ME-specific responses but also made a similar contribution to the l-ME and nME responses. Moreover, segregate analysis of both total CD8+IFN-γ+ (p = 0.99) and total CD8+IFN-γ+ MIP-1β+ (p = 0.27) subsets did not reveal any significant association with the appearance of escape mutants. Thus, we observed that the MIP-1β-producing CD8+T cells represent the dominant proportion of cells detectable in the early stage of infection prior to virus escape, and that this was strongly associated with immune pressure resulting in selection of the early escape mutants.

Bottom Line: Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants.However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection.Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, Duke University Medical Center, Durham, North Carolina, United States of America. gflmp@duke.edu

ABSTRACT
In the present study, we analyzed the functional profile of CD8+ T-cell responses directed against autologous transmitted/founder HIV-1 isolates during acute and early infection, and examined whether multifunctionality is required for selection of virus escape mutations. Seven anti-retroviral therapy-naïve subjects were studied in detail between 1 and 87 weeks following onset of symptoms of acute HIV-1 infection. Synthetic peptides representing the autologous transmitted/founder HIV-1 sequences were used in multiparameter flow cytometry assays to determine the functionality of HIV-1-specific CD8+ T memory cells. In all seven patients, the earliest T cell responses were predominantly oligofunctional, although the relative contribution of multifunctional cell responses increased significantly with time from infection. Interestingly, only the magnitude of the total and not of the poly-functional T-cell responses was significantly associated with the selection of escape mutants. However, the high contribution of MIP-1β-producing CD8+ T-cells to the total response suggests that mechanisms not limited to cytotoxicity could be exerting immune pressure during acute infection. Lastly, we show that epitope entropy, reflecting the capacity of the epitope to tolerate mutational change and defined as the diversity of epitope sequences at the population level, was also correlated with rate of emergence of escape mutants.

Show MeSH
Related in: MedlinePlus