Fitness Cost of Escape Mutations in p24 Gag in Association with Control of Human Immunodeficiency Virus Type 1

irsiCaixa Foundation, University Hospital Germans Trias i Pujol, Barcelona, Spain.
Journal of Virology (Impact Factor: 4.44). 05/2006; 80(7):3617-23. DOI: 10.1128/JVI.80.7.3617-3623.2006
Source: PubMed


Mutational escape by human immunodeficiency virus (HIV) from cytotoxic T-lymphocyte (CTL) recognition is a major challenge for vaccine design. However, recent studies suggest that CTL escape may carry a sufficient cost to viral replicative capacity to facilitate subsequent immune control of a now attenuated virus. In order to examine how limitations can be imposed on viral escape, the epitope TSTLQEQIGW (TW10 [Gag residues 240 to 249]), presented by two HLA alleles associated with effective control of HIV, HLA-B*57 and -B*5801, was investigated. The in vitro experiments described here demonstrate that the dominant TW10 escape mutation, T242N, reduces viral replicative capacity. Structural analysis reveals that T242 plays a critical role in defining the start point and in stabilizing helix 6 within p24 Gag, ensuring that escape occurs at a significant cost. A very similar role is played by Thr-180, which is also an escape residue, but within a second p24 Gag epitope associated with immune control. Analysis of HIV type 1 gag in 206 B*57/5801-positive subjects reveals three principle alternative TW10-associated variants, and each is strongly linked to concomitant additional variants within p24 Gag, suggesting that functional constraints operate against their occurrence alone. The extreme conservation of p24 Gag and the predictable nature of escape variation resulting from these tight functional constraints indicate that p24 Gag may be a critical immunogen in vaccine design and suggest novel vaccination strategies to limit viral escape options from such epitopes.

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    • "Inheritance of protective MHC Class I (MHC-I) alleles, important for CD8+ T cell recognition of target cells (such as HLA-B*57), has been associated with delayed progression to AIDS [14], [15], [16], [17] and found to be enriched in HIV-1 controller cohorts [18], [19]. CD8+ T cell responses directed against the HIV-1 Gag protein are increased in individuals with protective MHC-I alleles [20], [21], [22], [23], [24], [25] and are associated with lower viral loads [26], [27], [28]. Gag-specific CD8+ T cell responses target virally infected target cells early in the viral life cycle before integration and viral replication occurs [29], and are believed to limit viral replication by targeting conserved epitopes that reduce viral fitness following the emergence of escape mutations [30], [31], [32], [33]. "
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    ABSTRACT: HIV-1 infected viremic controllers maintain durable viral suppression below 2000 copies viral RNA/ml without anti-retroviral therapy (ART), and the immunological factor(s) associated with host control in presence of low but detectable viral replication are of considerable interest. Here, we utilized a multivariable analysis to identify which innate and adaptive immune parameters best correlated with viral control utilizing a cohort of viremic controllers (median 704 viral RNA/ml) and non-controllers (median 21,932 viral RNA/ml) that were matched for similar CD4+ T cell counts in the absence of ART. We observed that HIV-1 Gag-specific CD8+ T cell responses were preferentially targeted over Pol-specific responses in viremic controllers (p = 0.0137), while Pol-specific responses were positively associated with viral load (rho = 0.7753, p = 0.0001, n = 23). Viremic controllers exhibited significantly higher NK and plasmacytoid dendritic cells (pDC) frequency as well as retained expression of the NK CD16 receptor and strong target cell-induced NK cell IFN-gamma production compared to non-controllers (p<0.05). Despite differences in innate and adaptive immune function however, both viremic controllers (p<0.05) and non-controller subjects (p<0.001) exhibited significantly increased CD8+ T cell activation and spontaneous NK cell degranulation compared to uninfected donors. Overall, we identified that a combination of innate (pDC frequency) and adaptive (Pol-specific CD8+ T cell responses) immune parameters best predicted viral load (R2 = 0.5864, p = 0.0021, n = 17) by a multivariable analysis. Together, this data indicates that preferential Gag-specific over Pol-specific CD8+ T cell responses along with a retention of functional innate subsets best predict host control over viral replication in HIV-1 infected viremic controllers compared to chronically-infected non-controllers.
    PLoS ONE 07/2014; 9(7):e103209. DOI:10.1371/journal.pone.0103209 · 3.23 Impact Factor
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    • "Mutations in KF11 are rare in Clade B HIV-1 isolates, but one patient was found to have the A163S mutation and we demonstrated that this was in fact an escape mutation in a prior study [38]. In agreement with other studies [40-44], we found that some of the escape mutants we generated were detrimental to viral fitness. While attenuating escape mutations may contribute to elite control [56], viruses from CPs have been observed to have similar escape mutations, although compensatory mutations may partially restore viral fitness [57,58]. "
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    ABSTRACT: Elite Controllers or Suppressors (ES) are HIV-1 positive individuals who maintain plasma viral loads below the limit of detection of standard clinical assays without antiretroviral therapy. Multiple lines of evidence suggest that the control of viral replication in these patients is due to a strong and specific cytotoxic T lymphocyte (CTL) response. The ability of CD8+ T cells to control HIV-1 replication is believed to be impaired by the development of escape mutations. Surprisingly, viruses amplified from the plasma of ES have been shown to contain multiple escape mutations, and it is not clear how immunologic control is maintained in the face of virologic escape. We investigated the effect of escape mutations within HLA*B-57-restricted Gag epitopes on the CD8+ T cell mediated suppression of HIV-1 replication. Using site directed mutagenesis, we constructed six NL4-3 based viruses with canonical escape mutations in one to three HLA*B-57-restricted Gag epitopes. Interestingly, similar levels of CTL-mediated suppression of replication in autologous primary CD4+ T cells were observed for all of the escape mutants. Intracellular cytokine staining was performed in order to determine the mechanisms involved in the suppression of the escape variants. While low baseline CD8+ T cells responses to wild type and escape variant peptides were seen, stimulation of PBMC with either wild type or escape variant peptides resulted in increased IFN-gamma and perforin expression. These data presented demonstrate that CD8+ T cells from ES are capable of suppressing replication of virus harboring escape mutations in HLA-B*57-restricted Gag epitopes. Additionally, our data suggest that ES CD8+ T cells are capable of generating effective de novo responses to escape mutants.
    Retrovirology 12/2013; 10(1):152. DOI:10.1186/1742-4690-10-152 · 4.19 Impact Factor
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    • "The HLA-B*57 and HLA-B*5801 alleles are over-represented in ES cohorts cohorts [3-9], and HLA-B*57 is the major genetic determinant of control of HIV-1 replication as identified in multiple genome wide association studies [10-14]. Additionally, HLA-B*57 is thought to present peptides from structurally conserved regions of Gag, and mutations in these Gag epitopes have been associated with viral attenuation [42,43]. Therefore, we asked whether CD8+ T cells from HLA-B*57/5801+ ES were able to target proteins from the incoming virion, prior to the productive infection of target CD4+ T cells. "
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    ABSTRACT: Elite controllers or suppressors have the remarkable capacity to maintain HIV-1 plasma RNA levels below the limit of detection of clinical assays (<50 copies/mL) without therapy and have a lower frequency of latently infected cells compared to chronic progressors. While it is unclear how this reduced seeding of the reservoir is achieved, it is possible that effective CTL responses play an in important role in limiting the size of the latent reservoir. Herein, we demonstrate that primary CD8+ T cells from HLA-B*57/5801 elite suppressors were able to efficiently eliminate resting and activated primary CD4+ T cells shortly after viral entry and prior to productive infection. CD8+ T cells from elite suppressors were significantly more effective at eliminating these cells than CD8+ T cells from chronic progressors. Nonproductively infected CD4+ T cells may represent a subpopulation of cells that are precursors to latently infected cells; therefore, the effective elimination of these cells may partially explain why elite suppressors have a much lower frequency of latently infected cells compared to chronic progressors. Thus, a vaccine strategy that elicits early and potent CD8+ T cell responses may have the capacity to limit the seeding of the latent reservoir in HIV-1 infection.
    Retrovirology 07/2013; 10(1):68. DOI:10.1186/1742-4690-10-68 · 4.19 Impact Factor
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