A comparison of antigen-specific T cell responses induced by six novel tuberculosis vaccine candidates

Abstract

Eradication of tuberculosis (TB), the world's leading cause of death due to infectious disease, requires a highly efficacious TB vaccine. Many TB vaccine candidates are in pre-clinical and clinical development but only a few can be advanced to large-scale efficacy trials due to limited global resources. We aimed to perform a statistically rigorous comparison of the antigen-specific T cell responses induced by six novel TB vaccine candidates and the only licensed TB vaccine, Bacillus Calmette-Guérin (BCG). We propose that the antigen-specific immune response induced by such vaccines provides an objective, data-driven basis for prioritisation of vaccine candidates for efficacy testing. We analyzed frequencies of antigen-specific CD4 and CD8 T cells expressing IFNγ, IL-2, TNF and/or IL-17 from adolescents or adults, with or without Mycobacterium tuberculosis (M.tb) infection, who received MVA85A, AERAS-402, H1:IC31, H56:IC31, M72/AS01E, ID93+GLA-SE or BCG. Two key response characteristics were analyzed, namely response magnitude and cytokine co-expression profile of the memory T cell response that persisted above the pre-vaccination response to the final study visit in each trial. All vaccines preferentially induced antigen-specific CD4 T cell responses expressing Th1 cytokines; levels of IL-17-expressing cells were low or not detected. In M.tb-uninfected and -infected individuals, M72/AS01E induced higher memory Th1 cytokine-expressing CD4 T cell responses than other novel vaccine candidates. Cytokine co-expression profiles of memory CD4 T cells induced by different novel vaccine candidates were alike. Our study suggests that the T cell response feature which most differentiated between the TB vaccine candidates was response magnitude, whilst functional profiles suggested a lack of response diversity. Since M72/AS01E induced the highest memory CD4 T cell response it demonstrated the best vaccine take. In the absence of immunological correlates of protection, the likelihood of finding a protective vaccine by empirical testing of candidates may be increased by the addition of candidates that induce distinct immune characteristics.

Fig 1

Pre-vaccination antigen-specific CD4 (A) and CD8 (B) T cell responses by vaccine and M.tb infection status. Frequencies of antigen-specific, Th1-cytokine expressing CD4 or CD8 T cells pre-vaccination. Points denote sample trimmed means and error bars denote 95% CI. Solid error bar lines indicate responses that significantly exceeded 0.005% after controlling the false discovery rate at 0.01. Dashed lines did not meet this significance criterion. “No vaccine” indicates the immune response to M.tb infection detected after megapool stimulation in unvaccinated, IGRA-positive individuals. Pre-vaccination responses to each individual antigen in each vaccine are shown in S1A Fig.

Fig 2. Longitudinal vaccine-induced antigen-specific CD4 and CD8 T cell response kinetics by M.tb infection status for the six novel TB vaccine candidates and BCG.

Non-vertical lines pass through median CD4 (orange) or CD8 (blue) T cell responses at each timepoint. Vaccine administration timepoints are denoted by the “V” symbols along the x-axes. Vertical solid (M.tb-uninfected) and dashed (M.tb-infected) lines indicate interquartile ranges. The plots are truncated between -0.1 and 2.5 for readability, suppressing lower and/or upper interquartile ranges for some vaccines for some timepoints.

Fig 3

Vaccine-induced memory CD4 (A) and CD8 (B) T cell responses by vaccine and M.tb infection status. Frequencies of antigen-specific Th1-cytokine expressing CD4 (a) or CD8 (B) responses at the final time point in each trial, relative to the pre-vaccination frequencies (i.e. memory response minus pre-vaccination response). Points denote sample trimmed means, and error bars 95% CI. Solid error bar lines indicate responses that significantly exceeded 0% after controlling the false discovery rate at 0.01. Dashed lines did not meet this significance criterion.

Fig 4. PCA biplots of cytokine co-expression profiles for vaccine-induced memory CD4 T cells.

Characterization of vaccine-induced memory CD4 T cells responses by their Th1 cytokine co-expression profiles for each vaccine in M.tb-uninfected (A) and -infected (B) individuals. PCA biplots show principal components 1 and 2, computed from the scaled vaccine-induced memory T cell responses by cytokine-expressing subset. The scaled response indicates the relative proportions of cytokine co-expressing subsets of the induced response. It ranges from -1 to 1 and is independent of the overall vaccine-induced response magnitude (see Materials and Methods for details). Thick curves denote 95% bootstrap-based confidence areas for bivariate means for each vaccine-induced response. Thin curves represent contour lines of the bootstrap kernel density. The cytokine co-expression combinations displayed (G+2+T+, for example, refers to IFNγ+IL-2+TNF+) by biplot axes had high axis predictivity values relative to other cytokine combinations (S6 Fig). Percentages of total variation captured by principal components 1 and 2 are given on plot axes. Points denote observations; not all observations are shown to highlight the confidence areas. The legend item “No vaccine” indicates the group of M.tb-infected individuals that did not receive a vaccine, but whose blood was stimulated with megapool.

Fig 5. Vaccine-induced cytokine co-expression profiles for vaccine-induced memory CD4 T cells.

Characterization of vaccine-induced memory CD4 T cells response by their Th1 cytokine co-expression profiles for each vaccine in M.tb-uninfected (A) and -infected (B) individuals. Points denote sample trimmed means of the scaled vaccine-induced memory CD4 response for each vaccine for each cytokine-expressing subset, and error bars 95% CI (see Materials and Methods for details). Solid error bar lines indicate responses that significantly exceeded 0% after controlling the false discovery rate at 0.01. Dashed lines did not meet this significance criterion. G+2+T+, for example, refers to IFNγ+IL-2+TNF+.