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.