Supplementary Figure 6: Comparison of established “exhaustion gene-expression profile” with VHL-deficient-expression profile shows significant correlation, but identifies differently expressed genes.
From: Hypoxia-inducible factors enhance the effector responses of CD8+ T cells to persistent antigen
(a) Flow chart of analysis. (a) Flow chart of analysis. (b) Fold-change versus P-value plot of VHL-deficient versus VHL-sufficient P14 cells at day 7 post-infection (data from Fig. 3a). Genes that were reported1 to be upregulated in wild-type exhausted versus wild-type effector cells are highlighted in red, those down in blue; selected genes are identified. Genes up- or downregulated in VHL-deficient versus VHL-sufficient P14 cells show significant correlation with the genes previously reported to be up- or downregulated with exhausted versus effector cells (P = 0.0008 and 0.0004, respectively); Chi-squared test assuming equal distribution of genes up- and downregulated for the VHL-deficient versus VHL-sufficient and exhausted versus effector comparisons. (c) Bar graph representation of the data in a,b identifying the 64 genes that were upregulated in exhausted versus effector CTL; fold-change for VHL-deficient versus VHL-sufficient P14 cells is plotted. (d) As in c, but the fold-change expression of VHL-deficient versus VHL-sufficient of the 109 genes identified in a,b as being downregulated in exhausted versus effector cells.
