Figure 3. Expression of Th1 genes in TFH cells, Tbet regulation of cytotoxic genes, and cytotoxic TFH genes upregulated after SIV infection.

(A) Gene expression plots for Ifng, Tbx21 (Tbet), and Prdm1 (Blimp1) taken from the RNAseq data analyzed in Figure 2. WT (red) TFH cell average mRNA levels were set to 1 and fold changes are shown for Bcl6FC (blue), Blimp1FC (green), and DKO (magenta) TFH cells. The mRNA levels are taken from log₂RPKM counts. n = 4. ANOVA with Tukey’s post hoc analysis was used to determine statistical significance. (B) Heatmap of the gene set of 23 CD8⁺ cytotoxic T cell genes described in Figure 2, D–F, versus published gene expression data for WT and Tbet-KO T cells (GSE105806). (C) Comparison of fold changes in genes from TFH cells from SIV⁺ infected macaques over uninfected TFH cells from uninfected macaques (published RNAseq data GSE69756). As a group, the 23 CD8⁺ cytotoxic T cell genes described in Figure 2, D–F, show a statistically significant increase within the SIV⁺ TFH RNAseq data set over the SIV^– TFH RNAseq data set (“cytotoxic” column), in comparison with all other noncytotoxic genes expressed in the TFH cells, which on average showed no statistically significant upregulation between the 2 types of TFH cells (“other” column). For statistical significance of overlap between 2 sets of genes, the P value was calculated based on hypergeometric distribution.