Identification of core Th and Treg cell signatures.
(A) Expression analysis of the indicated chemokine receptors and transcription factors that define the different T cell populations. Values represent batch-effect–corrected counts per million. (B) PCA of all samples run on all expressed genes. Cluster centers representing naive T cells (1), Th cells (2), and Treg cells (3) returned by k-means clustering. (C) Venn diagrams showing the overlap in genes that were significantly (adjusted p value <0.05 and absolute log2 fold-change >1) upregulated (left) or downregulated (right) when comparing Treg cells with their mirror Th counterpart as indicated. Numbers indicate genes that were up-/downregulated in all comparisons (core of the Venn diagrams), or genes that were differentially expressed in only one comparison. (D) Heatmap showing expression of 31 genes identified by Pesenacker et al. as activation-independent Treg markers in the indicated samples. Bolded genes were significantly differentially expressed in all comparisons of mirror Th and Treg populations. (E) Volcano plots showing pairwise comparisons of mirror Th and Treg cell populations. Genes identified by Pesenacker et al. (13) as higher in Treg cells are highlighted in red, those higher in Th cells in blue. The χ2 test statistic and p values indicate whether the sets of up- and downregulated identified by Pesenacker et al. (13) are differentially distributed in the indicated Treg cell versus Th cell comparison.
