Figure 3. Differences in Th1/Th2 activation and neuroinflammation signaling pathways in CD4 Kdm6a KO mice.

(A) Scatterplot shows upregulated (red) and downregulated (blue) genes in CD4⁺ T cells in cKO as compared with WT. Differentially expressed genes were identified with edgeR (FDR < 0.1, logFC > 1 or logFC < –1, logCPM > 1). Other genes filtered out with this threshold are shown as gray dots. (B) The expression difference of 5 genes was validated with RT- PCR using biological replicates of 3 WT and 3 cKO: increased in cKO (Klra7: P = 0.0018, Ccl5: P = 0.0012), decreased in cKO (P2rx7: P = 0.0017, Tlr1: P = 0.0017, Cxcl10: P = 0.0204, t tests). In box-and-whisker plots, thick lines inside boxes represent the median of the data. Lower and upper ends of boxes show quantiles (25% and 75%), and whiskers show minimum and maximum values. P values were determined by t test. (C and D) Top 10 canonical pathways for the differentially expressed genes between WT and cKO CD4⁺ T cells. Significantly expressed genes (FDR < 0.1, logCPM > 1) were classified into 2 groups, and canonical pathway analysis was performed for each: (C) upregulated genes (logFC > 1) and (D) downregulated genes (logFC < –1), each in cKO as compared with WT. Genes within the top upregulated pathways in C (Th1 and Th2 activation pathway) and downregulated pathway in D (neuroinflammation signaling pathway) were visualized for their significance levels with volcano plots (E and F, respectively; pink dots represent Th1 and Th2 activation pathway genes, and green dots represent neuroinflammation signaling pathway genes). Gray circles represent all other genes not in these pathways, with the blue line as a threshold of significance (FDR = 0.1: any gene above this line considered significantly different). (G) Heatmaps for genes within the top canonical pathways: Th1 and Th2 activation pathway and neuroinflammation signaling pathway (red indicates upregulated, green represents downregulated).