Figure 5 from Epigenetic Induction of Cancer-Testis Antigens and Endogenous Retroviruses at Single-Cell Level Enhances Immune Recognition and Response in Glioma

CTA induction but not downstream interferon-downstream stimulation by DAC is correlated with CpG demethylation in glioma cells. A, Heatmap and hierarchical clustering of differentially expressed CTA. Scale represents z-score of DESeq2 counts. B, Violin plot of beta value distribution between treatment conditions for CpG probes corresponding to differentially upregulated CTA (P-value = 0.028; Wilcoxon rank sum test with continuity correction). C, Scatter plot of all CpG island probes containing intersectional DNA methylation log₂FoldChange and RNA expression log₂FoldChange of annotated genes in black (n = 115,801 CpG island probes). CpG island probes corresponding to CTA with Pearson correlation are highlighted in (red; n = 535 CpG probes; n = 65 CTA genes). D, Enricher analysis of DESEQ2 differentially upregulated genes (Hallmark IFNγ P = 0.00548; Hallmark IFNα P = 0.00548; Hallmark inflammatory response P = 0.0426) and downregulated genes (Hallmark mTORC1 signaling P = 1.59e⁻³; Hallmark mitotic spindle P = 1.59e⁻³, Hallmark G2M Checkpoint P = 7.77e⁻⁵; Hallmark E2F targets P = 7.77e⁻⁵). Hallmark MSigDB signature adjusted P values determined using Fisher exact test adjusted by Benjamini–Hochberg correction. E, Violin plot of beta value distribution between treatment conditions for CpG probes corresponding to differentially upregulated DAC_UP_MSigDB_Hallmark genes (P-value = 0.497; Wilcoxon rank sum test with continuity correction). F, Scatter plot of intersectional DNA methylation log₂FoldChange and RNA expression log₂FoldChange CpG island probes. CpG probes corresponding to the Hallmark Interferon Alpha Response gene set with Pearson correlation are highlighted in blue (n = 471 probes; n = 53 genes).