Extended Data Fig. 7: TE expression in SETDB1 KO A375 cells.
From: Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity
a, Distribution of TE types (top) and LTR subfamilies (bottom) induced in SETDB1 KO A375 cells by RNA-seq. b, Volcano plot of Hallmark IFN-alpha response genes in A375 cells by RNA-seq. Fold-change (x-axis) and statistical significance (y-axis) in SETDB1 KO versus control are shown. c, Percentage of TEs induced in Setdb1 KO A375 cells that retain intact viral ORFs compared to control TEs. Statistics by Fisher’s exact test. d, Diagram showing the total number of predicted, unique TE-encoded MHCI peptides induced in SETDB1 KO A375 cells by RNA-seq. Binding predictions are based on A375-specific HLA types (see Methods). Subsets of predicted TE-encoded MHCI peptides with (1) high expression in control cells and further induction upon SETDB1 KO, or (2) no detectable expression in control cells and strong induction only upon SETDB1 KO, are highlighted. ***P < 0.001. ****P < 0.0001.
