Fig. 5

Cryptic transcript expression in tumors. a–c Cryptic transcript expression in tumors characterized by TCGA. Shown is cryptic transcript expression in tumors with high or low methylation of cryptic transcript promoter regions (blue or red; > or ≤ the median methylation level of each tumor type), and in normoxic or hypoxic (light or dark color) tumors. Data are shown for a all tumor types combined, b stratified into those that are responding or non-responding to immunotherapy following the classification described by Turajlik and colleagues [38], and c for each tumor type separately. P values by t-test, red values indicating inverse correlations. d DNA methylation levels at cryptic transcript promoters (left) and cryptic transcript expression (right) in tumors profiled in TCGA, stratified into tumor types that are responsive (n = 2280) or non-responsive (n = 2214) to checkpoint immunotherapy. ***P < 0.001 by t-test. e Heatmap showing the expression (Z-score, blue to red) of the 59 cryptic transcripts associated with cytolytic activity in tumors responsive to immunotherapy from TCGA. The boxplot on the right depicts the log fold change in expression of the same 59 cryptic transcripts in hypoxic versus normoxic MCF7 cells (24 h, 0.5% O₂), and of MCF7 cells after 4-day exposure to aza versus vehicle-treated hypoxic MCF7 cells (P < 0.05 for all cryptic transcripts, either for hypoxia versus vehicle, or for hypoxia plus aza versus aza alone). At the bottom, cytolytic activity of each TCGA sample is depicted. LUAD; lung adenocarcinoma; LUSC, lung squamous cell carcinoma; HNSC, head and neck squamous cell carcinoma; BLCA, bladder urothelial carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; SKCM, skin cutaneous melanoma