Fig. 4
Effective treatments correlate with overexpression of a large number of functionally relevant genes. a Number of differentially expressed genes (DEG) (red, upregulated; blue, downregulated) detected by RNAseq on tumors in progression (non-responders, NR) and regression (responders, R) upon anti-PD1 or anti-PD1 and vaccine combination versus untreated tumors (n = 3–5/group) (median log2 FC < −1 or >1; Benjamini–Hochberg corrected p value < 0.05). b Venn diagram showing the overlap of the DEG plotted in panel A between anti-PD1 and combination therapy. c Heat map of the 1412 DEG found in responders to the combination therapy compared to untreated for each group of treatment. d Gene Ontology (GO) enrichment analysis performed on DEG genes found in responders to GAd and anti-PD1 combination versus untreated. The 22 biological processes with at least the 40% of genes significantly modulated are shown (Bonferroni corrected p value < 0.01). Genes upregulated upon combination treatment and anti-PD1 are shown in green, those upregulated only by combination treatment are shown in red. Pathways with a significant difference in percentage of modulated genes in responders to the combo versus responders to anti-PD1 are marked with an asterisk (p < 0.05, two-tailed, Fisher test)
