Fig. 3: Co-inhibition of CDK8/19 paralyzes long-term transcriptional adaptations by antagonizing the early response to ERK inhibition.
a Venn diagram depicting differentially expressed genes (p < 10−3) in MIA PaCa-2, SW1573, and SW620 cells treated with SCH772984 (1 µM) relative to DMSO (1:1000) for one week, performed in triplicate, with statistical significance determined by Wald test using the Benjamini and Hochberg method to correct for multiple hypothesis testing. b Reverse volcano plot depicting gene set enrichment analysis using gene sets from the MsigDB Biologic Process Ontology based on the gene expression data from Fig. 3a; Venn diagram depicting enriched gene sets with an FDR < 0.1 (insert). c In MIA PaCa-2, SW1573, and SW620 cells, odds that genes significantly dysregulated by treatment with SCH772984 for one week (1 µM, p < 0.001 by Wald statistic) are further up- or downregulated by co-treatment with Senexin A (1 µM), relative to genes that are not significantly dysregulated by treatment with ERK inhibition; p-value calculated according to Sheskin method. d In these same cell lines, percent of transcripts significantly dysregulated by SCH772984 (1 µM) for which treatment with Senexin A (1 µM) antagonizes or cooperates with these gene expression changes. e Heatmap (top) depicts differential expression of all genes within the assigned 67 DPGP clusters for MIA PaCa-2 cells treated with SCH772984 (1 µM) relative to DMSO (1:1000) at the indicated time points; restricted cubic splines of the mean differential expression of each cluster at each time point (bottom). f Restricted cubic spline of all genes in representative clusters 1 and 3 treated with SCH772984 (1 µM) alone or in combination with Senexin A (1 µM), with the bolded curves representing mean expression changes of each cluster according to treatment condition; the curves on the top reflect equivalent time points for the two treatment conditions, while on the bottom the SCH772984 alone curve is right-shifted by the indicated time intervals. g Bubble charts reflecting the mean expression changes of each cluster according to treatment condition at one week (left) versus three weeks (right), with the size of each bubble reflecting the number of genes in each cluster. h Bubble charts reflecting the mean expression changes of each cluster for MIA PaCa-2 cells treated with SCH772984 (1 µM) for three weeks compared to SCH772984 (1 µM) and Senexin A (1 µM) for five weeks, with the size of each bubble reflecting the number of genes in each cluster. ****p < 0.0001. Error bars represent standard deviations.
