Fig. 3
Loss of ARID1A results in deregulated expression of MEK/ERK pathway target genes. Forty-eight genes are commonly downregulated in the HCT116 and DLD1 cell lines (a). Gene set enrichment analysis shows that gene sets containing targets of the MEK/ERK pathway are enriched in the parental condition (a). The genes EREG, F3, and JAG1 are highly expressed in cell lines with KRASG13D mutations as analyzed using on the Morpheus tool to analyze data from the Cancer Cell Line Encyclopedia (CCLE) [36] (b). The scale represents the minimum expression in a particular row (blue) to the maximum expression in that row (red). Treatment with 20 nM trametinib for 24 h leads to a reduction of phosphorylated ERK (pERK) (c). The expression of EREG, F3, and JAG1 was significantly reduced by trametinib treatment and ARID1A deletion. Treatment with trametinib in ARID1A-deficient cells did not lead to a further reduction of gene expression (d). ARID1A mutations are significantly mutually exclusive with KRAS mutations in the TCGA colorectal cancer patient cohort (e). The y-axis represents −log10 (p value) and the blue dots represent significantly mutually exclusive or co-occurring mutations. pERK and JUND levels remain unchanged in ARID1A-deficient cells. HSC70 is used as a loading control. The AP1 transcription network gene set [41] is enriched in the parental condition (f). qRT-PCRs were performed for biological triplicates and technical duplicates. Error bars represent the standard deviation between three biological replicates. Significance was calculated using an unpaired t test, *p < 0.05, **p < 0.01, ***p < 0.001