GSE193943
PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production
We have identified a synthetically lethal relationship between the loss of chromatin modulator, ARID1A, and the inhibition of PLK1 kinase through a mechanism that involves mitochondrial dysfunction.  Using normal gastric epithelium cell line, GES1, we performed a comparative gene expression analysis comparing the various permutations of wild type (WT) and ARID1A knockout (KO) genotypes and untreated cells or those treated with PLK1 inhibitor,Volasertib. Consistent with ARID1A's role as a chromatin modulator, there was widespread gene expression modulation observed when comparing the WT cells with the ARID1A KO cells. In particular, we noted that oxidative phosphorylation and ROS pathway genes were enriched in ARID1A KO cells compared to wild type cells. Volasertib treatment appeared to exacerbate the effects on gene expression induced by ARID1A KO. We also investigated how ARID1A KO and Volasertib treatment specifically modulated the expression of mitochondrial encoded genes using a more recent human genome build, hg38 (as opposed to hg19), that enabled the correct alignment of these mitochondrial genes. For this analysis, in addition to GES1s, we used the ovarian cancer cell line, OVCAR3. To answer the question of which genes facilitate preferential cell killing of Volasertib-treated ARID1A KO cells, using normal breast epithelial cells, MCF10A, we performed a genome-wide CRISPR screen using the Brunello library.  We identified many genes whose knockout made ARID1A KO cells resistant to Volasertib, many of which were involved in mitochondrial process. Overall design: RNAseq: GES1s: WT, ARID1A KO, WT+Volasertib treatment, ARID1A KO+Volasertib treatment; 2 indpendent biological replicates each. OVCAR3: WT, ARID1A KO; 2 indpendent biological replicates each. CRISPR screen: MCF10A: WT, ARID1A KO, WT+Volasertib treatment, ARID1A KO+Volasertib treatment.