The effect of SETD1A knockout on gene expression in ATM- or BRCA-deficient cells.

Background: Cells deficient in DNA repair factors breast cancer susceptibility 1/2 (BRCA1/2) or ataxia-telangiectasia mutated (ATM) are sensitive to poly-ADP ribose polymerase (PARP) inhibitors. Building on our previous findings, we asked how the lysine methyltransferase SETD1A contributed to PARP inhibitor-mediated cell death and determined the mechanisms responsible. Methods: We used cervical, breast, lung and ovarian cancer cells bearing mutations in BRCA1 or ATM and depleted SETD1A using siRNA or CRISPR/Cas9. We assessed the effects of the PARPi Olaparib on cell viability, homologous recombination, and DNA repair. We assessed underlying transcriptional perturbations using RNAseq. We also used data from The Cancer Genomics Atlas (TCGA) to investigate overall patient survival. Results: Loss of SETD1A from both BRCA1-deficient and ATM-deficient cancer cells was associated with resistance to Olaparib, explained by an partial restoration of homologous recombination. Mechanistically, SETD1A-dependent transcription of the crossover junction endonuclease EME1 correlated with sensitivity to Olaparib in these cells. Accordingly, when SETD1A or EME1 was lost, BRCA1 or ATM-mutated cells became resistant to Olaparib, and homologous recombination was partially restored. Conclusions: Loss of SETD1A or EME1 may explain why patients develop resistance to PARP inhibitors in the clinic. To investigate the effect of SETD1A knockout on gene expression in backgrounds of HR-deficiency we treated Hela Kyoto inducible cas9 cells expressing SETD1A CRISPR gRNA with control, ATM or BRCA1 siRNA +/- doxycycline treatment. We performed gene expression analysis using data obtained from RNA-Seq experiments from three individual repeats.