BRCA1secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance

Abstract

AbstractBRCA1splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out the mutation-containing exon, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers ofBRCA1exon skipping remain undetermined.We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) withBRCA1exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi.BRCA1exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondaryBRCA1splice site mutations (SSMs), predictedin silicoto drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots andBRCA1minigene modelling. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials.We demonstrate that SSMs driveBRCA1exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.Statement of significanceFew PARPi resistance mechanisms have been confirmed in the clinical setting. While secondary/reversion mutations typically restore a gene’s reading frame, we have identified secondary mutations in patient cohorts that hijack splice sites to enhance mutation-containing exon skipping, resulting in the overexpression ofBRCA1hypomorphs, which in turn promote PARPi resistance.