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

Abstract

BRCA1 splice isoforms Δ11 and Δ11q can contribute to PARP inhibitor (PARPi) resistance by splicing-out mutation-containing exons, producing truncated, partially-functional proteins. However, the clinical impact and underlying drivers of BRCA1 exon skipping remain undetermined. We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for splice isoform expression and therapy response. This included a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi regimen. BRCA1 exon 11-deficient isoform expression was generally elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary BRCA1 splice site mutations (SSMs), predicted in silico to drive exon skipping. Predictions were confirmed using qRT-PCR, RNA sequencing, western blots and BRCA1 minigene modelling. SSMs were also enriched in post-PARPi OC patient cohorts from the ARIEL2 and ARIEL4 clinical trials. We demonstrate that SSMs drive BRCA1 exon 11 skipping and PARPi resistance, and should be clinically monitored, along with frame-restoring secondary mutations.

CHK1 inhibitor SRA737 is active in PARP inhibitor resistant and CCNE1 amplified ovarian cancer

“…PDX were generated by transplanting fresh surgical or biopsy tumor fragments (1-4 mm 3 ) subcutaneously on the flank of 6–8 week old female NSG mice (PDX #29, 48 PDX #111, 49 PDX #201, 50 PDX #206, 51 PDX #1177 52 ). Any IHC validation not previously published, including for new PDX models #206 and #931, is shown in Figure S2 .…”

A Molecular Characterization of the Allelic Expression of the BRCA1 Founder Δ9–12 Pathogenic Variant and Its Potential Clinical Relevance in Hereditary Cancer

“…The evidence suggests that transcripts of BRCA1 PVs may evade nonsense-mediated mRNA decay (NMD) mechanisms via isoform splicing events or the upregulation of WT isoforms, thereby rescuing the homologous recombination (HR) response pathway involving BRCA1. This phenomenon has been associated with resistance to PARP inhibitors and platinum-based therapies [ 14 , 15 , 16 , 17 , 18 , 19 ]. However, it remains unknown whether the BRCA1 Δ9–12 mutation generates a translatable transcript or modulates the expression of WT isoforms.…”