BRCA1 secondary splice-site mutations drive exon-skipping and PARP inhibitor resistance

Nesic, K; Krais, JJ; Wang, Y; Vandenberg, CJ; Patel, P; Cai, KQ; Kwan, T; Lieschke, E; Ho, GY; Barker, HE; Bedo, J; Casadei, S; Farrell, A; Radke, M; Shield-Artin, K; Penington, JS; Geissler, F; Kyran, E; Betsch, R; Xu, L; Zhang, F; Dobrovic, A; Olesen, I; Kristeleit, R; Oza, A; McNeish, I; Ratnayake, G; Traficante, N; DeFazio, A; Bowtell, DDL; Harding, TC; Lin, K; Swisher, EM; Kondrashova, O; Scott, CL; Johnson, N; Wakefield, MJ

Author(s): Nesic, K; Krais, JJ; Wang, Y; Vandenberg, CJ; Patel, P; Cai, KQ; Kwan, T; Lieschke, E; Ho, GY; Barker, HE; Bedo, J; Casadei, S; Farrell, A; Radke, M; Shield-Artin, K; Penington, JS; Geissler, F; Kyran, E; Betsch, R; Xu, L; Zhang, F; Dobrovic, A; Olesen, I; Kristeleit, R; Oza, A; McNeish, I; Ratnayake, G; Traficante, N; DeFazio, A; Bowtell, DDL; Harding, TC; Lin, K; Swisher, EM; Kondrashova, O; Scott, CL; Johnson, N; Wakefield, MJ;
Details: Publication Year 2024-08-05,Volume 23,Issue #1,Page 158
Journal Title: Molecular Cancer
Abstract: PARP inhibitor (PARPi) therapy has transformed outcomes for patients with homologous recombination DNA repair (HRR) deficient ovarian cancers, for example those with BRCA1 or BRCA2 gene defects. Unfortunately, PARPi resistance is common. Multiple resistance mechanisms have been described, including secondary mutations that restore the HR gene reading frame. BRCA1 splice isoforms △11 and △11q can contribute to PARPi resistance by splicing out the mutation-containing exon, producing truncated, partially functional proteins. However, the clinical impacts and underlying drivers of BRCA1 exon skipping are not fully understood.We analyzed nine ovarian and breast cancer patient derived xenografts (PDX) with BRCA1 exon 11 frameshift mutations for exon skipping and therapy response, including a matched PDX pair derived from a patient pre- and post-chemotherapy/PARPi. BRCA1 exon 11 skipping was elevated in PARPi resistant PDX tumors. Two independent PDX models acquired secondary BRCA1 splice site mutations (SSMs) that drive exon skipping, confirmed using qRT-PCR, RNA sequencing, immunoblotting and minigene modelling. CRISPR/Cas9-mediated disruption of splicing functionally validated exon skipping as a mechanism of PARPi resistance. SSMs were also enriched in post-PARPi ovarian cancer patient cohorts from the ARIEL2 and ARIEL4 clinical trials.Few 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 of BRCA1 hypomorphs, which in turn promote PARPi resistance. Thus, BRCA1 SSMs can and should be clinically monitored, along with frame-restoring secondary mutations.
Publisher: BMC
Keywords: Humans; *Poly(ADP-ribose) Polymerase Inhibitors/pharmacology/therapeutic use; *Exons; *Drug Resistance, Neoplasm/genetics; *BRCA1 Protein/genetics; Female; Animals; Mice; *Ovarian Neoplasms/genetics/drug therapy/pathology; *RNA Splice Sites; Mutation; Breast Neoplasms/genetics/drug therapy/pathology; Xenograft Model Antitumor Assays; Cell Line, Tumor
Research Division(s): Bioinformatics; Bioinformatics; Cancer Biology And Stem Cells
PubMed ID: 39103848
Publisher's Version: https://doi.org/10.1186/s12943-024-02048-1
Open Access at Publisher's Site: https://doi.org/10.1186/s12943-024-02048-1
Terms of Use/Rights Notice: Refer to copyright notice on published article.
Documents: s12943-024-02048-1.pdf - (2.42MB, application/pdf)

Creation Date: 2024-08-14 09:49:43

Last Modified: 2024-08-23 02:56:06