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.

K. Nesic reports funding from the AACR-AstraZeneca Ovarian Cancer Fellowship, Stafford Fox Medical Research Foundation, other support from Bev Gray PhD Top Up Scholarship and Australian Postgraduate Award (APA) stipend, and nonfinancial support from Clovis Oncology during the conduct of the study. O. Kondrashova is supported by an NHMRC Emerging Leader 1 Investigator Grant (APP2008631) and reports personal fees from XING Technologies outside the submitted work. C.J. Vandenberg reports grants from Stafford Fox Medical Research Foundation during the conduct of the study. E. Lieschke reports grants from Stafford Fox Medical Research Foundation and nonfinancial support from Clovis Oncology during the conduct of the study. K. Shield-Artin reports grants from Stafford Fox Medical Research Foundation during the conduct of the study. H. E. Barker reports grants from Stafford Fox Medical Research Foundation and Cancer Council Victoria during the conduct of the study. N. Traficante reports grants from AstraZeneca Pty Ltd. during the conduct of the study and grants from AstraZeneca Pty Ltd. outside the submitted work. D. Bowtell reports grants from AstraZeneca Pty Ltd. during the conduct of the study and research support grants from AstraZeneca, Roche-Genentech and BeiGene (paid to institution) outside the submitted work; and personal consulting fees from Exo Therapeutics, that are outside the submitted work. Australian Ovarian Cancer Study reports grants from AstraZeneca Pty Ltd. during the conduct of the study and grants from AstraZeneca Pty Ltd. outside the submitted work. There are no other conflicts of interest in relation to the work under consideration for publication, nor other relationships / conditions / circumstances that present a potential conflict of interest. DeFazio reports grants from AstraZeneca outside the submitted work. Dobrovic reports grants from National Breast Cancer Foundation of Australia during the conduct of the study. Thomas C. Harding, Kevin Lin and Tanya Kwan are employees of Clovis Oncology. M.J. Wakefield reports grants from Stafford Fox Foundation during the conduct of the study. C.L. Scott reports grants from Stafford Fox Medical Research Foundation, National Health and Medical Research Council, Victorian Cancer Agency, Herman Trust, University of Melbourne, Cancer Council Victoria, Sir Edward Dunlop Cancer Research Fellow, Cooperative Research Centre Cancer Therapeutics, and Australian Cancer Research Foundation during the conduct of the study; other support from Sierra Oncology and other support from Clovis Oncology outside the submitted work; and unpaid advisory boards: AstraZeneca, Clovis Oncology, Roche, Eisai, Sierra Oncology, Takeda, MSD. No disclosures were reported by the other authors.

This work was supported by fellowships and grants from the National Health and Medical Research Council (NHMRC Australia; Project grant 1062702 (CLS); Investigator grant 2009783 (CLS)); the Stafford Fox Medical Research Foundation (CLS); Cancer Council Victoria (Sir Edward Dunlop Fellowship in Cancer Research (CLS)); the Victorian Cancer Agency (Clinical Fellowships CRF10–20, CRF16014 (CSL)); the National Institute of Health (2P50CA083636) (to EMS) and the Wendy Feuer Ovarian Cancer Research Fund (to EMS); the Bev Gray Ovarian Cancer Scholarship (PhD top–up scholarship) and Research Training Program Scholarship (PhD Scholarship) (KN); the American Association of Cancer Research (AACR–AstraZeneca Ovarian Cancer Research Fellowship 2022 (KN)); the Swiss Cancer Research foundation (KFS5445 08–2021) (FG); NHMRC Emerging Leader 1 Investigator Grant (APP2008631) (OK), and Stand Up to Cancer (EMS). This work was supported by US National Institutes of Health (NIH) Grants R01CA214799 and R01GM135293 to NJ. J.J.K. was supported by an American Cancer Society–Tri State CEOs Against Cancer Postdoctoral Fellowship, PF–19–097–01–DMC, Ovarian Cancer Research Alliance and Phil and Judy Messing grant 597484. This work was made possible through the Australian Cancer Research Foundation, the Victorian State Government Operational Infrastructure Support and Australian Government NHMRC IRIISS. All authors, the WEHI Stafford Fox Rare Cancer Program and the AOCS would like to thank all of the patients who participated in these research programs. The AOCS would also like to acknowledge the contribution of the study nurses, research assistants, and all clinical and scientific collaborators to the study. The complete AOCS Study Group can be found at www.aocstudy.org. The Australian Ovarian Cancer Study gratefully acknowledges additional support from Ovarian Cancer Australia and the Peter MacCallum Foundation. The Australian Ovarian Cancer Study Group was supported by the U.S. Army Medical Research and Materiel Command under DAMD17–01–1–0729, The Cancer Council Victoria, Queensland Cancer Fund, The Cancer Council New South Wales, The Cancer Council South Australia, The Cancer Council Tasmania and The Cancer Foundation of Western Australia (Multi-State Applications 191, 211 and 182) and the National Health and Medical Research Council of Australia (NHMRC; ID199600; ID400413 and ID400281)

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IRB of Fox Chase Cancer Center (PA USA) gave ethical approval for this work. Human Research Ethics Committee at the Royal Womens Hospital (Melbourne Australia) gave ethical approval for this work. Human Research Ethics Committee of WEHI (Melbourne Australia) gave ethical approval for this work (HREC #10/05 and #G16/02). Human Research Ethics Committee of QIMR Berghofer (Brisbane Australia) gave ethical approval for this work (P3456 and P2095).

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