Abstract
Background Little is known about mechanisms of resistance to PARP inhibitors and platinum chemotherapy in patients with metastatic breast cancer and BRCA1/2 mutations. Further investigation of resistance in clinical cohorts may point to strategies to prevent or overcome treatment failure.
Patients and Methods We obtained tumor biopsies from metastatic breast cancer patients with BRCA1/2 deficiency before and after acquired resistance to PARP inhibitor or platinum chemotherapy. Whole exome sequencing was performed on each tumor, germline DNA, and circulating tumor DNA. Tumors underwent RNA sequencing, and immunohistochemical staining for RAD51 foci on tumor sections was performed for functional assessment of intact homologous recombination.
Results Pre- and post-resistance tumor samples were sequenced from 8 patients (4 with BRCA1 and 4 with BRCA2 mutation; 4 treated with PARP inhibitor and 4 with platinum). Following disease progression on DNA-damaging therapy, four patients (50%) acquired at least one somatic reversion alteration likely to result in functional BRCA1/2 protein detected by tumor or circulating tumor DNA sequencing. Two patients with germline BRCA1 deficiency acquired genomic alterations anticipated to restore homologous recombination through increased DNA end resection: loss of TP53BP1 in one patient and amplification of MRE11A in another. RAD51 foci were acquired post-resistance in all patients with genomic reversion, consistent with reconstitution of homologous recombination. All patients whose tumors demonstrated RAD51 foci post-resistance were intrinsically resistant to subsequent lines of DNA-damaging therapy.
Conclusions Genomic reversion in BRCA1/2 was the most commonly observed mechanism of resistance, occurring in 4 of 8 patients. Novel sequence alterations leading to increased DNA end resection were seen in two patients, and may be targetable for therapeutic benefit. The presence of RAD51 foci by immunohistochemistry was consistent with BRCA1/2 protein functional status from genomic data and predicted response to later DNA-damaging therapy, supporting RAD51 focus formation as a clinically useful biomarker.
Footnotes
Key message: We analyzed mechanisms of resistance to PARP inhibitor or platinum chemotherapy in 8 patients with BRCA1/2-mutant metastatic breast cancer. Four patients acquired resistance by genomic reversion to a functional BRCA1/2 protein two patients acquired resistance by upregulating DNA end resection. RAD51 foci by immunohistochemistry correlated with clinical response to PARP inhibitor/platinum.
Funding: Supported by an American Society of Clinical Oncology Young Investigator Award (AGW), the Breast Cancer Research Foundation (AGW, NUL), Specialized Program of Research Excellence (SPORE) in Breast Cancer NIH grant P50 CA168504 (AGW, IEK, ADD, EPW, NUL, GIS, NW), an NCI-Cancer Therapy Evaluation Program (CTEP) Biomarker Supplement to NIH grant UM1 CA186709 (BK, ADD, GIS), the Fashion Footwear Association of New York (to Dana-Farber Cancer Institute Breast Oncology Program), the National Comprehensive Cancer Network/Pfizer Collaborative Grant Program (NUL), Friends of Dana-Farber Cancer Institute (to N.U.L.), Yale Cancer Center grant 1UM1CA86689-05 (PL), Department of Defense W81XWH-13-1-0032 (N.W.), AACR Landon Foundation 13-60-27- WAGL (N.W.), Susan G. Komen CCR15333343 (N.W.), The V Foundation (N.W.), The Breast Cancer Alliance (N.W.), The Cancer Couch Foundation (N.W.), Twisted Pink (N.W.), Hope Scarves (N.W.), ACT NOW (to Dana-Farber Cancer Institute Breast Oncology Program). In addition, we thank Dana-Farber/Harvard Cancer Center in Boston, MA, for the use of the Specialized Histopathology Core, which provided immunohistochemical staining. Dana-Farber/Harvard Cancer Center is supported in part by an NCI Cancer Center Support Grant # NIH 5 P30 CA06516.
Conflicts of Interest: A.W. receives institutional research funding from Genentech and MacroGenics. S.W. reports consulting/advisory board role for Foundation Medicine, InfiniteMD, Eli Lilly, and Puma Biotechnology; and equity in InfiniteMD. S.S.F. filed a patent (WO2017161175A1) on methods applied in this study. S.I. receives research funding support from Genentech, PharmaMar, AstraZeneca, Merck (all to institution); and consulting fees from Genentech, Hengrui, Puma, Immunomedics, and Myriad. P.L reports serving on advisory boards at AbbVie (2018-2019), Alexion (2016-2017), Ariad (2016-2017), GenMab (2016-2018), Glenmark (2016-2017), Menarini (2016-2017), Novartis (2016-2017), CytomX (2016-2019), Omniox (2016-2017), Ignyta (2016-2017), Genentech (2016-2019), Takeda (2017-2020), SOTIO Consultant (2018-2019), Cybrexa (2018-2019), Agenus (2018-2020), IQVIA (2019-2020), TRIGR (2019-2020), Pfizer (2019-2020), I-MAB (2019-2020), ImmunoMet (2018-2020), Black Diamond (2019-2020), Sartarius (2019-2020), and Glaxo-Smith Kline (2019-2020); data safety monitoring boards/committees at Agios (2016-2019), Five Prime (2017-2020), Halozyme (2016-2019), FivePrime (2017-2019), and Tyme (2018-2020); and reports work with the imCORE Alliance at Roche-Genentech (2016-2019). V.A.A. filed a patent (WO2017161175A1) on methods applied in this study. S.M.T reports receiving institutional research support from Merck, Bristol-Myers Squibb, Exelixis, Eli Lilly, Pfizer, Novartis, AstraZeneca, Eisai, Nektar, Odenate, Sanofi, and Genentech and has served on advisory boards for Genentech, Eli Lilly, Novartis, Pfizer, Nektar, Immunomedics, Nanostring, Daiichi-Sankyo, Bristol-Meyers Squibb, Sanofi, Athenex, AstraZeneca, Eisai, Puma, and Merck. U.M. reports serving on advisory boards (paid) at Astrazeneca, Myriad Genetics, Clovis, Eli Lilly, Mersana, Geneos, Fuji Film, Cerulean; and consulting (paid) for Merck, 2X Oncology and Immunogen. I.E.K. receives institutional research funding from Genentech/Roche, Pfizer, Daiichi-Sankyo; has advisory board (honoraria) roles at Genentech/Roche, Daiichi-Sankyo, Macrogenics, Context Therapeutics, Taiho Oncology; and reports DSMC (honoraria) at Merck; and reports DSMB (honoraria) at Novartis. E.P.W. institutional research funding from Genentech/Roche and Merck; consultant/honoraria from Carrick Therapeutics, Genentech/Roche, Genomic Health, GSK, Jounce, Lilly, Merck, Seattle Genetics; advisory board/honoraria from Leap. A.D.D. reports receiving commercial research grants from Eli Lilly & Company, Sierra Oncology, and EMD Serono and is a consultant/advisory board member for Eli Lilly & Company, Sierra Oncology, and EMD Serono. G.I.S. has received research funding from Eli Lilly, Merck KGaA/EMD-Serono, Merck, and Sierra Oncology. He has served on advisory boards for Pfizer, Eli Lilly, G1 Therapeutics, Roche, Merck KGaA/EMD-Serono, Sierra Oncology, Bicycle Therapeutics, Fusion Pharmaceuticals, Cybrexa Therapeutics, Astex, Almac, Ipsen, Bayer, Angiex, and Daiichi Sankyo. N.U.L. reports institutional research funding from Genentech, Merck, Pfizer, Seattle Genetics; and consulting/ad board roles at Puma, Daichii, Seattle Genetics. N.W. was previously a stockholder and consultant for Foundation Medicine; has been a consultant/advisor for Novartis and Eli Lilly; and has received sponsored research support from Novartis and Puma Biotechnology. None of these entities had any role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript. All other authors report no conflicts of interest.