Swisher, Elizabeth M.

AbstractBackgroundBRCA1 methylation has been associated with homologous recombination deficiency, a biomarker of platinum sensitivity. Studies evaluating BRCA1-methylated tubal and ovarian cancer (OC) do not consistently support improved survival following platinum chemotherapy. We examine the characteristics of BRCA1-methylated OC in a meta-analysis of individual participant data.MethodsData of 2636 participants across 15 studies were analyzed. BRCA1-methylated tumors were defined according to their original study. Associations between BRCA1 methylation and clinicopathological characteristics were evaluated. The effects of methylation on overall survival (OS) and progression-free survival (PFS) were examined using mixed-effects models. All statistical tests were 2-sided.Results430 (16.3%) tumors were BRCA1-methylated. BRCA1 methylation was associated with younger age and advanced-stage, high-grade serous OC. There were no survival differences between BRCA1-methylated and non–BRCA1-methylated OC (median PFS = 20.0 vs 18.5 months, hazard ratio [HR] = 1.01, 95% CI = 0.87 to 1.16; P = .98; median OS = 46.6 vs 48.0 months, HR = 1.02, 95% CI = 0.87 to 1.18; P = .96). Where BRCA1/2 mutations were evaluated (n = 1248), BRCA1 methylation displayed no survival advantage over BRCA1/2-intact (BRCA1/2 wild-type non–BRCA1-methylated) OC. Studies used different methods to define BRCA1 methylation. Where BRCA1 methylation was determined using methylation-specific polymerase chain reaction and gel electrophoresis (n = 834), it was associated with improved survival (PFS: HR = 0.80, 95% CI = 0.66 to 0.97; P = .02; OS: HR = 0.80, 95% CI = 0.63 to 1.00; P = .05) on mixed-effects modeling.ConclusionBRCA1-methylated OC displays similar clinicopathological features to BRCA1-mutated OC but is not associated with survival. Heterogeneity within BRCA1 methylation assays influences associations. Refining these assays may better identify cases with silenced BRCA1 function and improved patient outcomes.

Abstract Background: The combination of cediranib (ced) and olaparib (olap) improves progression-free survival and overall response rates (ORR) in women with recurrent plat sensitive high-grade serous (HGS) ovarian cancer compared to olap alone. In this Phase 2 study of ced/olap in women with relapsed ovarian cancer (NCT02345265), we observed an ORR of 74% with ced/olap in plat sensitive relapsed patients (pts) and an ORR of 20% in plat resistant pts. BROCA-HR was performed to characterize tumor HRD status and to correlate this with the activity of ced/olap in the plat sensitive and resistant settings. Methods: Pts with relapsed ovarian cancer across 11 centers were enrolled to 2 cohorts, either plat sensitive or resistant. All pts received ced 30mg daily and olap tablets 200mg BID. Archival, pre-treatment, and on-treatment biopsies were collected on all pts where safely feasible; pts also had the option of undergoing a post-progression biopsy. A baseline blood sample was collected for germline testing and matched control. Available samples were sequenced with BROCA-HR, and HRD status was determined by (1) presence of an HR-related mutation or (2) an increase in loss of heterozygosity (LOH) score. Results: 72 pts were enrolled, with 70 pts receiving study treatment (35 plat sensitive and 35 plat resistant). BROCA-HR analysis is complete on 60 samples, with 10 samples in final analysis. The concordance of HRD status by presence of an HR-related mutation or by LOH score was relatively low (agreement=36/60=60%, Cohen's Kappa=0.28). In 19 pts with a germline BRCA mutation, 16 were HRD+ by LOH (LOH high), 2 were HRD- by LOH (LOH low), and 1 not quantifiable. 3 pts had a somatic BRCA mutation; 1 was LOH high, 1 LOH low, and 1 not quantifiable. 4 pts had non-BRCA somatic HR-related mutations (3 CDK12; 1 ATR); 3 were LOH high and 1 LOH low. Of the 34 pts without HR-related mutations, 15 were LOH high, 16 were LOH low, and 3 not quantifiable. In 29 plat sensitive pts with BROCA-HR results, 18 were HRD+ by mutation (12 germline BRCA, 3 somatic BRCA, 3 somatic other), and 16 were HRD+ by LOH (LOH high). The ORR in plat sensitive pts by HRD status with available HRD results was: 22/29=75.9% (13/18=72% HRDmut+; 9/11=82% HRDmut-); (12/16=75% LOH high; 6/9= 67% LOH low). In 31 plat resistant pts with BROCA-HR results, 8 were HRD+ by mutation (7 germline BRCA, 0 somatic BRCA, 1 somatic other), and 19 were HRD+ by LOH. The ORR in plat resistant pts by HRD status with available HRD results was: 7/31=22.6% (4/8=50% HRDmut+; 3/23=13% HRDmut-, P=0.05); (7/19=37% LOH high; 0/11= 0% LOH low, P=0.03). Updated results with the full data set are pending. Conclusion: Ced/olap has clinical activity in women with relapsed ovarian cancer, both in the plat sensitive and plat resistant settings. In women with plat sensitive disease, where response rates are high, HRD status by presence of an HR-related mutation or LOH status does not appear to provide significant additional information regarding likelihood of response. In women with plat resistant disease, the presence of HRD by an HR-related mutation or LOH status is correlated with a higher likelihood of response. Citation Format: Joyce F Liu, Su-Chun Cheng, Robert M Wenham, Andrea E Wahner Hendrickson, Deborah K Armstrong, Nancy Chan, David E Cohn, Jung-Min Lee, Richard T Penson, Mihaela Cristea, James Abbruzzese, Koji Matsuo, Alexander B Olawaiye, Jennifer Curtis, Geoffrey Shapiro, Ursula A Matulonis, Elise Kohn, Percy Ivy, Elizabeth M Swisher. Correlation of homologous recombination deficiency (HRD) status by BROCA-HR sequencing with response to combination cediranib and olaparib in relapsed ovarian cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr A074. doi:10.1158/1535-7163.TARG-19-A074

5073 Background: Recent molecular exploration of high-grade epithelial ovarian cancer (OC) has revealed potential targets for novel therapy based on altered DNA repair function, deregulated pathways and recurrent amplifications (Cancer Genome Atlas Research Network. 2011. Nature 474). Improved pre-clinical models allowing analysis of specific molecular subsets of ovarian cancer are urgently required to test novel treatment strategies. Methods: We have generated a novel xenograft model of human high-grade serous OC (HG-SOC). Histologic, functional and molecular analysis of the novel xenograft cohort (at baseline and following xenotransplantation) allows stratification of individual HG-SOC for testing with appropriate targeted therapy. We perform functional analysis of in vitro Homologous Recombination (HR) DNA repair and drug response capabilities on fresh human HG-SOC immediately following surgical resection. Molecular classification (similar to Tothill [Clin Canc Res. 2008;14]); analysis of NHEJ pathway (Proc Natl Acad Sci. 2011;108) and other DNA repair genes (Proc Natl Acad Sci USA 2011;108) is performed. In vivo drug response is studied in murine xenografts. Results: Sixteen chemotherapy-naive potentially HG-SOC samples and associated clinical data have been collected. Functional evidence of DNA repair (HR) capability and response to DNA damaging agents will be presented, including IHC for markers of DNA damage (gH2AX), DNA repair (RAD51AP1) and apoptosis (capsase 3 cleavage). Molecular classification, DNA repair gene and DNA repair pathway analyses are underway. Twelve HG-SOC have been transplanted and 6 of the first 8 have successfully xenografted, with serial transplantation and phenotyping of xenograft derivatives underway. In vivo drug response will be presented. Conclusions: This xenograft model will enable us to address hypotheses generated by recent molecular analyses of human HG-SOC (Cancer Genome Atlas Research Network. 2011. Nature 474; Clin Canc Res. 2008;14). Clinical, functional and molecular annotation will allow pre-clinical drug testing based on the plausible hypothesis approach.

Abstract Germline loss-of-function mutations in BRCA1 interacting protein C-terminal helicase 1 (BRIP1) are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand cross-link (ICL) repair and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants, for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next-generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 patients with ovarian cancer revealed nearly 2% of patients carry a very rare missense variant (minor allele frequency < 0.0001) in BRIP1. This is 3-fold higher than the frequency of all rare BRIP1 missense alleles reported in more than 60,000 individuals of the general population (P < 0.0001, χ2 test). Using CRISPR-Cas9 gene editing technology and rescue assays, we functionally characterized 20 of these missense variants, focusing on the altered protein's ability to repair ICL damage. A total of 75% of the characterized variants rendered the protein hypomorph or null. In a clinical cohort of >117,000 patients with breast and ovarian cancer who underwent panel testing, the combined OR associated with BRIP1 hypomorph or null missense carriers compared with the general population was 2.30 (95% confidence interval, 1.60–3.30; P < 0.0001). These findings suggest that novel missense variants within the helicase domain of BRIP1 may confer risk for both breast and ovarian cancer and highlight the importance of functional testing for additional variants. Significance: Functional characterization of rare variants of uncertain significance in BRIP1 revealed that 75% demonstrate loss-of-function activity, suggesting rare missense alleles in BRIP1 confer risk for both breast and ovarian cancer.

Abstract A key resistance mechanism to platinum-based chemotherapies and PARP inhibitors in BRCA-mutant cancers is the acquisition of BRCA reversion mutations that restore protein function. To estimate the prevalence of BRCA reversion mutations in high-grade ovarian carcinoma (HGOC), we performed targeted next-generation sequencing of circulating cell-free DNA (cfDNA) extracted from pretreatment and postprogression plasma in patients with deleterious germline or somatic BRCA mutations treated with the PARP inhibitor rucaparib. BRCA reversion mutations were identified in pretreatment cfDNA from 18% (2/11) of platinum-refractory and 13% (5/38) of platinum-resistant cancers, compared with 2% (1/48) of platinum-sensitive cancers (P = 0.049). Patients without BRCA reversion mutations detected in pretreatment cfDNA had significantly longer rucaparib progression-free survival than those with reversion mutations (median, 9.0 vs. 1.8 months; HR, 0.12; P < 0.0001). To study acquired resistance, we sequenced 78 postprogression cfDNA, identifying eight additional patients with BRCA reversion mutations not found in pretreatment cfDNA. Significance: BRCA reversion mutations are detected in cfDNA from platinum-resistant or platinum-refractory HGOC and are associated with decreased clinical benefit from rucaparib treatment. Sequencing of cfDNA can detect multiple BRCA reversion mutations, highlighting the ability to capture multiclonal heterogeneity. This article is highlighted in the In This Issue feature, p. 151