Radke, Marc R.

Abstract Purpose: Our goal was to determine if the HRDefine biomarker combining methylation and mutation assessment of key homologous recombination repair genes identifies BRCA wildtype (BRCAwt) ovarian cancer (OC) with outcomes similar to BRCA mutated (BRCAm) OC within the context of a frontline PARP inhibitor trial for advanced ovarian cancer. Methods: We performed an exploratory biomarker analysis of blood and neoplastic samples from the VELIA trial, a phase 3 study evaluating the PARP inhibitor veliparib as frontline maintenance therapy in OC. We developed a highly sensitive droplet digital PCR assay for quantitative BRCA1 and RAD51C promoter methylation and assessed germline/somatic mutations using the BROCA next generation sequencing platform. Cases were grouped into: BRCAm, HRDefine positive (BRCAwt HRDefine+), and HRDefine negative (BRCAwt HRDefine-). Carcinomas were considered HRDefine+ if quantitative BRCA1 or RAD51C promoter methylation was >/= 60% or if a germline or somatic pathogenic variant (PV) was identified in the following non-BRCA HRR repair genes: RAD51C, RAD51D, PALB2, BARD1. For this analysis, the control group included the two study arms with placebo maintenance compared to the investigational arm of veliparib with chemotherapy and continued as maintenance (veliparib throughout group). HRDefine was compared to the Myriad genomic instability score (GIS) used as HRD assessment in the trial. Progression free survival (PFS) was compared using log rank tests. Results: Among 1140 VELIA participants, biomarker analysis could be performed for 487 cases. Of these, 255 (52%) were BRCAm, 60 (12%) were BRCAwt HRDefine+, and 172 (35%) were BRCAwt HRDefine-. BRCAwt HRDefine+ was driven by promoter methylation (57%), germline (40%), or somatic (3%) PVs. Median PFS (months, all arms combined) was 26 months (BRCAm), 27 months (BRCAwt HRDefine+), and 15 months (BRCAwt HRDefine-), with corresponding hazard ratios (HR) of 0.50 (95% CI: 0.39-0.65) and 0.50 (0.34-0.73) versus HRDefine-. All HRDefine+ molecular subgroups were associated with longer PFS, including RAD51C/D mutations (HR 0.44, 0.25-0.77) and promoter methylation (HR 0.60, 0.36-0.97). HRDefine positivity was significantly associated with improved PFS compared to HRDefine-/GIS low (n=60 vs n=111, median PFS 27 versus 14 months, HR 0.44, 0.30-0.65), while the HRDefine- cases with high GIS demonstrated a trend toward an intermediate PFS (n=56, median 18 months, HR 0.67, 0.45-1.01). When compared by treatment arm, median PFS was significantly longer in the veliparib throughout arm compared to control only for the BRCAm group (32 months vs 23 months, HR 0.61, 0.42-0.87), though the analysis was underpowered for the BRCAwt HRDefine+ sub-group (30 months vs 25 months, HR 0.79, 0.4-1.57). Conclusions: HRDefine identifies BRCAwt OC associated with a PFS that is like that of BRCAm cases and may improve stratification for PARP inhibitor therapy beyond current HRD assays. GIS may have some, albeit reduced, prognostic implication that is independent of HRDefine. Citation Format: Isabel V. Rodriguez, Marc Radke, Ronit Katz, Persephone Miller, Paula Ladd, Nithisha Khasnavis, Jennifer Ochoa, Melanie Dillon, Heather Lankes, Peter Ansell, Carol Aghajanian, Gini Fleming, Michael Birrer, Scott Kaufmann, Charles Leath, Kathleen Moore, Theresa Werner, Linda Van Le, Robert L. Coleman, Elizabeth M. Swisher. Application of HRDefine: a biomarker for identifying root causes of homologous recombination deficiency to a phase 3, randomized, placebo-controlled trial of veliparib in front-line treatment of advanced ovarian cancer (VELIA/GOG-3005) [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Ovarian Cancer Research; 2025 Sep 19-21; Denver, CO. Philadelphia (PA): AACR; Cancer Res 2025;85(18_Suppl):Abstract nr A044.

Mutations in homologous recombination (HR) genes, including BRCA1 , BRCA2 , and the RAD51 paralog RAD51C , predispose to tumorigenesis and sensitize cancers to DNA-damaging agents and poly(ADP ribose) polymerase inhibitors. However, ∼800 missense variants of unknown significance have been identified for RAD51C alone, impairing cancer risk assessment and therapeutic strategies. Here, we interrogated >50 RAD51C missense variants, finding that mutations in residues conserved with RAD51 strongly predicted HR deficiency and disrupted interactions with other RAD51 paralogs. A cluster of mutations was identified in and around the Walker A box that led to impairments in HR, interactions with three other RAD51 paralogs, binding to single-stranded DNA, and ATP hydrolysis. We generated structural models of the two RAD51 paralog complexes containing RAD51C, RAD51B-RAD51C-RAD51D-XRCC2 and RAD51C-XRCC3. Together with our functional and biochemical analyses, the structural models predict ATP binding at the interface of RAD51C interactions with other RAD51 paralogs, similar to interactions between monomers in RAD51 filaments, and explain the failure of RAD51C variants in binding multiple paralogs. Ovarian cancer patients with variants in this cluster showed exceptionally long survival, which may be relevant to the reversion potential of the variants. This comprehensive analysis provides a framework for RAD51C variant classification. Importantly, it also provides insight into the functioning of the RAD51 paralog complexes.

Abstract In high-grade serous ovarian carcinoma (HGSC), deleterious mutations in DNA repair gene RAD51C are established drivers of defective homologous recombination and are emerging biomarkers of PARP inhibitor (PARPi) sensitivity. RAD51C promoter methylation (meRAD51C) is detected at similar frequencies to mutations, yet its effects on PARPi responses remain unresolved. In this study, three HGSC patient-derived xenograft (PDX) models with methylation at most or all examined CpG sites in the RAD51C promoter show responses to PARPi. Both complete and heterogeneous methylation patterns were associated with RAD51C gene silencing and homologous recombination deficiency (HRD). PDX models lost meRAD51C following treatment with PARPi rucaparib or niraparib, where a single unmethylated copy of RAD51C was sufficient to drive PARPi resistance. Genomic copy number profiling of one of the PDX models using SNP arrays revealed that this resistance was acquired independently in two genetically distinct lineages. In a cohort of 12 patients with RAD51C-methylated HGSC, various patterns of meRAD51C were associated with genomic “scarring,” indicative of HRD history, but exhibited no clear correlations with clinical outcome. Differences in methylation stability under treatment pressure were also observed between patients, where one HGSC was found to maintain meRAD51C after six lines of therapy (four platinum-based), whereas another HGSC sample was found to have heterozygous meRAD51C and elevated RAD51C gene expression (relative to homozygous meRAD51C controls) after only neoadjuvant chemotherapy. As meRAD51C loss in a single gene copy was sufficient to cause PARPi resistance in PDX, methylation zygosity should be carefully assessed in previously treated patients when considering PARPi therapy. Significance: Homozygous RAD51C methylation is a positive predictive biomarker for sensitivity to PARP inhibitors, whereas a single unmethylated gene copy is sufficient to confer resistance.

Abstract Acquired PARP inhibitor (PARPi) resistance in BRCA1- or BRCA2-mutant ovarian cancer often results from secondary mutations that restore expression of functional protein. RAD51C is a less commonly studied ovarian cancer susceptibility gene whose promoter is sometimes methylated, leading to homologous recombination (HR) deficiency and PARPi sensitivity. For this study, the PARPi-sensitive patient-derived ovarian cancer xenograft PH039, which lacks HR gene mutations but harbors RAD51C promoter methylation, was selected for PARPi resistance by cyclical niraparib treatment in vivo. PH039 acquired PARPi resistance by the third treatment cycle and grew through subsequent treatment with either niraparib or rucaparib. Transcriptional profiling throughout the course of resistance development showed widespread pathway level changes along with a marked increase in RAD51C mRNA, which reflected loss of RAD51C promoter methylation. Analysis of ovarian cancer samples from the ARIEL2 Part 1 clinical trial of rucaparib monotherapy likewise indicated an association between loss of RAD51C methylation prior to on-study biopsy and limited response. Interestingly, the PARPi resistant PH039 model remained platinum sensitive. Collectively, these results not only indicate that PARPi treatment pressure can reverse RAD51C methylation and restore RAD51C expression, but also provide a model for studying the clinical observation that PARPi and platinum sensitivity are sometimes dissociated.

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