Abstract A008: Characterizing the role of somatic and constitutional methylation in ovarian cancer
Authors: Isabel V. Rodriguez, Shu Ying Liang, Ksenija Nesic, Christopher Pennil, Marc R. Radke, Jennifer L. Ochoa, Barbara Norquist, Elizabeth Swisher
Journal: Cancer Research (2024)

Abstract Epigenetic silencing of homologous recombination repair genes through promoter methylation in ovarian cancer may lead to a homologous recombination deficiency (HRD) phenotype with prognostic and therapeutic implications. The objectives of this study were to evaluate somatic promoter methylation as a marker of HRD in BRCA wild-type ovarian cancer, assess impact of chemotherapy on promoter methylation, and to determine the frequency of constitutional methylation and its association with methylated ovarian cancers. BRCA1 and RAD51C quantitative methylation was assessed using a highly sensitive and specific digital droplet PCR (ddPCR) assay in of banked whole blood and cancer DNA from individuals with epithelial ovarian cancer, and in blood from individuals without personal or family history of cancer (benign controls). Cut-offs for positive methylation: &amp;gt;/= 1% for blood (constitutional methylation) and &amp;gt;/= 20% for neoplastic tissues (cancer methylation), with neoplastic samples further divided into low methylation (20-59%) and high methylation &amp;gt;/= 60%. Germline/somatic mutations and genome wide loss of heterozygosity (LOH) were assessed using next generation sequencing. 335 BRCA wild-type neoplastic samples were tested, with 12% positive for BRCA1 promoter methylation and 3% positive for RAD51C methylation. Subjects with highly methylated cancers had increased overall survival compared to unmethylated cancers (75 vs 44 months, HR 0.59, p=0.03). Increasing quantitative methylation was positively correlated with LOH score (R=0.65, p &amp;lt;0.001). Of 7 highly methylated paired primary and recurrent ovarian cancer samples, 6/7 (86%) demonstrated decrease in quantitative methylation at time of recurrence. For the constitutional methylation analysis, 275 neoplastic samples had a paired blood sample for assessment, and 223 benign controls were tested. A higher percentage of subjects with BRCA1 methylated cancers had constitutional methylation (29%), compared with 1.7% of unmethylated caners and 1.4% of benign controls (p&amp;lt;0.001). Subjects with BRCA1 constitutional methylation and cancer methylation were diagnosed at a younger age than those without methylation (p&amp;lt;0.01). Subjects with methylated ovarian cancers had increased overall survival compared to unmethylated cancers consistent with an HRD phenotype, and they were more likely to have positive LOH scores suggesting these patients may benefit from PARP inhibitor therapy. Exposure to cancer directed therapy was associated with loss of methylation. BRCA1 constitutional methylation occurred predominantly in ovarian cancers with BRCA1 methylation, therefore, may represent a predisposition to development of methylated ovarian cancers. Citation Format: Isabel V. Rodriguez, Shu Ying Liang, Ksenija Nesic, Christopher Pennil, Marc R. Radke, Jennifer L. Ochoa, Barbara Norquist, Elizabeth Swisher. Characterizing the role of somatic and constitutional methylation in ovarian cancer [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr A008.