Abstract 4101: Blood based biomarkers of DNA methylation associated with platinum resistance in high grade serous ovarian cancer
Authors: Daniela Matei, Horacio Cardenas, Elnaz Abbasi Farid, Zhen Fu, Collin M. Coon, Adam Vieth, Kenneth P. Nephew
Journal: Cancer Research (2025)

Abstract High grade serous ovarian cancer (OC) is initially a responsive tumor to platinum (Pt)-based therapy. Tumor suppressor genes (TSGs) are implicated in OC initiation and progression and can be inactivated through genetic or epigenetic events. DNA methylation has been shown to silence TSGs and other cancer-related genes and is detectable in cancer cells and in blood. Here we aimed to develop a blood-based methylation assay associated with cancer and cancer recurrence in OC. We evaluated genome-wide DNA methylation in de-identified peripheral blood mononuclear cells (PBMCs) from women: without cancer (controls, n=20), newly diagnosed OC (prior to treatment, Pt-sensitive, n=50), and platinum-resistant recurrent HGSOC before and after treatment with a hypomethylating agent (HMA, Pt-resistant, n=31). The Pt-resistant patients were enrolled on NCT02901899 clinical trial testing guadecitabine and pembrolizumab. DNA extracted from PBMCs was analyzed by using Infinium MethylationEPIC BeadChips. DNA methylation analysis used R package SeSAMe to derive beta (β) values and identify differential methylated loci (DMLs) and differential methylated regions (DMRs) between groups. Bioinformatics analysis was conducted to identify biological pathways and processes, determined using Ingenuity Pathway Analysis (IPA) and KEGG, GO:BP, REAC databases. Deconvolution analyses used the HEpiDISH algorithm to determine the cellular make-up of the samples. Comparing controls vs. Pt-sensitive groups, there were 30, 369 DMLs (adj. p&amp;lt;0.05, β&amp;gt;10%), with most loci being demethylated. Enriched pathways related to presence of cancer included: mechanisms of cancer, neutrophil degranulation, and cancer-related signaling pathways (PI3K/AKT, STAT3, HGF, interleukins). The number of DMLs was greater (880, adj. p&amp;lt;0.05, β&amp;gt;10%) in Pt-resistant vs Pt-sensitive and enriched pathways associated with Pt-resistant OC included: pathways in cancer, metabolic pathways, platelet activation, ABC transporters and signaling pathways (calcium, PI3K/AKT, MAPK, Ras, ErbB, Hippo, Wnt). Massive genome-wide hypomethylation 5 days after treatment with the HMA was seen (13, 742, adj. p&amp;lt;0.05, β&amp;gt;10%), consistent with observed LINE1 hypomethylation in PBMCs, and genome-wide hypomethylation persisted 30 days after end of HMA treatment. Enriched pathways among hypomethylated genes included: Th17 cell differentiation, virus infection, focal adhesion, signaling (chemokine, cGMP-PKG, Rap1) and hormone (thyroid, parathyroid, oxytocin, growth hormone) pathways. Deconvolution analysis identified decreased B and NK cells, monocytes, and eosinophils and a trend towards decreased CD4+ and CD8+ cells in Pt-sensitive OC vs controls. In contrast, neutrophils were increased in cancer vs control patients. We propose new DMLs associated with Pt-sensitive vs. Pt-resistant OC. These findings can lead to new biomarkers for HGSOC. Citation Format: Daniela Matei, Horacio Cardenas, Elnaz Abbasi Farid, Zhen Fu, Collin M. Coon, Adam Vieth, Kenneth P. Nephew. Blood based biomarkers of DNA methylation associated with platinum resistance in high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 4101.