Farid, E. A. | Search bioRxiv

bioRxiv2026

Blood Based Biomarkers of DNA Methylation Associated with Platinum Resistance in High Grade Serous Ovarian Cancer

BackgroundHigh grade serous ovarian cancer (HGSC) is initially a responsive tumor to platinum (Pt)-based therapy. Pt resistance in HGSC is associated with epigenetic modifications and hypomethylating agents (HMAs) have been studied as carboplatin resensitizing agents. As DNA methylation is detectable in cancer cells and in blood, here we aimed to develop a blood-based methylation signature associated with cancer and cancer recurrence in HGSC. ResultsWe evaluated genome-wide DNA methylation in de-identified peripheral blood mononuclear cells (PBMCs) from women 1) without cancer (controls, n=20); 2) newly diagnosed HGSC (prior to treatment, Pt-naive, n=60) 3) Pt-resistant recurrent HGSC before and after treatment with the novel HMA/DNA methyltransferase inhibitor (DNMTI) guadecitabine (Pt-resistant, n=30). The Pt-resistant patients were enrolled in NCT02901899 clinical trial testing guadecitabine and the PD-1 inhibitor pembrolizumab. DNA extracted from PBMCs was analyzed by using Infinium MethylationEPIC BeadChips. There were 30,369 differentially methylated loci (DMLs) in Pt-naive patients vs. controls (adj. p < 0.05, {beta} >10%), with most loci being demethylated. Enriched pathways in PBMCs from cancer patients included mechanisms of cancer, neutrophil degranulation, and cancer-related signaling pathways (PI3K/AKT, STAT3, HGF, interleukins). The number of DMLs was greater (880 DMLs; adj. p<0.05, {beta}>10%) in Pt-resistant vs. Pt-naive patients, and top enriched pathways associated with Pt-resistant HGSC included pathways in cancer, metabolic pathways, platelet activation, ABC transporters and signaling pathways (calcium, PI3K/AKT, MAPK, Ras, ErbB, Hippo, Wnt). Massive genomewide hypomethylation 5 days after treatment with guadecitabine was observed (13,742 DMLs; adj. p<0.05, {beta}>10%), which persisted 30 days after discontinuation of treatment. Pathways enriched by hypomethylated genes in PBMCs following guadecitabine treatment interestingly included pathways related to neuronal signaling, such as glutaminergic receptor signaling, axonal guidance signaling, synaptic long-term depression, synaptogenesis signaling and serotonin receptor signaling. Deconvolution analysis of the methylome data of PBMCs from Pt-resistant recurrent HGSC before versus after HMA treatment predicted increased naive B cells, memory and naive CD+ T cells, naive CD4+ T cells, and neutrophils and decreased monocytes. ConclusionsWe propose new DMLs associated with Pt-naive versus Pt-resistant HGSC. These findings can lead to new biomarkers for HGSC.

genomics↗

bioRxiv2026

Effects of the Hypomethylating Agent Guadecitabine on Peripheral Blood Mononuclear Cell Methylomes and Immune Cell Populations in Small-Cell Lung Cancer Patients

BackgroundSmall-cell lung cancer (SCLC) represents 15% of lung cancers and with a 5-year survival rate under 7% remains one of the deadliest malignancies. Although initially responsive to chemotherapy, rapid recurrence and resistance are common. Epigenetic modifications, particularly DNA methylation, contribute to tumor progression and therapy resistance. Guadecitabine, a hypomethylating agent (HMA), has shown promising clinical activity when combined with carboplatin in preclinical models. We evaluated the combination of guadecitabine with carboplatin as a second-line treatment for extensive-stage SCLC (NCT03913455). Here we report methylome changes in peripheral blood mononuclear cell (PBMCs) collected at baseline and during treatment from patients on the trial. ResultsPMBC DNA was analyzed using Infinium HumanMethylationEPIC v1.0 bead chips. Data were processed and differentially methylated positions (DMPs) were identified and analyzed for pathway enrichment using bioinformatic approaches and immune deconvolution analyses were conducted to investigate the impact on immune cell composition. Direct comparison of PBMCs between cycle 2 day 5 (C2D5; post-treatment) vs cycle 1 day 1 (C1D1; pre-treatment) revealed a greater number of hypomethylated DMPs (380 DMPs in C2D5 vs C1D1 PBMCs; p < 0.05, |{beta}| > 20%). Moreover, when first compared with normal PBMCs from cancer-free controls, the number of hypomethylated DMPs was even greater in C2D5 than in C1D1 (1,771 vs 237 DMPs, respectively; p < 0.05, |{beta}| > 20%). Long interspersed nucleotide elements-1 (LINE-1) were also significantly hypomethylated in PBMCs after HMA treatment (C2D5), compared to C1D1. Pathway analysis of hypomethylated DMPs revealed significant alterations in key signaling pathways including NF-{kappa}B, Rho GTPase, pulmonary fibrosis, and p75 NTR in C1D1 vs C2D5. When normal PBMCs were compared to C1D1 PBMCs, changes in IL-3 signaling, Fc{gamma} receptor-mediated phagocytosis, and molecular mechanisms of cancer were observed. Deconvolution analysis revealed a significantly higher percentage of monocytes in C1D1 PBMCs vs normal PBMCs. However, after HMA treatment, percentages of monocytes and B cells decreased, while eosinophil percentage increased in C1D1 compared to C2D5 PBMCs. ConclusionIn the first study on the global impact of HMA treatment on PBMC methylomes in SCLC patients, DNA methylation changes associated with biological pathways related to PBMC function reveal shifts in distinct immune cell populations. SummaryMethylome changes in peripheral blood mononuclear cell (PBMCs) from small cell lung cancer (SCLC) patients treated with an epigenetic therapy revealed global hypomethylation and altered cancer signaling processes associated with tumor progression, immune response, therapy resistance and significant change in the proportion of immune cells. Integrating blood-based methylation biomarkers into clinical trials of epigenetic therapy and methylomic analysis of PBMCs provides direct monitoring of treatment effects in cancer patients, which may improve patient selection and enable real-time response assessment in patients receiving hypomethylating agents.

genomics↗