University Medical Center Rotterdam, Department of Medical Oncology, Erasmus MC, 3015 GD Rotterdam, The Netherlands.
Institute of Graduate Studies in Sciences, Istanbul University, Istanbul 34116, Turkey.
Genes (Basel). 2024 Jun 7;15(6):750. doi: 10.3390/genes15060750.
Patients with advanced-stage epithelial ovarian cancer (EOC) receive treatment with a poly-ADP ribose-polymerase (PARP) inhibitor (PARPi) as maintenance therapy after surgery and chemotherapy. Unfortunately, many patients experience disease progression because of acquired therapy resistance. This study aims to characterize epigenetic and genomic changes in cell-free DNA (cfDNA) associated with PARPi resistance.
Blood was taken from 31 EOC patients receiving PARPi therapy before treatment and at disease progression during/after treatment. Resistance was defined as disease progression within 6 months after starting PARPi and was seen in fifteen patients, while sixteen patients responded for 6 to 42 months. Blood cfDNA was evaluated via Modified Fast Aneuploidy Screening Test-Sequencing System (mFast-SeqS to detect aneuploidy, via Methylated DNA Sequencing (MeD-seq) to find differentially methylated regions (DMRs), and via shallow whole-genome and -exome sequencing (shWGS, exome-seq) to define tumor fractions and mutational signatures.
Aneuploid cfDNA was undetectable pre-treatment but observed in six patients post-treatment, in five resistant and one responding patient. Post-treatment ichorCNA analyses demonstrated in shWGS and exome-seq higher median tumor fractions in resistant (7% and 9%) than in sensitive patients (7% and 5%). SigMiner analyses detected predominantly mutational signatures linked to mismatch repair and chemotherapy. DeSeq2 analyses of MeD-seq data revealed three methylation signatures and more tumor-specific DMRs in resistant than in responding patients in both pre- and post-treatment samples (274 vs. 30 DMRs, 190 vs. 57 DMRs, Χ-test < 0.001).
Our genome-wide Next-Generation Sequencing (NGS) analyses in PARPi-resistant patients identified epigenetic differences in blood before treatment, whereas genomic alterations were more frequently observed after progression. The epigenetic differences at baseline are especially interesting for further exploration as putative predictive biomarkers for PARPi resistance.
晚期上皮性卵巢癌（EOC）患者在手术后和化疗后接受多聚 ADP 核糖聚合酶（PARP）抑制剂（PARPi）维持治疗。不幸的是，许多患者因获得性治疗耐药而发生疾病进展。本研究旨在描述与 PARPi 耐药相关的无细胞 DNA（cfDNA）中的表观遗传和基因组变化。
采集 31 名接受 PARPi 治疗的 EOC 患者在治疗前和治疗期间/后疾病进展时的血液。耐药性定义为 PARPi 治疗开始后 6 个月内疾病进展，15 名患者耐药，16 名患者对 6 至 42 个月有反应。通过改良快速非整倍体筛查试验-测序系统（mFast-SeqS）检测非整倍体，通过甲基化 DNA 测序（MeD-seq）检测差异甲基化区域（DMR），通过浅层全基因组和外显子组测序（shWGS、exome-seq）检测肿瘤分数和突变特征。
治疗前未检测到 cfDNA 非整倍体，但 6 名患者在治疗后观察到，其中 5 名耐药患者和 1 名有反应患者。治疗后 ichorCNA 分析显示，在 shWGS 和 exome-seq 中，耐药患者的中位肿瘤分数高于敏感患者（7%和 9%对 7%和 5%）。SigMiner 分析检测到主要与错配修复和化疗相关的突变特征。DeSeq2 分析 MeD-seq 数据显示，在治疗前和治疗后样本中，耐药患者的甲基化标记物和肿瘤特异性 DMRs 均多于有反应患者（274 个 vs. 30 个 DMRs，190 个 vs. 57 个 DMRs，Χ检验<0.001）。
我们对 PARPi 耐药患者的全基因组下一代测序（NGS）分析发现，治疗前血液中存在表观遗传差异，而治疗后更常观察到基因组改变。基线时的表观遗传差异尤其值得进一步探索，作为 PARPi 耐药的潜在预测生物标志物。
