Background:Ovarian cancer remains the most lethal gynecological cancer, primarily due to its asymptomatic nature in early stages and consequent late diagnosis. Early detection improves survival, but current biomarkers lack sensitivity and specificity. Cell-free DNA (cfDNA) released from tumor cells captures tumor-associated epigenetic alterations and represents a promising source for minimally invasive biomarkers. Among these, aberrant DNA methylation occurs early in tumorigenesis and may reflect underlying disease biology. This study aimed to investigate genome-wide cfDNA methylation profiles in patients with ovarian cancer, benign ovarian conditions, and healthy controls to identify cancer-associated methylation patterns that may inform future biomarker development.Results:We performed genome-wide cfDNA methylation profiling using cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) on plasma samples from 40 patients with high-grade serous ovarian carcinoma, 38 patients with benign ovarian conditions, and 38 healthy postmenopausal women. A total of 536 differentially methylated regions (DMRs) were identified between ovarian cancer and controls (n = 76), with 97% showing hypermethylation in ovarian cancer. DMRs were enriched in CpG islands and gene bodies and depleted in repetitive elements, consistent with known cancer-associated methylation patterns. Fifteen genes showed robust hypermethylation across analyses. These genes exhibited methylation across intronic, exonic, and upstream regulatory regions. Separate comparisons of ovarian cancer to each control group (benign and healthy) supported the reproducibility of these findings. Gene Ontology enrichment analysis revealed enrichment in gland development, embryonic morphogenesis, and endocrine regulation, suggesting biological relevance to ovarian tumorigenesis.Conclusions:This study identifies consistent cfDNA hypermethylation patterns in ovarian cancer, affecting genes involved in developmental regulation and hormone-related processes. Our findings underscore the potential of cfMeDIP-seq for detecting tumor-specific methylation signatures in plasma and highlight these 15 hypermethylated genes as biologically relevant targets for future studies on cfDNA methylation in ovarian cancer.
背景：卵巢癌仍是致死率最高的妇科恶性肿瘤，主要因其早期症状隐匿导致诊断延迟。早期发现可提高生存率，但现有生物标志物缺乏敏感性与特异性。肿瘤细胞释放的游离DNA（cfDNA）携带肿瘤相关表观遗传学改变，是极具前景的微创生物标志物来源。其中DNA异常甲基化在肿瘤发生早期即出现，可能反映潜在疾病生物学特征。本研究旨在系统分析卵巢癌患者、良性卵巢疾病患者及健康对照人群的全基因组cfDNA甲基化谱，以识别可能指导未来生物标志物开发的癌症相关甲基化模式。 结果：我们采用游离甲基化DNA免疫沉淀测序技术（cfMeDIP-seq）对40例高级别浆液性卵巢癌患者、38例良性卵巢疾病患者及38例健康绝经后女性的血浆样本进行全基因组cfDNA甲基化分析。在卵巢癌组与对照组（n=76）间共鉴定出536个差异甲基化区域（DMRs），其中97%在卵巢癌中呈现高甲基化。DMRs富集于CpG岛和基因体区域，在重复序列中则呈现缺失，这与已知的癌症相关甲基化模式一致。综合分析显示15个基因存在显著高甲基化，其甲基化区域涵盖内含子、外显子及上游调控区。卵巢癌组分别与两个对照组（良性疾病组和健康组）的独立比较验证了该结果的可靠性。基因本体富集分析显示这些基因在腺体发育、胚胎形态发生及内分泌调控等生物学过程中显著富集，提示其与卵巢肿瘤发生存在生物学关联。 结论：本研究揭示了卵巢癌中稳定存在的cfDNA高甲基化模式，主要影响参与发育调控和激素相关过程的基因。我们的发现证实了cfMeDIP-seq技术在检测血浆中肿瘤特异性甲基化特征的潜力，并提示这15个高甲基化基因可作为未来卵巢癌cfDNA甲基化研究的生物学相关靶标。
Genome-Wide cfDNA Methylation Profiling Reveals Robust Hypermethylation Signatures in Ovarian Cancer
肿瘤(癌症)患者之家