PO.PR01.02 · 预防研究
全基因组启动子DNA甲基化特征与韩国遗传性乳腺癌风险：一项用于II期验证的初步研究
Genome-wide promoter DNA methylation signatures and risk of hereditary breast cancer in Korea: A pilot study for phase II validation
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
乳腺癌仍是全球女性癌症相关死亡的主要原因之一。表观遗传失调，尤其是CpG岛的DNA甲基化，可调节参与细胞增殖、分化和凋亡的基因的转录活性。启动子区域的异常甲基化日益被认为是乳腺癌早期和无创检测的一种有前景的生物标志物。本初步研究作为II期验证项目的初始阶段而设计，旨在识别与遗传性乳腺癌相关的全基因组甲基化特征。我们使用Illumina HumanMethylation BeadChip对16例遗传性乳腺癌患者和28例正常对照的DNA甲基化谱进行了分析。全基因组共检测了775,008个CpG位点。其中，217,366个CpG显示出显著的差异甲基化（min p = 6.87×10⁻⁹；min FDR = 0.003），批次校正后有136个CpG仍具有显著性（min p = 5.98×10⁻⁹；min FDR = 4.63×10⁻³）。在启动子区域（164,796个CpG）内，有32个位点在FDR < 0.05时显著（min p = 2.14×10⁻⁷；min FDR = 0.012）。低甲基化（27.5%）略多于高甲基化（23.5%），聚类分析显示多个基因集中的甲基化改变在启动子水平呈聚集性，提示遗传性乳腺癌中存在广泛但平衡的表观遗传改变。为进行外部验证，将把发现位点交叉映射到TCGA-BRCA、GEO（如GSE69914）和METABRIC数据集中重叠的CpG。将使用minfi对Beta值进行标准化，并通过ComBat进行协调以最大限度地减少批次效应。将使用limma重新评估启动子水平的甲基化差异，并通过方向一致性和FDR校正的显著性来确认重复性。此外，在初步发现集中FDR > 0.05的CpG位点将被保留用于II期分析，该分析涉及400例BRCA1/2遗传性乳腺癌患者和400例匹配对照，采用靶向甲基化检测。这一扩大队列将允许对临界和新发现的CpG位点进行验证，并评估启动子甲基化作为早期检测和风险预测的精准生物标志物。总的来说，我们的结果提示启动子甲基化特征反映了遗传性乳腺癌中一种可重复且具有生物学意义的表观遗传模式，值得在独立人群中开展大规模验证。本研究得到了韩国政府（MSIT）资助的韩国国家研究基金会（NRF）基金（No. RS-2024-00345260）以及韩国保健福祉部国家癌症控制研发计划（1420190）的支持。
查看英文原文 English abstract
Breast cancer remains one of the leading causes of cancer-related mortality among women worldwide. Epigenetic dysregulation, particularly DNA methylation of CpG islands, can modulate the transcriptional activity of genes involved in cell proliferation, differentiation, and apoptosis. Aberrant methylation in promoter regions has been increasingly recognized as a promising biomarker for early and non-invasive detection of breast cancer. This pilot study, designed as the initial phase for a Phase II validation project, aimed to identify genome-wide methylation signatures associated with hereditary breast cancer. We analyzed DNA methylation profiles using the Illumina HumanMethylation BeadChip in 16 hereditary breast cancer patients and 28 normal controls. A total of 775,008 CpG sites were examined across the genome. Of these, 217,366 CpGs showed significant differential methylation (min p = 6.87×10⁻⁹; min FDR = 0.003), and 136 CpGs remained significant after batch correction (min p = 5.98×10⁻⁹; min FDR = 4.63×10⁻³). Within promoter regions (164,796 CpGs), 32 sites were significant at FDR < 0.05 (min p = 2.14×10⁻⁷; min FDR = 0.012). Hypomethylation (27.5%) was slightly more frequent than hypermethylation (23.5%), and clustering analysis revealed promoter-level aggregation of methylation changes across multiple gene sets, indicating widespread but balanced epigenetic alterations in hereditary breast cancer. For external validation, discovery loci will be cross-mapped to overlapping CpGs in TCGA-BRCA, GEO (e.g., GSE69914), and METABRIC datasets. Beta-values will be normalized using minfi and harmonized by ComBat to minimize batch effects. Promoter-level methylation differences will be reassessed with limma, and replication will be confirmed by directional concordance and FDR-adjusted significance. Furthermore, CpG sites with FDR > 0.05 in the pilot discovery set will be retained for a Phase II analysis involving 400 BRCA1/2 hereditary breast cancer patients and 400 matched controls, using targeted methylation assays. This extended cohort will allow validation of borderline and novel CpG loci and evaluation of promoter methylation as a precision biomarker for early detection and risk prediction. Collectively, our results suggest that promoter methylation signatures reflect a reproducible and biologically meaningful epigenetic pattern in hereditary breast cancer and warrant large-scale validation in independent populations. This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. RS-2024-00345260) and the National R&D Program for Cancer Control, Ministry of Health & Welfare, Republic of Korea (1420190).
利益披露 Disclosure
S. Park, None..
S. Lee, None.