血浆游离DNA中甲基化IRF4两个片段与ZEB2一片段的双基因检测组合用于胃癌检测

A dual-gene panel of two fragments of methylated IRF4 and one of ZEB2 in plasma cell-free DNA for gastric cancer detection

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Epigenetics

影响因子:3.2

分区:生物学3区 / 生化与分子生物学3区遗传学3区

发表日期:2024 Dec

作者: Chunxiao Bu, Zhilong Wang, Xianping Lv, Yanteng Zhao

DOI: 10.1080/15592294.2024.2374988

摘要

早期检测对于提高胃癌（GC）患者的生存率至关重要。我们旨在识别用于检测GC的甲基化游离DNA（cfDNA）标记物面板。从癌症基因组图谱（TCGA）和基因表达数据库（GEO）中筛选差异甲基化的CpG位点（DMCs）。所选DMCs在组织样本（40例胃癌，36例健康白细胞）和血浆样本（37例胃癌，12例良性胃病，43例健康人）中进行验证和筛选。随后，在常规血浆样本（35例胃癌，39例对照疾病，40例健康人）中采用实时甲基化特异性PCR（MSP）评估所选标记组合。结果分析采用2-ΔΔCt值和Ct值的比较方法。通过生物信息学筛选出30个DMCs，经过生物验证筛选出5个，最终选择IRF4的两个片段（IRF4-1和IRF4-2）及ZEB2作为检测标记组合，表现良好。Ct值法因其良好的结果和实用性被采用，IRF4-1和IRF4-2在一个荧光通道中，而ZEB2在另一个通道中，实现对任何阶段胃癌组的检测灵敏度达74.3%，特异性为92.4%。总之，该IRF4和ZEB2在血浆cfDNA中的检测面板具有良好的诊断性能和临床应用潜力。

Abstract

Early detection is crucial for increasing the survival rate of gastric cancer (GC). We aimed to identify a methylated cell-free DNA (cfDNA) marker panel for detecting GC. The differentially methylated CpGs (DMCs) were selected from datasets of The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The selected DMCs were validated and further selected in tissue samples (40 gastric cancer and 36 healthy white blood cell samples) and in a quarter sample volume of plasma samples (37 gastric cancer, 12 benign gastric disease, and 43 healthy individuals). The marker combination selected was then evaluated in a normal sample volume of plasma samples (35 gastric cancer, 39 control diseases, and 40 healthy individuals) using real-time methylation-specific PCR (MSP). The analysis of the results compared methods based on 2-ΔΔCt values and Ct values. In the results, 30 DMCs were selected through bioinformatics methods, and then 5 were selected for biological validation. The marker combination of two fragments of IRF4 (IRF4-1 and IRF4-2) and one of ZEB2 was selected due to its good performance. The Ct-based method was selected for its good results and practical advantages. The assay, IRF4-1 and IRF4-2 in one fluorescence channel and ZEB2 in another, obtained 74.3% sensitivity for the GC group at any stage, at 92.4% specificity. In conclusion, the panel of IRF4 and ZEB2 in plasma cfDNA demonstrates good diagnostic performance and application potential in clinical settings.