Department of Magnetic Resonance Imaging,The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
Henan Academy of Medical Sciences, Zhengzhou, Henan, China.
Epigenetics. 2024 Dec;19(1):2374988. doi: 10.1080/15592294.2024.2374988. Epub 2024 Jul 14.
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 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.
早期检测对于提高胃癌（GC）的生存率至关重要。我们旨在确定用于检测 GC 的甲基化细胞游离 DNA（cfDNA）标记物组合。从 The Cancer Genome Atlas（TCGA）和 Gene Expression Omnibus（GEO）数据库的数据集中选择差异甲基化 CpG（DMC）。在组织样本（40 例胃癌和 36 例健康白细胞样本）和四分之一体积的血浆样本（37 例胃癌、12 例良性胃病和 43 例健康个体）中验证和进一步选择所选 DMC。然后，使用实时甲基化特异性 PCR（MSP）在正常样本体积的血浆样本（35 例胃癌、39 例对照疾病和 40 例健康个体）中评估选定的标记组合。结果分析比较了基于 2 值和 Ct 值的方法。在结果中，通过生物信息学方法选择了 30 个 DMC，然后选择了 5 个进行生物学验证。由于其良好的性能，选择了两个 IRF4 片段（IRF4-1 和 IRF4-2）和一个 ZEB2 的标记组合。基于 Ct 的方法因其良好的结果和实用优势而被选中。该测定法，IRF4-1 和 IRF4-2 在一个荧光通道中，ZEB2 在另一个荧光通道中，在任何阶段对 GC 组的灵敏度均为 74.3%，特异性为 92.4%。总之，血浆 cfDNA 中的 IRF4 和 ZEB2 组合在临床环境中具有良好的诊断性能和应用潜力。
