用于胃癌检测的血浆游离 DNA 中两个甲基化 IRF4 片段和一个 ZEB2 片段的双基因组。
A dual-gene panel of two fragments of methylated IRF4 and one of ZEB2 in plasma cell-free DNA for gastric cancer detection.
发表日期:2024 Dec
作者:
Chunxiao Bu, Zhilong Wang, Xianping Lv, Yanteng Zhao
来源:
Epigenetics & Chromatin
摘要:
早期发现对于提高胃癌(GC)的生存率至关重要。我们的目的是鉴定用于检测 GC 的甲基化游离 DNA (cfDNA) 标记物组。差异甲基化 CpG (DMC) 选自癌症基因组图谱 (TCGA) 和基因表达综合 (GEO) 数据库的数据集。选定的 DMC 在组织样本(40 例胃癌和 36 例健康白细胞样本)和四分之一样本体积的血浆样本(37 例胃癌、12 例良性胃病和 43 例健康个体)中进行了验证和进一步选择。然后使用实时甲基化特异性 PCR (MSP) 在正常样本量的血浆样本(35 例胃癌、39 例对照疾病和 40 例健康个体)中评估所选标记组合。结果分析比较了基于2-ΔΔCt值和Ct值的方法。结果中,通过生物信息学方法筛选出30个DMC,然后筛选出5个进行生物学验证。 IRF4的两个片段(IRF4-1和IRF4-2)和ZEB2的一个片段的标记组合因其良好的性能而被选择。基于CT的方法因其良好的结果和实用优势而被选择。该检测(一个荧光通道中的 IRF4-1 和 IRF4-2 以及另一个荧光通道中的 ZEB2)在任何阶段对 GC 组的灵敏度为 74.3%,特异性为 92.4%。总之,血浆 cfDNA 中的 IRF4 和 ZEB2 组合表现出良好的诊断性能和在临床环境中的应用潜力。
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.