两个甲基化IRF4片段的双基因面板和无血浆细胞DNA中的一个Zeb2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
影响因子:3.20000
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
摘要
早期检测对于增加胃癌（GC）的存活率至关重要。我们旨在确定用于检测GC的无甲基化细胞DNA（CFDNA）标记面板。从癌症基因组图集（TCGA）和基因表达综合（GEO）数据库的数据集中选择差异化甲基化的CPGS（DMC）。验证了选定的DMC，并在组织样品（40个胃癌和36个健康的白细胞样品）和四分之一的血浆样品（37种胃癌，12种良性胃病和43个健康个体）中进一步选择。然后，使用实时甲基化特异性PCR（MSP）评估选定的标记组合在正常样品体积（35个胃癌，39个对照疾病和40个健康个体）中评估。对结果的分析比较了基于2-ΔΔCT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DMC进行生物学验证。由于其良好的性能，选择了IRF4（IRF4-1和IRF4-2）和ZEB2的两个片段的标记组合。基于CT的方法的良好结果和实际优势选择了基于CT的方法。一个荧光通道中的IRF4-1和IRF4-2在另一个荧光通道中的IRF4-1和IRF4-2，在任何阶段的特异性为92.4％，对GC组的敏感性为74.3％。总之，等离子体CFDNA中的IRF4和ZEB2小组在临床环境中表现出良好的诊断性能和应用潜力。
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.