Fan Zhiyuan, Hao Jiajie, He Feifan, Jiang Hao, Wang Jinwu, Li Minjuan, Li Xinqing, Chen Ru, Wei Wenqiang
Office of National Central Cancer Registry, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
State Key Laboratory of Molecular Oncology, Center for Cancer Precision Medicine, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
Sci China Life Sci. 2024 Dec;67(12):2701-2712. doi: 10.1007/s11427-024-2642-8. Epub 2024 Aug 30.
Gastric cardia adenocarcinoma (GCA) and esophageal squamous cell carcinoma (ESCC) present significant health challenges in China, often diagnosed at advanced stages with poor prognoses. However, effective biomarkers for early detection remain elusive. This study aimed to integrate methylome and transcriptome data to identify DNA methylation markers for the early detection of GCA and ESCC. In the discovery stage, we conducted Infinium MethylationEPIC array analysis on 36 paired GCA and non-tumor adjacent tissues (NAT), identifying differentially methylated CpG sites (DMCs) between GCA/ESCC and NAT through combined analyses of in-house and publicly available data. In the validation stage, targeted pyrosequencing and quantitative real-time RT-PCR were performed on paired tumor and NAT samples from 50 GCA and 50 ESCC patients. In the application stage, an independent set of 438 samples, including GCA, ESCC, high- and low-grade dysplasia (HGD/LGD), and normal controls, was tested for selected DMCs using pyrosequencing. Our analysis validated three GCA-specific, two ESCC-specific, and one tumor-shared DMCs, exhibiting significant hypermethylation and decreased expression of target genes in tumor samples compared with NAT. Leveraging these DMCs, we developed a GCA-specific 4-marker panel (cg27284428, cg11798358, cg07880787, and cg00585116) with an area under the receiver operating characteristic curve (AUC) of 0.917, effectively distinguishing between cardia HGD/GCA patients and cardia LGD/normal controls. Similarly, an ESCC-specific 3-marker panel (cg14633892, cg04415798, and cg00585116) achieved an AUC of 0.865 in distinguishing esophageal HGD/ESCC cases. Furthermore, integrating cg00585116, age, and alcohol consumption yielded a tumor-shared logistic model with good discrimination for two cancer/HGD (AUC, 0.767; 95% confidence interval, 0.720-0.813). The mean AUC of the model after 5-fold cross-validation was 0.764. In summary, our study identifies novel DNA methylation markers capable of accurately distinguishing GCA/ESCC and HGD from LGD and normal controls. These findings offer promising prospects for targeted DNA methylation assays in future minimally invasive cancer screening methods.
贲门腺癌（GCA）和食管鳞状细胞癌（ESCC）在中国带来了重大的健康挑战，这些癌症往往在晚期才被诊断出来，预后较差。然而，用于早期检测的有效生物标志物仍然难以捉摸。本研究旨在整合甲基化组和转录组数据，以识别用于GCA和ESCC早期检测的DNA甲基化标志物。在发现阶段，我们对36对GCA及其非肿瘤相邻组织（NAT）进行了Infinium MethylationEPIC阵列分析，通过对内部和公开可用数据的综合分析，确定了GCA/ESCC与NAT之间差异甲基化的CpG位点（DMC）。在验证阶段，对来自50例GCA和50例ESCC患者的配对肿瘤和NAT样本进行了靶向焦磷酸测序和定量实时RT-PCR。在应用阶段，使用焦磷酸测序对包括GCA、ESCC、高级别和低级别发育异常（HGD/LGD）以及正常对照在内的438个独立样本集进行了选定DMC的检测。我们的分析验证了3个GCA特异性、2个ESCC特异性和1个肿瘤共享的DMC，与NAT相比，肿瘤样本中这些位点表现出显著的高甲基化以及靶基因表达降低。利用这些DMC，我们开发了一个GCA特异性的4标记物组合（cg27284428、cg11798358、cg07880787和cg00585116），其受试者工作特征曲线下面积（AUC）为0.917，能够有效区分贲门HGD/GCA患者与贲门LGD/正常对照。同样，一个ESCC特异性的3标记物组合（cg14633892、cg04415798和cg00585116）在区分食管HGD/ESCC病例时的AUC为0.865。此外，将cg00585116、年龄和饮酒情况相结合，得到了一个对两种癌症/HGD具有良好区分能力的肿瘤共享逻辑模型（AUC，0.767；95%置信区间，0.720 - 0.813）。5折交叉验证后模型的平均AUC为0.764。总之，我们的研究识别出了能够准确区分GCA/ESCC和HGD与LGD及正常对照的新型DNA甲基化标志物。这些发现为未来微创癌症筛查方法中的靶向DNA甲基化检测提供了有希望的前景。
