Abstract
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.
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Data availability
The methylation data generated in this study are deposited in the OMIX, China National Center for Bioinformation/Beijing Institute of Genomics, Chinese Academy of Sciences (http://bigd.big.ac.cn/omix, accession number OMIX004975). Other data supporting the findings of the present study are available from the corresponding author upon reasonable request.
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Acknowledgement
This work was supported by CAMS Innovation Fund for Medical Sciences (2021-I2M-1–010), National Key Research and Development Program of China (2016YFC0901404), and the National Natural Science Foundation of China (81974493). We thank the Gene Expression Omnibus database for providing public platform and researchers for their valuable data sets. WQ. W. and ZY.F. conceived and designed the study. ZY.F., FF.H., MJ.L., XQ.L., JW.W., R.C., and H.J. collected data and performed quality control. ZY.F. and JJ.H. performed the experiments and analyzed the data. ZY.F. completed the initial drafting of the manuscript. JJ.H. and WQ.W. critically revised the manuscript. All authors read and approved the final manuscript.
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Fan, Z., Hao, J., He, F. et al. Novel DNA methylation markers for early detection of gastric cardia adenocarcinoma and esophageal squamous cell carcinoma. Sci. China Life Sci. (2024). https://doi.org/10.1007/s11427-024-2642-8
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DOI: https://doi.org/10.1007/s11427-024-2642-8