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Updated: Aug 19, 2025
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Identification of DNA methylation signatures for hepatocellular carcinoma detection and microvascular invasion
Yijie Hao1,2, Qingxia Yang2,3, Qiye He4
1Center of Hepato-Pancreato-Biliary Surgery, The First Affiliated Hospital, Sun Yat-sen University, No.58 Zhongshan Er Road, Guangzhou, 510080, Guangdong Province, China.
Background And Aim:
Preoperative evaluation of microvascular invasion (MVI) in patients with hepatocellular carcinoma (HCC) is important for surgical strategy determination. We aimed to develop and establish a preoperative predictive model for MVI status based on DNA methylation markers.
Methods:
A total of 35 HCC tissues and the matched peritumoral normal liver tissues as well as 35 corresponding HCC patients' plasma samples and 24 healthy plasma samples were used for genome-wide methylation sequencing and subsequent methylation haplotype block (MHB) analysis. Predictive models were constructed based on selected MHB markers and 3-cross validation was used.
Results:
We grouped 35 HCC patients into 2 categories, including the MVI- group with 17 tissue and plasma samples, and MVI + group with 18 tissue and plasma samples. We identified a tissue DNA methylation signature with an AUC of 98.0% and a circulating free DNA (cfDNA) methylation signature with an AUC of 96.0% for HCC detection. Furthermore, we established a tissue DNA methylation signature for MVI status prediction, and achieved an AUC of 85.9%. Based on the MVI status predicted by the DNA methylation signature, the recurrence-free survival (RFS) and overall survival (OS) were significantly better in the predicted MVI- group than that in the predicted MVI + group.
Conclusions:
In this study, we identified a cfDNA methylation signature for HCC detection and a tissue DNA methylation signature for MVI status prediction with high accuracy.
