Clinical Epigenetics (Jun 2025)

A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling

  • Jialing Sun,
  • Xinfeng Sun,
  • Weihuang He,
  • Bingding Huang,
  • Wenxing Feng,
  • Zhiyi Han,
  • Ruyun Ruan,
  • Yuanke Pan,
  • Jinxin Zhu,
  • Jing Li,
  • Xin Zhong,
  • Mengqing Ma,
  • Rui Hu,
  • Minling Lv,
  • Qi Huang,
  • Wei Zhang,
  • Mingji Feng,
  • Jinyu Yi,
  • Pin Cui,
  • Xiaozhou Zhou

DOI
https://doi.org/10.1186/s13148-025-01909-w
Journal volume & issue
Vol. 17, no. 1
pp. 1 – 13

Abstract

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Abstract Background Early detection of hepatocellular carcinoma (HCC) can greatly improve the survival rate of patients. Plasma cfDNA methylation has been shown to have the potential to be a non-invasive method for diagnosing HCC. However, the identified HCC plasma cfDNA methylation sites were less sensitive to early HCC diagnosis. Therefore, we aimed to develop a highly sensitive marker panel based on cell-free DNA (cfDNA) methylation for the detection of HCC. Methods The study included 374 participants, including 102 healthy individuals, 51 HBV patients, 50 cirrhosis patients, and 171 HCC patients (56 at stage 0 or A according to BCLC staging). Two cfDNA methylation sequencing assays (whole genome bisulfite sequencing (WGBS) and targeted bisulfite sequencing (TBS)) were used along with machine learning modeling to detect HBV-related HCC based on differentially methylated regions (DMR) among the four participant groups. Results TBS analysis achieved an overall sensitivity of 96.67% at a specificity of 93.7% than alpha-fetoprotein (AFP) of 18%-60%, to discriminate all stages of HCC patients from healthy people, and sensitivity of 90.0% at a specificity of 93.75% to discriminate early-stage HCC patients from healthy people. A number of significant DMRs between HCC and non-cancer groups were identified, providing candidate biomarkers for HCC detection. Among these DMRs, one that locates in the promoter region of GJA4, was found to be consistently present in the whole process of HBV-related HCC carcinogenesis. Using data from TCGA, comparison of expression profile of GJA4 between 160 healthy people and 369 HCC patients further supported this scenario. Conclusions: This study provides biomarkers for detecting, staging and early detection of HCC using plasma cfDNA methylome profiling. Additionally, the dynamic alteration of GJA4 promoter methylation may serve as a molecular clue for studying HBV-related HCC carcinogenesis and prognosis.

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