A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling
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...
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BMC
2025-06-01
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| Series: | Clinical Epigenetics |
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| Online Access: | https://doi.org/10.1186/s13148-025-01909-w |
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| author | 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 |
| author_facet | 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 |
| author_sort | Jialing Sun |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-673af040acbb4f92ad17a86e46d1aed3 |
| institution | OA Journals |
| issn | 1868-7083 |
| language | English |
| publishDate | 2025-06-01 |
| publisher | BMC |
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| series | Clinical Epigenetics |
| spelling | doaj-art-673af040acbb4f92ad17a86e46d1aed32025-08-20T02:06:19ZengBMCClinical Epigenetics1868-70832025-06-0117111310.1186/s13148-025-01909-wA liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profilingJialing Sun0Xinfeng Sun1Weihuang He2Bingding Huang3Wenxing Feng4Zhiyi Han5Ruyun Ruan6Yuanke Pan7Jinxin Zhu8Jing Li9Xin Zhong10Mengqing Ma11Rui Hu12Minling Lv13Qi Huang14Wei Zhang15Mingji Feng16Jinyu Yi17Pin Cui18Xiaozhou Zhou19Department of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineShenzhen Rapha Biotechnology IncorporateCollege of Big Data and Internet, Shenzhen Technology UniversityDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineCollege of Big Data and Internet, Shenzhen Technology UniversityCollege of Big Data and Internet, Shenzhen Technology UniversityCollege of Big Data and Internet, Shenzhen Technology UniversityDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineShenzhen Rapha Biotechnology IncorporateDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineShenzhen Rapha Biotechnology IncorporateDepartment of Liver Disease, the Fourth Clinical Medical School, Guangzhou University of Chinese MedicineAbstract 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.https://doi.org/10.1186/s13148-025-01909-wHBV-HCC carcinogenesiscfDNAMethylation profileEarly detectionDMR |
| spellingShingle | 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 A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling Clinical Epigenetics HBV-HCC carcinogenesis cfDNA Methylation profile Early detection DMR |
| title | A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling |
| title_full | A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling |
| title_fullStr | A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling |
| title_full_unstemmed | A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling |
| title_short | A liquid biopsy approach detects HCC and identifies GJA4 as a potential biomarker for HBV-HCC via plasma cfDNA methylome profiling |
| title_sort | liquid biopsy approach detects hcc and identifies gja4 as a potential biomarker for hbv hcc via plasma cfdna methylome profiling |
| topic | HBV-HCC carcinogenesis cfDNA Methylation profile Early detection DMR |
| url | https://doi.org/10.1186/s13148-025-01909-w |
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