Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA
Abstract Background Epigenetic variants carried by circulating tumor DNA can be used as biomarkers for early detection of hepatocellular carcinoma (HCC) by noninvasive liquid biopsy. However, traditional methylation analysis method, bisulfite sequencing, with disadvantages of severe DNA damage, is l...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-01-01
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| Series: | Clinical Epigenetics |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s13148-022-01420-6 |
| _version_ | 1797958677521498112 |
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| author | Ping Guo Hailing Zheng Yihan Li Yuntong Li Yue Xiao Jin Zheng Xingqiang Zhu Huan Xu Zhi He Qian Zhang Jinchun Chen Mingshan Qiu Min Jiang Pingguo Liu Hongliang Chen |
| author_facet | Ping Guo Hailing Zheng Yihan Li Yuntong Li Yue Xiao Jin Zheng Xingqiang Zhu Huan Xu Zhi He Qian Zhang Jinchun Chen Mingshan Qiu Min Jiang Pingguo Liu Hongliang Chen |
| author_sort | Ping Guo |
| collection | DOAJ |
| description | Abstract Background Epigenetic variants carried by circulating tumor DNA can be used as biomarkers for early detection of hepatocellular carcinoma (HCC) by noninvasive liquid biopsy. However, traditional methylation analysis method, bisulfite sequencing, with disadvantages of severe DNA damage, is limited in application of low-amount cfDNA analysis. Results Through mild enzyme-mediated conversion, enzymatic methyl sequencing (EM-seq) is ideal for precise determination of cell-free DNA methylation and provides an opportunity for HCC early detection. EM-seq of methylation control DNA showed that enzymatic conversion of unmethylated C to U was more efficient than bisulfite conversion. Moreover, a relatively large proportion of incomplete converted EM-seq reads contains more than 3 unconverted CH site (CH = CC, CT or CA), which can be removed by filtering to improve accuracy of methylation detection by EM-seq. A cohort of 241 HCC, 76 liver disease, and 279 normal plasma samples were analyzed for methylation value on 1595 CpGs using EM-seq and targeted capture. Model training identified 283 CpGs with significant differences in methylation levels between HCC and non-HCC samples. A HCC screening model based on these markers can efficiently distinguish HCC sample from non-HCC samples, with area under the curve of 0.957 (sensitivity = 90%, specificity = 97%) in the test set, performing well in different stages as well as in serum α-fetoprotein/protein induced by vitamin K absence-II negative samples. Conclusion Filtering of reads with ≥ 3 CHs derived from incomplete conversion can significantly reduce the noise of EM-seq detection. Based on targeted EM-seq analysis of plasma cell-free DNA, our HCC screening model can efficiently distinguish HCC patients from non-HCC individuals with high sensitivity and specificity. |
| first_indexed | 2024-04-11T00:22:24Z |
| format | Article |
| id | doaj.art-dd47e1dabedd4009af95bdd5b133f241 |
| institution | Directory Open Access Journal |
| issn | 1868-7083 |
| language | English |
| last_indexed | 2024-04-11T00:22:24Z |
| publishDate | 2023-01-01 |
| publisher | BMC |
| record_format | Article |
| series | Clinical Epigenetics |
| spelling | doaj.art-dd47e1dabedd4009af95bdd5b133f2412023-01-08T12:14:49ZengBMCClinical Epigenetics1868-70832023-01-0115111110.1186/s13148-022-01420-6Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNAPing Guo0Hailing Zheng1Yihan Li2Yuntong Li3Yue Xiao4Jin Zheng5Xingqiang Zhu6Huan Xu7Zhi He8Qian Zhang9Jinchun Chen10Mingshan Qiu11Min Jiang12Pingguo Liu13Hongliang Chen14School of Medicine, Huaqiao UniversityXiamen Vangenes Biotechnology CO., LTDXiamen Hospital of Beijing University of Chinese MedicineZhongshan Hospital, Xiamen UniversityXiamen Vangenes Biotechnology CO., LTDXiamen Vangenes Biotechnology CO., LTDXiamen Vangenes Biotechnology CO., LTDXiamen Vangenes Biotechnology CO., LTDXiamen Vangenes Biotechnology CO., LTDXiamen Hospital of Beijing University of Chinese MedicineXiamen Hospital of Beijing University of Chinese MedicineXiamen Hospital of Beijing University of Chinese MedicineThe Second Affiliated Hospital of Fujian University of Traditional Chinese MedicineZhongshan Hospital, Xiamen UniversityXiamen Vangenes Biotechnology CO., LTDAbstract Background Epigenetic variants carried by circulating tumor DNA can be used as biomarkers for early detection of hepatocellular carcinoma (HCC) by noninvasive liquid biopsy. However, traditional methylation analysis method, bisulfite sequencing, with disadvantages of severe DNA damage, is limited in application of low-amount cfDNA analysis. Results Through mild enzyme-mediated conversion, enzymatic methyl sequencing (EM-seq) is ideal for precise determination of cell-free DNA methylation and provides an opportunity for HCC early detection. EM-seq of methylation control DNA showed that enzymatic conversion of unmethylated C to U was more efficient than bisulfite conversion. Moreover, a relatively large proportion of incomplete converted EM-seq reads contains more than 3 unconverted CH site (CH = CC, CT or CA), which can be removed by filtering to improve accuracy of methylation detection by EM-seq. A cohort of 241 HCC, 76 liver disease, and 279 normal plasma samples were analyzed for methylation value on 1595 CpGs using EM-seq and targeted capture. Model training identified 283 CpGs with significant differences in methylation levels between HCC and non-HCC samples. A HCC screening model based on these markers can efficiently distinguish HCC sample from non-HCC samples, with area under the curve of 0.957 (sensitivity = 90%, specificity = 97%) in the test set, performing well in different stages as well as in serum α-fetoprotein/protein induced by vitamin K absence-II negative samples. Conclusion Filtering of reads with ≥ 3 CHs derived from incomplete conversion can significantly reduce the noise of EM-seq detection. Based on targeted EM-seq analysis of plasma cell-free DNA, our HCC screening model can efficiently distinguish HCC patients from non-HCC individuals with high sensitivity and specificity.https://doi.org/10.1186/s13148-022-01420-6Enzymatic methyl sequencingLiquid biopsyHepatocellular carcinomaCancer screeningIncomplete Conversion |
| spellingShingle | Ping Guo Hailing Zheng Yihan Li Yuntong Li Yue Xiao Jin Zheng Xingqiang Zhu Huan Xu Zhi He Qian Zhang Jinchun Chen Mingshan Qiu Min Jiang Pingguo Liu Hongliang Chen Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA Clinical Epigenetics Enzymatic methyl sequencing Liquid biopsy Hepatocellular carcinoma Cancer screening Incomplete Conversion |
| title | Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA |
| title_full | Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA |
| title_fullStr | Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA |
| title_full_unstemmed | Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA |
| title_short | Hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell-free DNA |
| title_sort | hepatocellular carcinoma detection via targeted enzymatic methyl sequencing of plasma cell free dna |
| topic | Enzymatic methyl sequencing Liquid biopsy Hepatocellular carcinoma Cancer screening Incomplete Conversion |
| url | https://doi.org/10.1186/s13148-022-01420-6 |
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