Genome-wide methylation profiling of the different stages of hepatitis B virus-related hepatocellular carcinoma development in plasma cell-free DNA reveals potential biomarkers for early detection and high-risk monitoring of hepatocellular carcinoma

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• 作者：Yangxing Zhao (24)
  Feng Xue (25)
  Jinfeng Sun (26)
  Shicheng Guo (27)
  Hongyu Zhang (28)
  Bijun Qiu (25)
  Junfeng Geng (29)
  Jun Gu (24)
  Xiaoyu Zhou (30)
  Wei Wang (24)
  Zhenfeng Zhang (24)
  Ning Tang (28)
  Yinghua He (28)
  Jian Yu (24)
  Qiang Xia (25)
  
  24. State Key Laboratory of Oncogenes and Related Genes ; Shanghai Cancer Institute ; Renji Hospital ; Shanghai Jiao Tong University School of Medicine ; LN 2200/25 ; Xietu Road ; Shanghai ; 200032 ; China
  25. Department of Liver Surgery ; Ren Ji Hospital ; School of Medicine ; Shanghai Jiao Tong University ; 160 Pujian Road ; Shanghai ; 200127 ; China
  26. Zhongshan Hospital ; Fudan University ; 180 Fenglin Road ; Shanghai ; 200032 ; China
  27. Ministry of Education Key Laboratory of Contemporary Anthropology School of Life Sciences ; Fudan University ; 220 Handan Road ; Shanghai ; 200433 ; China
  28. Shanghai Cancer Institute ; Renji Hospital ; Shanghai Jiao Tong University School of Medicine ; LN 2200/25 ; Xietu Road ; Shanghai ; 200032 ; China
  29. Department of General Thoracic Surgery ; Shanghai Chest Hospital ; Shanghai Jiao Tong University ; 241 West Huaihai Road ; Shanghai ; 200030 ; China
  30. Key Laboratory of Contraceptive Drugs and Devices of NPFPC ; Shanghai Institute of Planned Parenthood Research ; 2140 Xietu Road ; Shanghai ; 200032 ; China
  
• 关键词：Plasma ; Cell ; free DNA ; HBV ; HCC development ; Genome ; wide ; DNA methylation
• 刊名：Clinical Epigenetics
• 出版年：2014
• 出版时间：December 2014
• 年：2014
• 卷：6
• 期：1
• 全文大小：2,831 KB
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• 刊物主题：Human Genetics; Gene Function;
• 出版者：BioMed Central
• ISSN：1868-7083

文摘

Background An important model of hepatocellular carcinoma (HCC) that has been described in southeast Asia includes the transition from chronic hepatitis B infection (CHB) to liver cirrhosis (LC) and, finally, to HCC. The genome-wide methylation profiling of plasma cell-free DNA (cfDNA) has not previously been used to assess HCC development. Using MethylCap-seq, we analyzed the genome-wide cfDNA methylation profiles by separately pooling healthy control (HC), CHB, LC and HCC samples and independently validating the library data for the tissue DNA and cfDNA by MSP, qMSP and Multiplex-BSP-seq. Results The dynamic features of cfDNA methylation coincided with the natural course of HCC development. Data mining revealed the presence of 240, 272 and 286 differentially methylated genes (DMGs) corresponding to the early, middle and late stages of HCC progression, respectively. The validation of the DNA and cfDNA results in independent tissues identified three DMGs, including ZNF300, SLC22A20 and SHISA7, with the potential for distinguishing between CHB and LC as well as between LC and HCC. The area under the curve (AUC) ranged from 0.65 to 0.80, and the odds ratio (OR) values ranged from 5.18 to 14.2. Conclusions Our data revealed highly dynamic cfDNA methylation profiles in support of HBV-related HCC development. We have identified a panel of DMGs that are predictive for the early, middle and late stages of HCC development, and these are potential markers for the early detection of HCC as well as the screening of high-risk populations.