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Methylation profiling of serum DNA from hepatocellular carcinoma patients using an Infinium Human Methylation 450 BeadChip

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Abstract

Background

Alterations in DNA methylation frequently occur in hepatocellular cancer (HCC). The methylation status of circulating DNA might serve as a potential biomarker for cancers.

Methods

Six early stage HCC patients with chronic hepatitis B virus (HBV) infection and six age-matched healthy controls were selected for genome-scale DNA methylation screening of serum by Illumina Infinium Human Methylation 450 BeadChip. The chosen methylation sites were reassessed by bisulfite sequencing in four healthy controls and four early stage HCC patients with chronic HBV infection and were used for bead array screening. Another 27 healthy controls and 31 early stage HCC patients with chronic HBV infection were also chosen for further bisulfite sequencing validation.

Results

Whole-genome methylation was significantly lower in serum from HCC patients than in that from healthy controls. After bioinformatics analysis, methylation at DBX2 and Thy-1 membrane glycoprotein (THY1) was reassessed by bisulfite sequencing. The correlation coefficients of DBX2 and THY1 between the Illumina 450 BeadChip and bisulfite sequencing were respectively 0.9145 and 0.8232. Twenty-seven healthy controls and 31 early stage HCC patients with chronic HBV infection were chosen for further validation. The diagnostic sensitivity and specificity of DBX2 for differentiating healthy controls and early stage HCC were 88.89 and 87.10 % and of THY1 were 85.19 and 80.65 %.

Conclusions

The results demonstrated that the 450K BeadChip is a useful tool for whole-genome serum DNA methylation screening of HCC, and some HCC-related DNA methylation sites were screened.

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Acknowledgments

This work was supported by the National High Technology Research and Development Program 863 (2011AA02A111), National Science and Technology Infrastructure (2009BAI86B05) and The National Natural Science Foundation of China (81071413).

Compliance with ethical requirements and Conflict of interest

All procedures followed were in accordance with the ethical standards of Ethics Committee of the Chinese PLA General Hospital and with the Helsinki Declaration of 1975, as revised in 2008. Informed consent was obtained from all patients for being included in the study. Pengjun Zhang, Xinyu Wen, Feng Gu, Xinxin Deng, Juan Li, Jin Dong, Jiao Jiao, and Yaping Tian declare that they have no conflict of interest.

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Authors and Affiliations

  1. State Key Laboratory of Kidney Disease, Department of Clinical Biochemistry, Chinese PLA General Hospital, 28 Fu-Xing Road, Beijing, China

    Pengjun Zhang, Xinyu Wen, Feng Gu, Xinxin Deng, Juan Li, Jin Dong, Jiao Jiao & Yaping Tian

  2. Medical College, Nankai University, Tianjin, China

    Yaping Tian

Authors
  1. Pengjun Zhang
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  2. Xinyu Wen
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  3. Feng Gu
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  4. Xinxin Deng
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  5. Juan Li
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  6. Jin Dong
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  7. Jiao Jiao
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  8. Yaping Tian
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Corresponding author

Correspondence to Yaping Tian.

Additional information

Zhang Pengjun, Wen Xinyu and Gu Feng have contributed equally.

Electronic supplementary material

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12072_2013_9437_MOESM1_ESM.tif

Supplementary Fig. 1 Gene interaction map of the 28 sites that were hypermethylated in the healthy control group compared to the HCC group using an edge weight cutoff of 0.689. Genes marked with a red line are involved in sequence-specific DNA binding. (TIFF 1278 kb)

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Zhang, P., Wen, X., Gu, F. et al. Methylation profiling of serum DNA from hepatocellular carcinoma patients using an Infinium Human Methylation 450 BeadChip. Hepatol Int 7, 893–900 (2013). https://doi.org/10.1007/s12072-013-9437-0

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  • DOI: https://doi.org/10.1007/s12072-013-9437-0

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