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Analysis of the Genome-Wide DNA Methylation Profile of Side Population Cells in Hepatocellular Carcinoma

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Abstract

Background

DNA methylation plays an important role in maintaining pluripotency and regulating the differentiation of stem cells, but the DNA methylation profile of stem cells in hepatocellular carcinoma (HCC) remains unclear.

Aims

To investigate the genome-wide DNA methylation profile of side population (SP) cells of HCC, a special subpopulation of cells enriched with cancer stem cells, by DNA methylation microarray analysis and to analyze the functions and signal pathways of the aberrantly methylated genes in SP cells.

Methods

Side population cells were isolated from HCC cell lines Huh7 and PLC/PRF/5 using flow cytometry, and the tumorigenicity of these SP cells was assessed in NOD/SCID mice. The genome-wide DNA methylation status of SP cells and non-SP (NSP) cells was detected and compared by DNA methylation microarray analysis. Genes with differential methylation between SP and NSP cells were further analyzed for their functions and roles in related signaling pathways.

Results

Subcutaneous inoculation of 1 × 103 SP cells yielded tumors in 60 % NOD/SCID mice, whereas no tumor was developed after the inoculation of 1 × 106 NSP cells. Genome-wide DNA methylation microarray analysis showed that 72 and 181 genes were hypermethylated and hypomethylated, respectively, in both Huh7 and PLC/PRF/5 SP cells as compared with their corresponding NSP cells. Analyses of signaling pathways revealed that hypermethylated and hypomethylated genes were related to four and eight pathways, respectively.

Conclusions

Hepatocellular carcinoma SP cells possessed a differential DNA methylation status compared with NSP cells, and the differentially methylated genes in SP cells were involved in 12 signaling pathways. Our results provide valuable clues for further investigations in elucidating the importance of epigenetic regulation in sustaining HCC SP cells and tumorigenesis.

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Acknowledgments

This work was supported by grants from National Natural Science Foundation of China (No. 30672051) and National Science and Technology Major Projects of China (No. 2008ZX10002-019 and 2008ZX10002-026).

Conflict of interest

None.

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Authors and Affiliations

  1. Department of Hepatobiliary Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, People’s Republic of China

    Jing-Ming Zhai, Xiao-Yu Yin, Xun Hou, Xiao-Yi Hao, Jian-Peng Cai & Li-Jian Liang

  2. Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510080, Guangdong, People’s Republic of China

    Long-Juan Zhang

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  1. Jing-Ming Zhai
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  2. Xiao-Yu Yin
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  5. Jian-Peng Cai
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Correspondence to Xiao-Yu Yin.

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Zhai, JM., Yin, XY., Hou, X. et al. Analysis of the Genome-Wide DNA Methylation Profile of Side Population Cells in Hepatocellular Carcinoma. Dig Dis Sci 58, 1934–1947 (2013). https://doi.org/10.1007/s10620-013-2663-4

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  • DOI: https://doi.org/10.1007/s10620-013-2663-4

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