Objective: To clarify the progression pattern of abnormal DNA methylation during the development of hepatocellular carcinoma (HCC) using a comprehensive methylation assay. Methods: We used an Infinium HumanMethylation450 BeadChip array that can analyze >485,000 CpG sites distributed throughout the genome for a comprehensive methylation study of 117 liver tissues consisting of 59 HCC and 58 noncancerous livers. Altered DNA methylation patterns during tumor progression were also analyzed. Results: We identified 38,330 CpG sites with significant differences in methylation levels between HCCs and noncancerous livers (DM-CpGs) using strict criteria. Of the DM-CpGs, 92% were hypomethylated and only 3,051 CpGs (8%) were hypermethylated in HCC. The DM-CpGs were more prevalent within intergenic regions with isolated CpGs. In contrast, DM-CpGs that were hypermethylated in HCC were predominantly located within promoter regions and CpG islands (p < 0.0001). The association between methylation profiles of DM-CpGs and tumor size was statistically significant, especially in hepatitis C virus (HCV)-positive cases (p = 0.0001). Conclusions: We clarified the unique characteristics of DM-CpGs in human HCCs. The stepwise progression of alterations in DNA methylation was a common feature of HCV-related hepatocarcinogenesis.

Keywords:
CpG sites, Cytosine residues, DNA methylation, Genome-wide profiling, Hypomethylation
1.
Kim do Y, Han KH: Epidemiology and surveillance of hepatocellular carcinoma. Liver Cancer 2012;1:2-14.
2.
Kudo M: Prediction of hepatocellular carcinoma incidence risk by ultrasound elastography. Liver Cancer 2014;3:1-5.
3.
Nishida N, Goel A: Genetic and epigenetic signatures in human hepatocellular carcinoma: a systematic review. Curr Genomics 2011;12:130-137.
4.
Moeini A, Cornella H, Villanueva A: Emerging signaling pathways in hepatocellular carcinoma. Liver Cancer 2012;1:83-93.
5.
Ramakrishna G, Rastogi A, Trehanpati N, Sen B, Khosla R, Sarin SK: From cirrhosis to hepatocellular carcinoma: new molecular insights on inflammation and cellular senescence. Liver Cancer 2013;2:367-383.
6.
Nishida N: Alteration of epigenetic profile in human hepatocellular carcinoma and its clinical implications. Liver Cancer, in press.
7.
Esteller M: Epigenetics in cancer. N Engl J Med 2008;358:1148-1159.
8.
Berdasco M, Esteller M: Aberrant epigenetic landscape in cancer: how cellular identity goes awry. Dev Cell 2010;19:698-711.
9.
Herman JG, Baylin SB: Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med 2003;349:2042-2054.
10.
Marabita F, Almgren M, Lindholm ME, Ruhrmann S, Fagerstrom-Billai F, Jagodic M, Sundberg CJ, Ekstrom TJ, Teschendorff AE, Tegner J, Gomez-Cabrero D: An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics 2013;8:333-346.
11.
Shen J, Wang S, Zhang YJ, Wu HC, Kibriya MG, Jasmine F, Ahsan H, Wu DP, Siegel AB, Remotti H, Santella RM: Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips. Epigenetics 2013;8:34-43.
12.
Song MA, Tiirikainen M, Kwee S, Okimoto G, Yu H, Wong LL: Elucidating the landscape of aberrant DNA methylation in hepatocellular carcinoma. PLoS One 2013;8:e55761.
13.
Kulis M, Queiros AC, Beekman R, Martin-Subero JI: Intragenic DNA methylation in transcriptional regulation, normal differentiation and cancer. Biochim Biophys Acta 2013;1829:1161-1174.
14.
Nishida N, Kudo M, Nishimura T, Arizumi T, Takita M, Kitai S, Yada N, Hagiwara S, Inoue T, Minami Y, Ueshima K, Sakurai T, Yokomichi N, Nagasaka T, Goel A: Unique association between global DNA hypomethylation and chromosomal alterations in human hepatocellular carcinoma. PLoS One 2013;8:e72312.
15.
Nishida N, Kudo M: Oxidative stress and epigenetic instability in human hepatocarcinogenesis. Dig Dis 2013;31:447-453.
16.
Mudbhary R, Hoshida Y, Chernyavskaya Y, Jacob V, Villanueva A, Fiel MI, Chen X, Kojima K, Thung S, Bronson RT, Lachenmayer A, Revill K, Alsinet C, Sachidanandam R, Desai A, SenBanerjee S, Ukomadu C, Llovet JM, Sadler KC: UHRF1 overexpression drives DNA hypomethylation and hepatocellular carcinoma. Cancer Cell 2014;25:196-209.
17.
Gao XD, Qu JH, Chang XJ, Lu YY, Bai WL, Wang H, Xu ZX, An LJ, Wang CP, Zeng Z, Yang YP: Hypomethylation of long interspersed nuclear element-1 promoter is associated with poor outcomes for curative resected hepatocellular carcinoma. Liver Int 2014;34:136-146.
18.
Nishida N, Kudo M, Nagasaka T, Ikai I, Goel A: Characteristic patterns of altered DNA methylation predict emergence of human hepatocellular carcinoma. Hepatology 2012;56:994-1003.
19.
Nishida N, Nagasaka T, Nishimura T, Ikai I, Boland CR, Goel A: Aberrant methylation of multiple tumor suppressor genes in aging liver, chronic hepatitis, and hepatocellular carcinoma. Hepatology 2008;47:908-918.
© 2014 S. Karger AG, Basel
2014
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