J Korean Med Sci.  2011 Nov;26(11):1428-1438. 10.3346/jkms.2011.26.11.1428.

Genes Associated with Recurrence of Hepatocellular Carcinoma: Integrated Analysis by Gene Expression and Methylation Profiling

• Yang JD
• Seol SY
• Leem SH
• Kim YH
• Sun Z
• Lee JS
• Thorgeirsson SS
• Chu IS
• Roberts LR
• Kang KJ

• KMID: 1123442
• DOI: http://doi.org/10.3346/jkms.2011.26.11.1428

Abstract

Gene expression is suppressed by DNA methylation. The goal of this study was to identify genes whose CpG site methylation and mRNA expression are associated with recurrence after surgical resection for hepatocellular carcinoma (HCC). Sixty-two HCCs were examined by both whole genome DNA methylation and transcriptome analysis. The Cox model was used to select genes associated with recurrence. A validation was performed in an independent cohort of 66 HCC patients. Among fifty-nine common genes, increased CpG site methylation and decreased mRNA expression were associated with recurrence for 12 genes (Group A), whereas decreased CpG site methylation and increased mRNA expression were associated with recurrence for 25 genes (Group B). The remaining 22 genes were defined as Group C. Complement factor H (CFH) and myosin VIIA and Rab interacting protein (MYRIP) in Group A; proline/serine-rich coiled-coil 1 (PSRC1), meiotic recombination 11 homolog A (MRE11A), and myosin IE (MYO1E) in Group B; and autophagy-related protein LC3 A (MAP1LC3A), and NADH dehydrogenase 1 alpha subcomplex assembly factor 1 (NDUFAF1) in Group C were validated. In conclusion, potential tumor suppressor (CFH, MYRIP) and oncogenes (PSRC1, MRE11A, MYO1E) in HCC are reported. The regulation of individual genes by methylation in hepatocarcinogenesis needs to be validated.

Keyword

Carcinoma, Hepatocellular; Gene Expression Profiling; Microarray analysis; DNA methylation; Survival

MeSH Terms

Adult
Aged
Carcinoma, Hepatocellular/*genetics/pathology/surgery
CpG Islands
*DNA Methylation
Female
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
Humans
Liver/pathology
Liver Neoplasms/*genetics/pathology/surgery
Male
Middle Aged
Neoplasm Recurrence, Local/*genetics
Oligonucleotide Array Sequence Analysis
Proportional Hazards Models
RNA, Messenger/biosynthesis
Transcriptome/genetics

Figure

• 

  Fig. 1 Flow chart of the experimental protocol.

• 

  Fig. 2 Selection of recurrence associated genes in the training and validation data set. MYRIP, Myosin VIIA and Rab interacting protein; CFH, Complement factor H; PSRC1, Proline/serine-rich coiled-coil 1; MRE11A, Meiotic recombination 11 homolog A; MYO1E, Myosin IE; MAP1LC3A, autophagy-related protein LC3 A; NDUFAF1, NADH dehydrogenase 1 alpha subcomplex assembly factor 1.

• 

  Fig. 3 Effect of individual gene expression and methylation on recurrence free survival. Patients were divided into two groups based on their gene expression and methylation status (over expression vs under expression; hypermethylation vs hypomethylation). Recurrence-free survival was compared between two groups in the training data set. Group A and B genes associated with recurrence both in the training and validation data sets were included in the figure. (A) 31-patients with PSRC1 mRNA expression level above median is more likely develop recurrence than the other 31 patients with PSRC1 mRNA expression level below median (P = 0.05). On the other hand 31 patients with PSRC1 CpG site methylation level above median is less likely to develop recurrence than the other 31 patients with PSRC1 CpG site methylation level below median (P = 0.06). (B) 31-patients with MRE11A mRNA expression level above median is more likely develop recurrence than the other 31 patients with MRE11A mRNA expression level below median (P = 0.05). On the other hand 31 patients with MRE11A CpG site methylation level above median is less likely to develop recurrence than the other 31 patients with MRE11A CpG site methylation level below median (P = 0.05). (C) MYO1E mRNA expression level was not associated with recurrence when patients were dichotomized (P = 0.67). On the other hand 31 patients with MYO1E CpG site methylation level above median is less likely to develop recurrence than the other 31 patients with MYO1E CpG site methylation level below median (P = 0.06). (D) MYRIP mRNA expression level (P = 0.32) and CpG site methylation level (P = 0.79) were not associated with recurrence when patients were dichotomized. (E) 31-patients with CFH mRNA expression level above median is less likely develop recurrence than the other 31 patients with CFH mRNA expression level below median (P = 0.02). On the other hand 31 patients with CFH CpG site methylation level above median is more likely to develop recurrence than the other 31 patients with PSRC1 CpG site methylation level below median (P = 0.02).

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