Genome-wide analysis of DNA methylation identifies novel cancer-related genes in hepatocellular carcinoma.
ABSTRACT Aberrant DNA methylation has been implicated in the development of hepatocellular carcinoma (HCC). Our aim was to clarify its molecular mechanism and to identify useful biomarkers by screening for DNA methylation in HCC. Methylated CpG island amplification coupled with CpG island microarray (MCAM) analysis was carried out to screen for methylated genes in primary HCC specimens [hepatitis B virus (HBV)-positive, n = 4; hepatitis C virus (HCV)-positive, n = 5; HBV/HCV-negative, n = 7]. Bisulfite pyrosequencing was used to analyze the methylation of selected genes and long interspersed nuclear element (LINE)-1 in HCC tissue (n = 57) and noncancerous liver tissue (n = 50) from HCC patients and in HCC cell lines (n = 10). MCAM analysis identified 332, 342, and 259 genes that were methylated in HBV-positive, HCV-positive, and HBV/HCV-negative HCC tissues, respectively. Among these genes, methylation of KLHL35, PAX5, PENK, and SPDYA was significantly higher in HCC tissue than in noncancerous liver tissue, irrespective of the hepatitis virus status. LINE-1 hypomethylation was also prevalent in HCC and correlated positively with KLHL35 and SPDYA methylation. Receiver operating characteristic curve analysis revealed that methylation of the four genes and LINE-1 strongly discriminated between HCC tissue and noncancerous liver tissue. Our data suggest that aberrant hyper- and hypomethylation may contribute to a common pathogenesis mechanism in HCC. Hypermethylation of KLHL35, PAX, PENK, and SDPYA and hypomethylation of LINE-1 could be useful biomarkers for the detection of HCC.
SourceAvailable from: Yogen Saunthararajah[Show abstract] [Hide abstract]
ABSTRACT: Hepatocellular Carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. However, the role of epigenetic changes such as aberrant DNA methylation in hepatocarcinogenesis remains largely unclear. In this study, we examined the methylation profiles of 59 HCC patients. Using consensus hierarchical clustering with feature selection, we identified three tumor subgroups based on their methylation profiles and correlated these subgroups with clinicopathological parameters. Interestingly, one tumor subgroup is different from the other 2 subgroups and the methylation profile of this subgroup is the most distinctly different from the non-tumorous liver tissues. Significantly, this subgroup of patients was found to be associated with poor overall as well as disease-free survival. To further understand the pathways modulated by the deregulation of methylation in HCC patients, we integrated data from both the methylation as well as the gene expression profiles of these 59 HCC patients. In these patients, while 4416 CpG sites were differentially methylated between the tumors compared to the adjacent non-tumorous tissues, only 536 of these CpG sites were associated with differences in the expression of their associated genes. Pathway analysis revealed that forty-four percent of the most significant upstream regulators of these 536 genes were involved in inflammation-related NFκB pathway. These data suggest that inflammation via the NFκB pathway play an important role in modulating gene expression of HCC patients through methylation. Overall, our analysis provides an understanding on aberrant methylation profile in HCC patients.PLoS ONE 08/2014; 9(8):e104158. DOI:10.1371/journal.pone.0104158 · 3.53 Impact Factor
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ABSTRACT: Runt-related transcription factor 3 (RUNX3) is a potential tumor suppressor that is frequently hypermethylated in hepatocellular carcinoma (HCC). The present meta-analysis of case-control studies was carried out to determine whether RUNX3 hypermethylation is associated with HCC. The PubMed, Embase, and Chinese National Knowledge Infrastructure databases were searched for all relevant studies published between May 2000 and May 2012. A total of 11 studies were identified, and 8 studies involving 491 patients with HCC and 409 patients without tumors were found to satisfy the inclusion criteria for the meta-analysis. All tissue samples were from Asian populations. There was significant heterogeneity between the studies. Over the entire sample, the odds ratio (OR) of RUNX3 promoter methylation was 18.5 [95% confidence interval (CI), 11.6-29.6] for HCC tissues relative to control tissues. The ORs of RUNX3 methylation were 16.6 (95%CI = 6.5-42.4) for tumor tissues relative to tumor-adjacent tissues in patients with HCC, 67.3 (95%CI = 13.0-348.5) for tumor tissues from patients with HCC relative to liver tissues from patients with non-neoplastic liver diseases, and 3.26 (95%CI = 1.54-6.90) for tissues from patients with hepatitis C virus (HCV)- related HCC relative to liver tissues from patients with HCC unrelated to HCV. There was no association between RUNX3 methylation and age, gender, pathological stage, or hepatitis B virus infection in HCC tissues. Methylation of the RUNX3 promoter strongly correlated with HCC in Asian populations, especially in individuals with HCV-related HCC, and may be a useful marker for HCC diagnosis in these populations.Genetics and molecular research: GMR 01/2014; 13(3):5182-9. DOI:10.4238/2014.July.7.11 · 0.85 Impact Factor
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ABSTRACT: Hepatitis B virus (HBV) infection is a major global health problem and many studies have underlined the importance of inter individual variability and somatic mutations during the clinical course of HBV infection. In recent years, high-throughput technologies have provided new possibilities to study the genetic basis of many diseases. We reviewed all literature available on genome-wide association studies (GWASs), whole genome, exome and RNA sequencing studies as well as studies on HBV infection and the pathogenesis of related liver disease. Many GWASs conclude that the genetic variants in the HLA region (HLA-DP, HLA-DQ, HLA-DR and MICA), KIF1B, DEPDC5 and PNPLA3 influence HBV infection, its clinical course and the response to hepatitis B vaccination. The next generation sequencing approach provides important clues on the mutational landscape of genes involved in signaling pathways in particular JAK/STAT, Wnt/β-catenin, p53 pathways and multiple chromatin regulator genes that significantly promote hepatocarcinogenesis. In addition, the hotspots of recurrent integrations of HBV-DNA into host chromosomes such as hTERT, PDGF receptor, MLL are involved in pathogenesis of hepatocellular carcinoma (HCC). Additionally, the transitions T > C/A > G, C > T/G > A, C > A/G > T and T > A/A > T remain specific for HCC induced by viral infection and the DNA methylation in the CpG island is proposed as a biomarker for HCC. We have described common mutations in the HBV genome (G1896A, rtM204V, rtM204I) which modulate the pathogenesis and carcinogenesis of the liver. Further GWASs in different ethnic groups and additional functional studies are required to warrant the significance of such defined genetic factors. Such findings continue to shape our understanding of the genetic architecture of host–virus interactions and provide new clues and directions in determining genetic markers that modulate HBV infection and related liver diseases. The studies using high-throughput technologies help identifying potential genetic threats however the utility of mutational information can be complex in predicting prognostic significance and shall pose challenges to its clinical implementation.Mutation Research/Reviews in Mutation Research 07/2014; 762. DOI:10.1016/j.mrrev.2014.06.001 · 7.33 Impact Factor