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Specific molecular signatures of non-tumor liver tissue may predict a risk of hepatocarcinogenesis.

Utsunomiya T, Shimada M, Morine Y, Tajima A, Imoto I - Cancer Sci. (2014)

Bottom Line: The bleak outcomes of HCC patients even after curative treatment have been, at least partially, attributed to its multicentric origin.Carcinogenetic risk estimation based on specific methylation signatures may be advantageous for close follow-up of patients who are at high risk of HCC development.Furthermore, epigenetic therapies for patients with chronic liver diseases may be helpful to reduce the risk of HCC development because epigenetic alterations are potentially reversible, and thus provide promising molecular targets for therapeutic intervention.

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Affiliation: Department of Surgery, University of Tokushima, Tokushima, Japan.

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Percentage of CpG sites according to their gene location (upper) and the CpG content in the genes (lower). “Common” indicates the 30 CpG sites, which were commonly hyper- or hypomethylated in both hepatitis B core antibody (HbcAb) (−) and HBcAb (+) liver tissues in comparison with normal control (NC) liver tissues.
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fig03: Percentage of CpG sites according to their gene location (upper) and the CpG content in the genes (lower). “Common” indicates the 30 CpG sites, which were commonly hyper- or hypomethylated in both hepatitis B core antibody (HbcAb) (−) and HBcAb (+) liver tissues in comparison with normal control (NC) liver tissues.

Mentions: Hepatitis C virus-related HCC is responsible for the greatest proportion of HCC patients in Japan, however, the proportion of HCC cases negative for hepatitis B surface antigen and hepatitis C antibody, so-called “NBNC-HCC”, is rapidly increasing.(61,62) However, there have been no studies specifically focusing on the implications of the molecular characteristics of non-tumor liver tissue in terms of hepatocarcinogenesis in patients with NBNC-HCC. Therefore, DNA methylation profiling of autosomal CpGs in non-tumor liver tissue of NBNC-HCC (n = 15) was compared with that in normal control (NC) liver tissue (n = 8) using the HumanMethylation450 BeadChip, as described previously.(63) The former (n = 15) included eight hepatitis B core antibody (HBcAb) positive (+) and seven HBcAb negative (−) patients. The latter (n = 7) were non-tumor liver tissue samples from patients who did not undergo any preoperative treatments, such as chemoradiotherapy. The methylation score for each CpG site was represented by a Beta-value calculated according to the normalized probe fluorescence intensity ratios between methylated and unmethylated signals, and Beta-values vary between 0 (fully unmethylated) and 1 (fully methylated). Figure 1 shows volcano plots showing 87 differentially methylated CpG sites in HBcAb (−) liver tissues and 603 CpG sites in HBcAb (+) liver tissue in comparison with NC liver tissue (Beta-value difference >0.2, P < 0.05). It is interesting to note that more differentially methylated CpG sites were identified in HBcAb (+) liver tissue samples compared with those from HBcAb (−) liver tissue, suggesting the possible epigenetic association of occult HBV infection with hepatocarcinogenesis. Thirty CpG sites were commonly hyper- or hypomethylated in both HBcAb (−) and HBcAb (+) liver tissue samples. The overlapping CpG sites were 100% consistent in the direction of methylation changes. The principal component analysis based on these differentially methylated CpG sites showed a clear separation of HBcAb (−) and HBcAb (+) liver tissue samples from NC liver tissue (Fig. 2). Therefore, specific DNA methylation profiling, which possibly contributes to the development of HCC, may exist in the non-tumor liver tissue of patients with NBNC-HCC. A Manhattan plot revealed that such DNA methylation alterations were spread across all chromosomes (data not shown). Table 1 lists the 30 CpG sites corresponding to 14 gene promoters that were commonly hyper- or hypomethylated in both HBcAb (−) and HBcAb (+) liver tissue samples. This genome-wide DNA methylation array system (HumanMethylation450 BeadChip) includes the promoter, gene body, and 3′-UTR.(64) In fact, high percentages of aberrant DNA methylation were observed in gene bodies rather than promoters (Fig. 3). A recent study showed that CpG sites located at promoter regions show a negative correlation whereas CpG sites in gene bodies show a positive correlation between DNA methylation and gene expression levels.(65) It is important to note that correlations between DNA methylation status and gene expression levels may be dependent on the location of CpG sites in the genes. In addition, cautious interpretation of these microarray data with special emphasis on potential signals generated by cross-reactive probes and polymorphic CpGs should also be recommended.(66)


Specific molecular signatures of non-tumor liver tissue may predict a risk of hepatocarcinogenesis.

Utsunomiya T, Shimada M, Morine Y, Tajima A, Imoto I - Cancer Sci. (2014)

Percentage of CpG sites according to their gene location (upper) and the CpG content in the genes (lower). “Common” indicates the 30 CpG sites, which were commonly hyper- or hypomethylated in both hepatitis B core antibody (HbcAb) (−) and HBcAb (+) liver tissues in comparison with normal control (NC) liver tissues.
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fig03: Percentage of CpG sites according to their gene location (upper) and the CpG content in the genes (lower). “Common” indicates the 30 CpG sites, which were commonly hyper- or hypomethylated in both hepatitis B core antibody (HbcAb) (−) and HBcAb (+) liver tissues in comparison with normal control (NC) liver tissues.
Mentions: Hepatitis C virus-related HCC is responsible for the greatest proportion of HCC patients in Japan, however, the proportion of HCC cases negative for hepatitis B surface antigen and hepatitis C antibody, so-called “NBNC-HCC”, is rapidly increasing.(61,62) However, there have been no studies specifically focusing on the implications of the molecular characteristics of non-tumor liver tissue in terms of hepatocarcinogenesis in patients with NBNC-HCC. Therefore, DNA methylation profiling of autosomal CpGs in non-tumor liver tissue of NBNC-HCC (n = 15) was compared with that in normal control (NC) liver tissue (n = 8) using the HumanMethylation450 BeadChip, as described previously.(63) The former (n = 15) included eight hepatitis B core antibody (HBcAb) positive (+) and seven HBcAb negative (−) patients. The latter (n = 7) were non-tumor liver tissue samples from patients who did not undergo any preoperative treatments, such as chemoradiotherapy. The methylation score for each CpG site was represented by a Beta-value calculated according to the normalized probe fluorescence intensity ratios between methylated and unmethylated signals, and Beta-values vary between 0 (fully unmethylated) and 1 (fully methylated). Figure 1 shows volcano plots showing 87 differentially methylated CpG sites in HBcAb (−) liver tissues and 603 CpG sites in HBcAb (+) liver tissue in comparison with NC liver tissue (Beta-value difference >0.2, P < 0.05). It is interesting to note that more differentially methylated CpG sites were identified in HBcAb (+) liver tissue samples compared with those from HBcAb (−) liver tissue, suggesting the possible epigenetic association of occult HBV infection with hepatocarcinogenesis. Thirty CpG sites were commonly hyper- or hypomethylated in both HBcAb (−) and HBcAb (+) liver tissue samples. The overlapping CpG sites were 100% consistent in the direction of methylation changes. The principal component analysis based on these differentially methylated CpG sites showed a clear separation of HBcAb (−) and HBcAb (+) liver tissue samples from NC liver tissue (Fig. 2). Therefore, specific DNA methylation profiling, which possibly contributes to the development of HCC, may exist in the non-tumor liver tissue of patients with NBNC-HCC. A Manhattan plot revealed that such DNA methylation alterations were spread across all chromosomes (data not shown). Table 1 lists the 30 CpG sites corresponding to 14 gene promoters that were commonly hyper- or hypomethylated in both HBcAb (−) and HBcAb (+) liver tissue samples. This genome-wide DNA methylation array system (HumanMethylation450 BeadChip) includes the promoter, gene body, and 3′-UTR.(64) In fact, high percentages of aberrant DNA methylation were observed in gene bodies rather than promoters (Fig. 3). A recent study showed that CpG sites located at promoter regions show a negative correlation whereas CpG sites in gene bodies show a positive correlation between DNA methylation and gene expression levels.(65) It is important to note that correlations between DNA methylation status and gene expression levels may be dependent on the location of CpG sites in the genes. In addition, cautious interpretation of these microarray data with special emphasis on potential signals generated by cross-reactive probes and polymorphic CpGs should also be recommended.(66)

Bottom Line: The bleak outcomes of HCC patients even after curative treatment have been, at least partially, attributed to its multicentric origin.Carcinogenetic risk estimation based on specific methylation signatures may be advantageous for close follow-up of patients who are at high risk of HCC development.Furthermore, epigenetic therapies for patients with chronic liver diseases may be helpful to reduce the risk of HCC development because epigenetic alterations are potentially reversible, and thus provide promising molecular targets for therapeutic intervention.

View Article: PubMed Central - PubMed

Affiliation: Department of Surgery, University of Tokushima, Tokushima, Japan.

Show MeSH
Related in: MedlinePlus