Global DNA methylation and hydroxymethylation differ in hepatocellular carcinoma and cholangiocarcinoma and relate to survival rate

Abstract

In addition to DNA methylation, hydroxymethylation of DNA is recognized as a novel epigenetic mark. Primary liver cancers, i.e., hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC), are highly prevalent but epigenetically poorly characterized, so far. In the present study we measured global methylcytosine (mCyt) and hydroxymethylcytosine (hmCyt) in HCC and CC tissues and in peripheral blood mononuclear cell (PBMC) DNA to define mCyt and hmCyt status and, accordingly, the survival rate. Both mCyt and hmCyt were measured by a liquid chromatography/tandem mass spectrometry method in neoplastic and homologous nonneoplastic tissues, i.e., liver and gallbladder, and in PBMCs of 31 HCC and 16 CC patients. Content of mCyt was notably lower in HCC than in CC tissues (3.97% versus 5.26%, respectively; P < 0.0001). Significantly reduced mCyt was also detected in HCC compared to nonneoplastic tissue (3.97% versus 4.82% mCyt, respectively; P < 0.0001), but no such difference was found for CC versus homologous nonneoplastic tissue. Hydroxymethylation was significantly decreased in HCC versus nonneoplastic liver tissue (0.044 versus 0.128, respectively; P < 0.0001) and in CC versus both liver and gallbladder nonneoplastic tissue (0.030 versus 0.124, P 5 0.026, and 0.030 versus 0.123, P 5 0.006, respectively). When the survival rate was evaluated according to mCyt PBMC content by Kaplan-Meier analysis, patients with mCyt 5.59% had a significantly higher life expectancy than those with mCyt <5.59% (P 5 0.034) at a follow-up period up to 48 months. Conclusion: A significant DNA hypomethylation distinguishes HCC from CC, while DNA hypohydroxymethylation characterizes both HCC and CC, and a PBMC DNA mCyt content 5.59% relates to a favorable outcome in primary liver cancers. (HEPATOLOGY 2015;62:496-504) M ethylation and hydroxymethylation of DNA are major epigenetic marks in human DNA consisting of modification of cytosines, respectively, as 5-methylcytosine (mCyt) and 5-hydroxymethylcytosine (hmCyt) in the dynamic processes of methylation and demethylation of DNA involved in the regulatory mechanisms of gene expression. [1][2][3] Methylation of DNA is the main epigenetic feature of mammalian DNA involved in several physiological processes through the transcriptional regulation of gene expression and chromatin conformational configuration 4 but also in pathologic conditions such as cancer disease development and progression. 5 Aberrant DNA methylation is an almost universal finding in cancer, where a global DNA hypomethylation, leading

Cholangiocarcinoma: current knowledge and future perspectives consensus statement from the European Network for the Study of Cholangiocarcinoma (ENS-CCA)

“…Information related to the effect of altered histone modifications in CCA and to the response of CCA to epigenetic-based therapies is limited [81][82][83] .…”

“…The contribution of chronic liver inflammation alongside an aberrant epigenetic landscape provides survival signals to the tumour (for example, IL-6-STAT3) 88,89 . Marked reduction in DNA hydroxymethylation character izes CCA tissue when compared with non-neoplastic tissue and a DNA mCyt content of ≥5.59% in peripheral blood mononuclear cells relates to a favourable outcome in primary liver cancers 81 . On the other hand, several promoters of genes involved in Wnt signalling are hypermethylated in CCA tissue 90 .…”

Reply

“…We thank Li et al (1) for their interest in the study and for the opportunity to further discuss our findings to gain deeper insights.…”

“…The question, appropriately brought up by Li et al, (1) on how a blood-positive screening assay may be helpful to detect the precise tissue origin of cancer disease is indeed open and challenging. Global DNA methylation can represent the overall epigenetic effect.…”

Hypomethylation and hypohydroxymethylation of DNA in hepatocellular carcinoma and cholangiocarcinoma

“…We read with great interest the article by Udali et al, (1) who demonstrated that there was significantly reduced DNA methylation in hepatocellular carcinoma (HCC) compared to cholangiocarcinoma (CC) and that there was no difference in DNA hydroxymethylation between HCC and CC. They also reported that high levels of methylcytosine (mCyt) in the DNA of peripheral blood mononuclear cells (PBMCs) were related to a better clinical outcome of patients with HCC or CC.…”