Abstract 4439: Relationship between DNA methylation of TET genes and levels of 5-methyl-cytosine and 5-hydroxymethyl-cytosine in hepatocellular carcinoma

Abstract

Abstract Long-term survival after hepatocellular carcinoma (HCC) diagnosis has clearly improved as a result of treatment by means of a liver transplant. However, a large number of cases do not meet the transplant criteria and undergo resection. In these patients, loss of global DNA hydroxymethylation has been linked to worse prognosis, but no association has been found in transplant patients. Differential epigenetic processing is a possible reason for this, and has not been previously explored. The process of DNA demethylation is mediated by the family of ten-eleven translocation (TET) proteins, that catalyze the conversion of 5-methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). There are three different TET protein variants: TET1, TET2 and TET3. Studies have shown that expression of at least TET1 is epigenetically regulated. In this study we investigated the association between DNA methylation of TET genes and global DNA methylation and hydroxymethylation in 66 tumor (T) and non-tumor (NT) paired samples of individuals treated at Columbia Presbyterian Medical Center in New York. Levels of 5mC and 5hmC were determined by UPLC/MS/MS, and DNA methylation of the TET promoters was obtained from Illumina Infinium 450k CpG array data. Mean levels of 5mC (T = 3.15±0.49% vs. NT = 3.80±0.12% (p<0.0001) and 5hmC (T = 0.11±0.04% vs. NT = 0.23±0.07%, p<0.0001) in tumor tissues were statistically significantly lower than in non-tumor tissues. In contrast, average DNA methylation levels of TET1 (T = 0.40±0.06% vs. NT = 0.35±0.02%, p<0.0001) were statistically significantly lower in non-tumor tissues than in tumor tissues. However, this was not the case for TET2 or TET3. TET1 DNA methylation levels negatively correlate with global DNA 5mC levels in tumor and non-tumor tissue (Spearman correlation coefficient: T = -0.47 (p = 0.002) and NT = -0.60 (p<0.0001)). In contrast, associations between gene DNA methylation and 5hmC DNA levels were different for the tumor and non-tumor tissue samples. 5hmC levels positively and statistically significantly correlated with TET1 and TET2 DNA methylation (Spearman corr. coef TET1 NT = 0.57 (p<0.0001), and TET2 NT = 0.56 (p<0.0001)) in non-tumor tissue while there was a statistically significant negative correlation with TET3 (Spearman corr. coef. TET3 T = -0.37 (p = 0.005)). No other associations were found between 5mC and 5hmC levels and TET gene DNA methylation levels. These findings suggest higher expression of TET1 correlates with a hypomethylated state and that the accumulation of 5hmC possibly results from a downregulation of TET1 and TET2 in non-tumor tissue. HCC carcinogenesis alters this process, and while further studies need to be conducted, TET3 seems to play a larger role in tumor cells. Our sample size was limited, but these results suggest that future research of 5hmC might help elucidate HCC underlying molecular events and aid in the design of prognostic markers. Citation Format: Lissette Delgado-Cruzata, Hui-Chen Wu, Jin Shen, Tiffany Thomas, Abby B. Siegel, Yu-Jing Zhang, Abhishek Goyal, Christine C. Hsu, Helen E. Remotti, Regina M. Santella. Relationship between DNA methylation of TET genes and levels of 5-methyl-cytosine and 5-hydroxymethyl-cytosine in hepatocellular carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4439.