Rapid and quantitative detection of CpG-methylation status using TaqMan PCR combined with methyl-binding-domain polypeptide

Analysis of DNA methylation in plasma for monitoring hepatocarcinogenesis

AIM

To explore whether the aberrant DNA methylation status in plasma could be used as a biomarker for hepatocellular carcinoma (HCC) screening among high-risk individuals.

METHODS

The promoter methylation status of ELF, RASSF1A, p16, and GSTP1 was investigated by methylation-specific polymerase chain reaction (PCR) in 34 paired HCC and nontumor liver tissue from HCC patients and 10 tissues from patients with liver cirrhosis (LC). Plasma samples from 31 HCC patients, 10 LC patients as well as 7 patients with benign hepatic conditions were also collected and characterized using the same method.

RESULTS

Among liver specimens, HCC tissues displayed a significantly higher methylation frequency of each gene compared with nontumor tissue (p<0.05). Moreover, the frequency was much higher in tumor tissues than in nontumor tissue, when the data from two or three genes were combined (p=0.001 and p<0.001, respectively). Among plasma samples, either the frequency of at least one methylated gene (p<0.001) or the average number of methylated genes (p<0.05) demonstrated a stepwise increase in patients with benign lesions, LC, and HCC. Furthermore, when positive results, that is, plasma methylation status of at least one gene were combined with the elevated AFP400 level (serum alpha-fetoprotein [AFP] level at a cutoff of 400 ng/mL), the diagnostic sensitivity of HCC could increase to 93.55%.

CONCLUSIONS

These results suggested that the methylation of tumor suppressor genes may participate in the development and progression of HCC. Additionally, it may be useful to combine the plasma DNA methylation status of a panel of gene markers and the serum AFP for HCC screening.

Aberrant DNA methylation in hepatocellular carcinoma tumor suppression (Review)

Aberrant DNA methylation leads to altered gene expression, resulting in cancerous features. Numerous tumor suppressor genes are silenced by DNA methylation during hepatocarcinogenesis. Promoter CpG island hypermethylation is an important mechanism for inactivating tumor suppressor genes in hepatocellular carcinoma (HCC). Hypermethylation of CpG islands in the p16 (INK4a) and p15 (INK4b) promoters may increase the risk of developing HCC, particularly hepatitis B virus-related HCC. Environmental factors can lead to geographic variations in the methylation status of CpG islands. Aberrant DNA methylation of CpG islands is catalyzed by DNA methyltransferases (DNMTs). Thus, abnormal variations of DNMTs can contribute to hepatocarcinogenesis. In hepatitis-related HCC, microRNAs participate in hepatocarcinogenesis by directly targeting DNMTs, during which hepatitis B virus X acts as a regulator. DNA methylation may also contribute to HCC tumorigenesis by regulating the cell cycle. Based on the importance of DNA methylation in tumor suppression of HCC, certain DNA methylations may predict the risk of tumor development, tumor staging, patient survival and HCC recurrence.

Promoter methylation of the RASSF1A gene may contribute to colorectal cancer susceptibility: a meta-analysis of cohort studies

This meta-analysis of published cohort studies was conducted to evaluate whether promoter methylation of the RASSF1A gene contributes to colorectal cancer (CRC) susceptibility. A range of electronic databases were searched without language restrictions. Meta-analysis was conducted using the STATA 12.0 software. Crude risk differences (RD) with their 95% confidence intervals (95%CI) were calculated. In this meta-analysis, 11 clinical cohort studies with a total of 630 CRC patients were included. The pooled results revealed that the frequency of RASSF1A gene methylation in cancer tissues was significantly higher than that in benign, adjacent, and normal tissues (cancer tissues vs. benign tissues: RD = 0.25, 95%CI = 0.13-0.38, P < 0.001; cancer tissues vs. adjacent tissues: RD = 0.32, 95%CI: 0.20-0.45, P < 0.001; cancer tissues vs. normal tissues: RD = 0.38, 95%CI: 0.26-0.50, P < 0.001; respectively). Subgroup analysis by ethnicity demonstrated that RASSF1A promoter methylation also exhibited a higher frequency in cancer tissues among both Asians and Caucasians (all P < 0.05). Our meta-analysis has shown positive correlations between RASSF1A promoter methylation and CRC susceptibility. Thus, detection of RASSF1A promoter methylation may be utilized as a valuable diagnostic marker for CRC.

Novel DNA binding domain-based assays for detection of methylated and nonmethylated DNA

Methylation of cytosine in the context of CpG dinucleotides is an epigenetic phenomenon in eukaryotes that plays important roles in genome function and transcription regulation. Aberrant changes in DNA methylation is an important feature of several human diseases such as cancer and neurological disorders. These discoveries have opened a new field of new therapies and diagnostics. During recent years, there has been a revolution in DNA methylation analysis technologies. This article focuses on methods with which to study DNA methylation that employ protein domains that specifically recognize either 5-methyl-cytosine in the CpG context or nonmethylated DNA, and methods developed for the detection of 5-hydroxymethylcytosine, the recently described epigenetic mark known as the sixth base of the epigenome.