Lower expression of p14ARF and p16INK4a correlates with higher DNMT3B expression in human oesophageal squamous cell carcinomas

DNA methylation patterns suggest the involvement of DNMT3B and TET1 in osteosarcoma development

DNA methylation may be involved in the development of osteosarcomas. Osteosarcomas commonly arise during the bone growth and remodeling in puberty, making it plausible to infer the involvement of epigenetic alterations in their development. As a highly studied epigenetic mechanism, we investigated DNA methylation and related genetic variants in 28 primary osteosarcomas aiming to identify deregulated driver alterations. Methylation and genomic data were obtained using the Illumina HM450K beadchips and the TruSight One sequencing panel, respectively. Aberrant DNA methylation was spread throughout the osteosarcomas genomes. We identified 3146 differentially methylated CpGs comparing osteosarcomas and bone tissue samples, with high methylation heterogeneity, global hypomethylation and focal hypermethylation at CpG islands. Differentially methylated regions (DMR) were detected in 585 loci (319 hypomethylated and 266 hypermethylated), mapped to the promoter regions of 350 genes. These DMR genes were enriched for biological processes related to skeletal system morphogenesis, proliferation, inflammatory response, and signal transduction. Both methylation and expression data were validated in independent groups of cases. Six tumor suppressor genes harbored deletions or promoter hypermethylation (DLEC1, GJB2, HIC1, MIR149, PAX6, and WNT5A), and four oncogenes presented gains or hypomethylation (ASPSCR1, NOTCH4, PRDM16, and RUNX3). Our analysis also revealed hypomethylation at 6p22, a region that contains several histone genes. Copy-number changes in DNMT3B (gain) and TET1 (loss), as well as overexpression of DNMT3B in osteosarcomas provide a possible explanation for the observed phenotype of CpG island hypermethylation. While the detected open-sea hypomethylation likely contributes to the well-known osteosarcoma genomic instability, enriched CpG island hypermethylation suggests an underlying mechanism possibly driven by overexpression of DNMT3B likely resulting in silencing of tumor suppressors and DNA repair genes.

Epigenetic Alterations in Oesophageal Cancer: Expression and Role of the Involved Enzymes

Oesophageal cancer is a life-threatening disease, accounting for high mortality rates. The poor prognosis of this malignancy is mostly due to late diagnosis and lack of effective therapies for advanced disease. Epigenetic alterations may constitute novel and attractive therapeutic targets, owing to their ubiquity in cancer and their reversible nature. Herein, we offer an overview of the most important studies which compared differences in expression of enzymes that mediate epigenetic alterations between oesophageal cancer and normal mucosa, as well as in vitro data addressing the role of these genes/proteins in oesophageal cancer. Furthermore, The Cancer Genome Atlas database was interrogated for the correlation between expression of these epigenetic markers and standard clinicopathological features. We concluded that most epigenetic players studied thus far are overexpressed in tumours compared to normal tissue. Furthermore, functional assays suggest an oncogenic role for most of those enzymes, supporting their potential as therapeutic targets in oesophageal cancer.

Associations of DNMT3B -149C>T and -2437T>A polymorphisms and lung cancer risk in Chinese population

BACKGROUND

DNMT3B polymorphisms are associated with the susceptibility of lung cancer. DNMT3B -2437T>A is a novel polymorphism, and its influence on the risk of lung cancer in Chinese was investigated in this study. In addition, effect of DNMT3B -149C>T polymorphism on lung cancer was also explored.

METHODS

Genotyping in subjects were performed by PCR-RFLP. Haplotype frequencies were estimated by estimating haplotype software. Adjusted odds ratios (ORs) with 95% confidence intervals (CIs) were calculated by unconditional logistic regression analysis.

RESULTS

Neither of the two polymorphisms was correlated with lung cancer (-149C>T: CT+TT vs CC: OR = 0.78, 95%CI, 0.57 to 1.05, P = 0.361; -2437T>A: AT+AA vs TT: OR = 0.99, 95%CI, 0.74 to 1.33, P = 0.168). In stratification analysis, T-allele carrier genotype of -149C>T polymorphism resulted in a reduced lung cancer risk at stage II, compared with CC (OR = 0.46, 95%CI, 0.28 to 0.77, P = 0.023). In haplotype analysis, when -149C/-2437T was used as reference, the other combined genotypes of the two polymorphisms had no significant effect on lung cancer risk (P > 0.05).

CONCLUSIONS

The two DNMT3B polymorphisms are not correlated with lung cancer risk among Chinese population nor the haplotype of them.

MTSS1, a novel target of DNA methyltransferase 3B, functions as a tumor suppressor in hepatocellular carcinoma

DNA methyltransferase 3B (DNMT3B) mediates gene silencing via epigenetic mechanisms during hepatocellular carcinoma (HCC) progression. We aimed to identify novel targets of DNMT3B and their potential regulatory mechanisms in HCC. Metastasis suppressor 1 (MTSS1) was one of the DNMT3B targets and selected for further study. DNMT3B overexpression was detected in 81.25% of clinical HCC specimens and was negatively associated with MTSS1 in HCC cells and clinical samples. The underlying mechanism by which DNMT3B silences MTSS1 was studied using a combination of methylation-specific polymerase chain reaction (PCR) and bisulfite genome sequencing, chromatin immunoprecipitation-PCR and luciferase reporter assays. We found that the MTSS1 promoter region was sparsely methylated, and the methylation inhibitors failed to abolish DNMT3B-mediated MTSS1 silencing. DNMT3B protein bound directly to the 5'-flanking region (-865/-645) of the MTSS1 gene to inhibit its transcription. The functional role of MTSS1 was investigated using in vitro and in vivo tumorigenicity assays. As a result, MTSS1 exerted tumor suppressor effects and arrested cells in the G2/M phase, but not the G1/S phase of the cell cycle when it was depleted or overexpressed in HCC cells. Taken together, MTSS1, a novel target of DNMT3B, is repressed by DNMT3B via a DNA methylation-independent mechanism. MTSS1 was further characterized as a novel tumor suppressor gene in HCC. These findings highlight how DNMT3B regulates MTSS1, and such data may be useful for the development of new treatment options for HCC.

Targeting epigenetic mediators of gene expression in thoracic malignancies

Lung and esophageal cancers and malignant pleural mesotheliomas are highly lethal neoplasms that are leading causes of cancer-related deaths worldwide. Presently, limited information is available pertaining to epigenetic mechanisms mediating initiation and progression of these neoplasms. The following presentation will focus on the potential clinical relevance of epigenomic alterations in thoracic malignancies mediated by DNA methylation, perturbations in the histone code, and polycomb group proteins, as well as ongoing translational efforts to target epigenetic regulators of gene expression for treatment of these neoplasms. This article is part of a Special Issue entitled: Chromatin in time and space.

The DNMT3B -579 G>T promoter polymorphism and risk of lung cancer

The present study aimed to investigate the association of the -579 G>T polymorphism in the DNMT3B promoter with susceptibility to lung cancer. A total of 174 lung cancer patients and 135 healthy controls from the northern part of China were enrolled, and were matched for gender and age. All subjects were genotyped by polymerase chain reaction-restriction-fragment length polymorphism analysis and confirmed by DNA sequencing. Stratification analyses were used to study the subgroups of subjects by age and gender, and evaluate the association between the -579 G>T polymorphism and the genetic susceptibility to lung cancer. The results revealed that individuals with the DNMT3B -579 GT genotype had a significantly decreased risk of lung cancer [odds ratio (OR), 0.517; 95% confidence interval (CI), 0.273-0.981] compared with those with a -579 TT genotype in the studied population. However, the deviation was significant (OR, 0.138, 95% CI, 0.034-0.549) between the risk of lung cancer and the GT and GG genotype, when the smoking factor was considered. The data from this study indicate that the DNMT3B genetic polymorphism varies among various races, ethnic groups and geographical areas. The DNMT3B -579 G>T polymorphism may contribute to the genetic susceptibility to lung cancer.

Genetic variation in the promoter of DNMT3B is associated with the risk of colorectal cancer

PURPOSE

DNA methyltransferase-3B (DNMT3B) plays an important role in the generation of aberrant methylation in carcinogenesis. Polymorphisms of the DNMT3B gene may influence DNMT3B enzyme activity on DNA methylation, thereby modulating the susceptibility to colorectal cancer (CRC).

METHODS

The polymorphisms in the promoter region of the DNMT3B gene [-149C>T (rs2424913) and -579G>T (rs1569686)] were detected by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), and a total of 544 CRC patients and 533 age- and sex-matched healthy controls were enrolled in the case-control study.

RESULTS

The results showed that the -579G allele was associated with a significantly decreased risk of CRC (adjusted OR, 0.50; 95%CI, 0.35-0.72; P = 0.0002) when compared with the -579TT genotype. However, the DNMT3B-149CT genotype was not associated with the risk of CRC (adjusted OR, 0.48; 95%CI, 0.18-1.30; P = 0.151). In addition, stratification analysis revealed that the increased risk was predominant in both colon cancer and rectal cancer showing no effect of primary occurrence site.

CONCLUSION

Our research demonstrated the -579G allele was a potential protective factor for the occurrence of CRC.

Gene regulation by methylation

Epigenetic gene regulation of specific genes strongly affects clinical outcome of malignant glioma. MGMT is the best studied gene for the connection of promoter methylation and clinical course in glioblastoma. While MGMT promoter methylation analysis currently does not alter treatment of glioblastoma patients, mainly because of a lack of convincing therapy to radiotherapy and concomitant administration of alkylating drugs, there is increasing interest on the part of patients and physicians in having this molecular parameter assessed. This chapter gives a short overview of the physiological characteristics of the epigenome in normal cells and tissues and the changes in epigenetic gene regulation following malignant transformation. It discusses the technical aspects, advantages, and shortcomings of currently used approaches for single-gene and genome-wide methylation analyses. Finally, an outlook is given on potential therapeutic avenues and targets to overcome tumor-suppressor gene silencing by aberrant promoter methylation in gliomas.

Inhibition of de novo Methyltransferase 3B is a Potential Therapy for Hepatocellular Carcinoma

BACKGROUND

Aberrant epigenetic patterns, including inactivation of tumor suppressor genes due to DNA methylation, have been described in many human cancers. Epigenetic therapeutic is a new and rapidly developing area of tumor treatment because DNA methyltransferase (DNMT) inhibitors can reverse its changes. We attempted to identify potential approach for epigenetic therapy of hepatocellular carcinoma.

METHODS

We knocked down the expression of DNMT 1 or DNMT 3B by siRNA, and inhibited DNA methyltranferases by 5-Aza-2'-deoxycytidine. We used high-density oligonucleotide gene expression microarrays to examine the induced genes in human hepatocellular carcinoma cell line SMMC-7721 after suppressing DNA methyltranferases. The 5' ends of up-regulated genes were analyzed by BLAST database to determine whether they have promoter CpG islands, and then the identical induced genes were compared among different inhibition of DNA methyltranferases.

RESULTS

Our results show that 9 genes were found to be over expressed by more than two-fold induced by DNMT1 siRNA and 5-Aza-CdR, and 30 genes were found to be over expressed by more than two-fold induced by DNMT3B siRNA and 5-Aza-CdR in SMMC-7721. Among them, 76.6% up-regulated genes conjectural contained 5' CpG islands. The DNMT3B siRNA could induce more genes identical to demethylation agent in SMMC-7721.

CONCLUSIONS

DNMT3B might be a new potential target for therapy of hepatocellular carcinoma.

Promoter polymorphisms of DNMT3B and the risk of colorectal cancer in Chinese: a case-control study

BACKGROUND

DNA-methyltransferase-3B (DNMT3B), which plays a role in DNA methylation, is usually aberrant expression involved in carcinogenesis. Polymorphisms of the DNMT3B gene may influence DNMT3B activity on DNA methylation in several cancers, thereby modulating the susceptibility to cancer.

METHODS

DNMT3B -579G>T genotypes and -149C>T were determined by PCR-RFLP and sequencing in 137 colorectal cancer patients and 308 controls matched for age and sex, who did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed colorectal cancer. The association between two SNPs of the DNMT3B promoter and the risk of the development of colorectal cancer was analyzed in a population of Chinese.

RESULTS

The allele frequency of -149C >T among patients and controls was 0.73% versus 0.65%, respectively. The allele frequency of -597G>T for patients and controls was 6.57% versus 11.53%, respectively. Individuals with at least one -149C>T allele were no at a significantly increase risk of colorectal cancer compared with those having a -149TT genotype. However, Individuals with at least one 579G>T allele were decreased risk of colorectal cancer compared with those having a -579TT genotype.

CONCLUSION

The relative distribution of -149C>T DNMT3B SNPs among a Chinese population can not be used as a stratification marker to predict an individual's susceptibility to colorectal cancer. However, the DNMT3B -579G>T polymorphism may contribute to the genetic susceptibility to colorectal cancer.

RASSF1A, BLU, NORE1A, PTEN and MGMT expression and promoter methylation in gliomas and glioma cell lines and evidence of deregulated expression of de novo DNMTs

Methylation of CpG islands in gene promoters can lead to gene silencing. Together with deletion or mutation, it may cause a loss of function of tumor suppressor genes. RASSF1A (3p21.3), NORE1A (1q32.1) and BLU (3p21.3) have been shown to be downregulated by methylation in cancer, and PTEN (10q23.3) and MGMT (10q26.1) are located in areas commonly deleted in astrocytomas. MGMT methylation predicts a better response and a longer overall survival in patients with glioblastomas treated with temozolomide. We analyzed 53 astrocytoma samples and 10 high-grade glioma cell lines. Gene expression was assessed by RT-PCR. Bisulfite sequencing, MSP and a melting curve analysis-based real-time PCR were performed to detect promoter methylation. Treatments with 5'-aza-2'-deoxicitidine were applied to restore gene expression in cell lines. Ninety-two percent of tumor samples were methylated for RASSF1A, 30%-57% for BLU and 47% for MGMT, suggesting promoter methylation of these genes to be a common event in glioma tumorigenesis. Only 4% of the tumors revealed a methylated promoter for NORE1A. No association between methylation and loss of expression could be established for PTEN. We identified de novo DNMTs overexpression in a subset of tumors which may explain the methylation phenotype of individual gliomas.

DNMT3B 579 G>T promoter polymorphism and risk of esophagus carcinoma in Chinese

AIM

To investigate the relationship between 579 G>T polymorphisms in the DNMT3B gene, which is involved in de novo methylation and associated with the risk of esophagus cancer (EC) in Chinese.

METHODS

DNMT3B 579 G>T genotypes were determined by PCR-RFLP in 194 EC patients and 210 healthy controls matched for age and sex, who did not receive radiotherapy or chemotherapy for newly diagnosed and histopathologically confirmed EC.

RESULTS

In control subjects, the frequency of T/T and G/T genotypes, and T and G alleles was 81.4%, 18.1%, 90.05% and 9.55%, respectively. The distribution of genotypes and allelotypes in the EC patients was not significantly different from that in the controls. When stratified by sex and age, there was still no significant association between the risks of EC and GT and GG genotypes. This study also showed a distinct difference in the distribution of DNMT3B and single nucleotide polymorphism (SNP) between Chinese and Koreans.

CONCLUSION

DNMT3B 579 G>T polymorphism may not be a stratification marker to predict the susceptibility to EC, at least in Chinese. DNMT3B promoter SNP is diverse in ethnic populations.