DNA methylation and mRNA expression of glutathione S-transferase alpha 4 are associated with intracranial aneurysms in a gender-dependent manner

Objective: We performed a case-control study to investigate the correlation between DNA methylation and mRNA expression of the glutathione S-transferase alpha 4 (GSTA4) gene and the risk of intracranial aneurysm (IA) in the Chinese Han population. Methods: After propensity score matching, 44 pairs of cases and controls were collected in this study. Fasting blood samples were collected for DNA and RNA extraction within 24 h of admission. Nine CpG dinucleotides were selected from the GSTA4 promoter region for DNA methylation pyrosequencing. mRNA expression of GSTA4 was measured by quantitative real-time polymerase chain reaction (RT-qPCR). In vitro cell experiments were conducted to verify the association between 5-aza-2'-deoxycytidine induced DNA hypomethylation and GSTA4 mRNA expression. Results: The mean methylation level of GSTA4 was much lower in IA patients, especially in IA patients, especially in unruptured IA (UIA), than that in controls (IA vs. Control, p < .001; ruptured IA (RIA) vs. Control, p = .005; UIA vs. Control, p < .001). With sex stratification, we further found that the association between GSTA4 methylation and IA risk presented only in women (mean methylation level: IA vs. Control, p < .001; RIA vs. Control, p = .009; UIA vs. Control, p < .001). GSTA4 mRNA expression was significantly higher in the IA group than in the control group (p < .01) and negatively correlated with DNA methylation in all individuals (r = -.746, p < .001). DNA hypomethylation can increase GSTA4 mRNA expression in human primary artery smooth muscle cells. The receiver operating characteristic (ROC) curve showed that GSTA4 mean methylation (AUC = .80, p < .001) was a reliable predictor of women intracranial aneurysm, among which CpG 1 exhibited the best predictive value (AUC = .89, p < .001). In addition, GSTA4 expression levels could also predict the risk of IA in women (AUC = .87, p = .005). Conclusion: Decreased DNA methylation and increased mRNA expression of the GSTA4 gene are associated with the risk of IA in women.

The DNA methylation profile of liver tumors in C3H mice and identification of differentially methylated regions involved in the regulation of tumorigenic genes

Background

C3H mice have been frequently used in cancer studies as animal models of spontaneous liver tumors and chemically induced hepatocellular carcinoma (HCC). Epigenetic modifications, including DNA methylation, are among pivotal control mechanisms of gene expression leading to carcinogenesis. Although information on somatic mutations in liver tumors of C3H mice is available, epigenetic aspects are yet to be clarified.

Methods

We performed next generation sequencing-based analysis of DNA methylation and microarray analysis of gene expression to explore genes regulated by DNA methylation in spontaneous liver tumors of C3H mice. Overlaying these data, we selected cancer-related genes whose expressions are inversely correlated with DNA methylation levels in the associated differentially methylated regions (DMRs) located around transcription start sites (TSSs) (promoter DMRs). We further assessed mutuality of the selected genes for expression and DNA methylation in human HCC using the Cancer Genome Atlas (TCGA) database.

Results

We obtained data on genome-wide DNA methylation profiles in the normal and tumor livers of C3H mice. We identified promoter DMRs of genes which are reported to be related to cancer and whose expressions are inversely correlated with the DNA methylation, including Mst1r, Slpi and Extl1. The association between DNA methylation and gene expression was confirmed using a DNA methylation inhibitor 5-aza-2′-deoxycytidine (5-aza-dC) in Hepa1c1c7 cells and Hepa1-6 cells. Overexpression of Mst1r in Hepa1c1c7 cells illuminated a novel downstream pathway via IL-33 upregulation. Database search indicated that gene expressions of Mst1r and Slpi are upregulated and the TSS upstream regions are hypomethylated also in human HCC. These results suggest that DMRs, including those of Mst1r and Slpi, are involved in liver tumorigenesis in C3H mice, and also possibly in human HCC.

Conclusions

Our study clarified genome wide DNA methylation landscape of C3H mice. The data provide useful information for further epigenetic studies of mice models of HCC. The present study particularly proposed novel DNA methylation-regulated pathways for Mst1r and Slpi, which may be applied not only to mouse HCC but also to human HCC.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4221-0) contains supplementary material, which is available to authorized users.

Targeting DNA hypermethylation: Computational modeling of DNA demethylation treatment of acute myeloid leukemia

In acute myeloid leukemia (AML) DNA hypermethylation of gene promoters is frequently observed and often correlates with a block of differentiation. Treatment of AML patients with DNA methyltransferase inhibitors results in global hypomethylation of genes and, thereby, can lead to a reactivation of the differentiation capability. Unfortunately, after termination of treatment both hypermethylation and differentiation block return in most cases. Here, we apply, for the first time, a computational model of epigenetic regulation of transcription to: i) provide a mechanistic understanding of the DNA (de-) methylation process in AML and; ii) improve DNA demethylation treatment strategies. By in silico simulation, we analyze promoter hypermethylation scenarios referring to DNMT dysfunction, decreased H3K4me3 and increased H3K27me3 modification activity, and accelerated cell proliferation. We quantify differences between these scenarios with respect to gene repression and activation. Moreover, we compare the scenarios regarding their response to DNMT inhibitor treatment alone and in combination with inhibitors of H3K27me3 histone methyltransferases and of H3K4me3 histone demethylases. We find that the different hypermethylation scenarios respond specifically to therapy, suggesting that failure of remission originates in patient-specific deregulation. We observe that inappropriate demethylation therapy can result even in enforced deregulation. As an example, our results suggest that application of high DNMT inhibitor concentration can induce unwanted global gene activation if hypermethylation originates in increased H3K27me3 modification. Our results underline the importance of a personalized therapy requiring knowledge about the patient-specific mechanism of epigenetic deregulation.

Biodegradable system for drug delivery of hydrolytically labile azanucleoside drugs

BACKGROUND

The archetypal DNA methyltransferase inhibitors, 5-azacytidine (AZA) and 5-aza-2'-deoxycytidine (DAC) are potent antineoplastic agents used in the treatment of mainly, blood malignancies. However, the administration of these drugs is confounded by their hydrolytic lability which decreases plasma circulation time. Here, we describe a new biodegradable, polyanhydride formulation for drug delivery that circumvents this drawback.

METHODS

Injectable/implantable polymeric microbeads containing dispersed microcrystals of hydrophilic AZA or DAC packed in a dry environment are protected from hydrolysis, until the hydrolytic zone reaches the core. Diclofenac is embedded into the formulation to decrease any local inflammation. The efficacy of the formulations was confirmed by monitoring the induced demethylation, and cytostatic/cytotoxic effects of continuous drug release from the time-course dissolution of the microbeads, using an in vitro developed cell based reporter system.

RESULTS

Poly(sebaccic acid-co-1,4-cyclohexanedicarboxylic acid) containing 30 wt. % drug showed zero-order release (R(2) = 0.984 for linear regression), and release rate of 10.0 %/h within the first 5 h, and subsequent slower release of the remaining drug, thus maintaining the level of drugs in the outer environment considerably longer than the typical plasma half-life of free azanucleosides. At lower concentrations, the differences between powder drug formulations and microbeads were very low or negligible, however, at higher concentrations, we discovered equivalent or increasing effects of the drugs loaded in microbeads.

CONCLUSIONS

The study provides evidence that microbead formulations of the hydrolytically labile azanucleoside drugs could prevent their chemical decomposition in aqueous solution, and effectively increase plasma circulation time.

Epigenetically regulated MIR941 and MIR1247 target gastric cancer cell growth and migration

Altered expression of microRNA (miRNA) can significantly contribute to cancer development and recent studies have shown that a number of miRNAs may be regulated by DNA methylation. Through a candidate gene approach, we identified MIR941 and MIR1247 to be transcriptionally silenced by DNA hypermethylation in several gastric cancer cell lines. We confirmed that these miRNAs are also densely methylated in primary gastric cancers but not in normal gastric tissues. In addition, we demonstrated that ectopic expression of these two miRNAs in AGS gastric cancer cells resulted in suppression of growth and migration. Furthermore, we tested genes predicted to be the targets of MIR941 and MIR1247 and identified 7 and 6 genes, whose expressions were significantly downregulated by transfection of MIR941 and MIR1247 mimics, respectively, in gastric cancer cell lines. Some of these genes are known to promote proliferation and invasion, phenotypes we observed upon ectopic expression of the two miRNAs. Thus, we examined these candidates more closely and found that downregulation of mRNA corresponded to a decrease in protein levels (observed by western blot). Our study provides unequivocal evidence that MIR941 and MIR1247 are transcriptionally regulated by DNA methylation in gastric cancer and that they have tumor suppressor properties through their inhibition of key cancer promoting genes in this context.

DNA methylation of E-cadherin is a priming mechanism for prostate development

In prostate and other epithelial cancers, E-cadherin (CDH1) is downregulated inappropriately by DNA methylation to promote an invasive phenotype. Though cancer frequently involves a reawakening of developmental signaling pathways, whether DNA methylation of Cdh1 occurs during organogenesis has not been determined. Here we show that DNA methylation of Cdh1 mediates outgrowth of developing prostate ducts. During the three-day gestational window leading up to and including prostate ductal initiation, Cdh1 promoter methylation increases and its mRNA and protein abundance decreases in epithelium giving rise to prostatic buds. DNA methylation is required for prostate specification, ductal outgrowth, and branching morphogenesis. All three endpoints are impaired by a DNA methylation inhibitor, which also decreases Cdh1 promoter methylation and increases Cdh1 mRNA and protein abundance. A CDH1 function-blocking antibody restores prostatic identity, bud outgrowth, and potentiates epithelial differentiation in the presence of the DNA methylation inhibitor. This is the first study to mechanistically link acquired changes in DNA methylation to the normal process of prostate organogenesis. We propose a novel mechanism whereby Cdh1 promoter methylation restricts Cdh1 abundance in developing prostate epithelium to create a permissive environment for prostatic bud outgrowth. Thus, DNA methylation primes the prostate primordium to respond to developmental cues mediating outgrowth, differentiation and maturation of the ductal network.

Functional epigenetic approach identifies frequently methylated genes in Ewing sarcoma

Using a candidate gene approach we recently identified frequent methylation of the RASSF2 gene associated with poor overall survival in Ewing sarcoma (ES). To identify effective biomarkers in ES on a genome-wide scale, we used a functionally proven epigenetic approach, in which gene expression was induced in ES cell lines by treatment with a demethylating agent followed by hybridization onto high density gene expression microarrays. After following a strict selection criterion, 34 genes were selected for expression and methylation analysis in ES cell lines and primary ES. Eight genes (CTHRC1, DNAJA4, ECHDC2, NEFH, NPTX2, PHF11, RARRES2, TSGA14) showed methylation frequencies of>20% in ES tumors (range 24-71%), these genes were expressed in human bone marrow derived mesenchymal stem cells (hBMSC) and hypermethylation was associated with transcriptional silencing. Methylation of NPTX2 or PHF11 was associated with poorer prognosis in ES. In addition, six of the above genes also showed methylation frequency of>20% (range 36-50%) in osteosarcomas. Identification of these genes may provide insights into bone cancer tumorigenesis and development of epigenetic biomarkers for prognosis and detection of these rare tumor types.

Real-time PCR analysis of genes encoding tumor antigens in esophageal tumors and a cancer vaccine

Tumor antigens are the primary target of therapeutic cancer vaccines. We set out to define and compare the expression pattern of tumor antigen genes in esophagus carcinoma biopsies and in an allogeneic tumor lysate-based cancer vaccine, MelCancerVac. Cells used for vaccine production were treated with the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine (5-aza-CdR) to determine whether this treatment could improve the profile of tumor antigen genes expressed in these cells. In addition, the presence of MAGE-A tumor antigen protein was evaluated in the purified tumor cell lysate used in the production of the vaccine. Quantitative PCR was used to assay 74 tumor antigen genes in patients with squamous cell carcinoma of the esophagus. 81% (13/16) of tumors expressed more than five cancer/testis (CT) antigens. A total of 96 genes were assayed in the tumor cell clone (DDM1.7) used to make tumor cell lysate for vaccine preparation. Gene expression in DDM1.7 cells was compared with three normal tissues; 16 tumor antigen genes were induced more than ten-fold relative to normal tissues. Treatment with 5-aza-CdR induced expression of an additional 15 tumor antigens to a total of 31. MAGE-A protein was detected in cell lysate by Western blot at an estimated concentration of 0.2 micrograms/ml or 0.01% of the total protein.

Relationship between tumor suppressor gene RUNX3 expression and cell proliferation and apoptosis in colonic cancer cell line Lovo

AIM: To investigate the expression and methylation status of tumor suppressor gene RUNX3 in human colon cancer cell line Lovo and explore the effects of 5-aza-2'-deoxycytidine (5-Aza-CdR) on the proliferation and apoptosis of Lovo cells and the expression of RUNX3 gene.

METHODS: Human colon cancer cell line Lovo was treated with 5-Aza-CdR, a specific methyltransferase inhibitor, at the concentrations of 0.4, 4 and 40 μmol/L for 3 d, and then cultured in RPMI 1640 medium for 5 d. The activation of Lovo cells was respectively observed by Tetrazolium salt colorimetric (MTT) assay before and after 5-Aza-CdR treatment. The change in expression of RUNX3 mRNA was observed by semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR). The apoptosis was analyzed by flow cytometry. The methylation status of gene promoter was determined by methylation-specific PCR (MSP).

RESULTS: Lovo cells treated with 5-Aza-CdR (0.4, 4, 40 μmol/L) displayed a slowed growth rate in different degrees in contrast with those in the control group and their growth rates decreased accordingly with the increase of 5-Aza-CdR concentration. There were significant increases in RUNX3 mRNA expression (0.46 ± 0.06, 0.71 ± 0.06, 0.84 ± 0.07 vs 0, P < 0.01) and apoptotic rates of Lovo cells (10.95% ± 2.09%, 17.61% ± 1.51%, 26.60% ± 1.89% vs 2.92% ± 0.93%, P < 0.01) after 5-Aza-CdR treatment in comparison with those in the control group. The level of RUNX3 mRNA expression and the apoptotic rates of Lovo cells were increased in correlation with 5-Aza-CdR concentration (F = 168.4, F = 145.7, P < 0.01). Methylation of RUNX3 promoter region was confirmed in Lovo cells of control group and detected partly in 5-Aza-CdR-treated group.

CONCLUSION: 5-Aza-CdR is able to reverse the methylation status of RUNX3 promoter region. The re-expression of RUNX3 gene can inhibit Lovo cell growth and partly induce Lovo cell apoptosis.

5-aza-2'-deoxycytidine induces demethylation of p16 gene in human gastric cancer cells and up-regulates its expression

AIM: To investigate the effects of 5-aza-2'-deoxycytidine (5-Aza-CdR) on methylation and expression of p16 gene in the human gastric cancer cell line SGC7901, and to discuss the mechanism of p16 gene silencing in human gastric cancer cells, as well as the regulating effect of the demethylating agent on p16 gene expression.

METHODS: SGC7901 cells were cultured in RPMI 1640 medium and were treated with different concentrations (1 × 10^-7 mol/L, 5 × 10^-7 mol/L, 1 × 10^-6 mol/L, 5 × 10^-6 mol/L) of DNA methyltransferase inhibitor 5-Aza-CdR. Methylation-specific polymerase chain reaction (MSP) was used to detect the promoter methylation state of the p16 gene. RT-PCR and Western blotting were used to detect expression of p16 mRNA and protein before and after treatment with 5-Aza-CdR, respectively.

RESULTS: Promoter hypermethylation of the p16 gene was detected in SGC7901 cells, and p16 was expressed at a low level before treatment. After treatment with 5-Aza-CdR, the promoter region of the p16 gene exhibited a demethylation state, and its expression was increased at the mRNA and protein levels.

CONCLUSION: Promoter hypermethylation is a major mechanism of p16 gene silencing in human gastric cancer cells, and can be reversed by the demethylating agent 5-Aza-CdR. Demethylating agents can regulate the expression of the p16 gene. The corresponding ratio of the group mRNA and protein expression prior to treatment when the concentration of 5-Aza-CdR is 1 × 10^-7, 5 × 10^-7, 1 × 10^-6, 5 × 10^-6 mol/L are 2.21 ± 0.36, 2.01 ± 0.31; 2.82 ± 0.39, 2.22 ± 0.33; 2.98 ± 0.42, 3.15 ± 0.43, 3.35 ± 0.55, and 3.75 ± 0.61 respectively.

Effects of 5-aza-2'-deoxycitydine on proliferation of human gastric cancer cell lines and abnormal methylation of Apaf-1 gene

AIM: To observe the effects of 5-aza-2'-deoxycitydine (5-Aza-CdR) on the proliferation of human gastric cancer cell lines SGC7901 and BGC823 as well as the methylation and epression of Apaf-1 gene.

METHODS: Human gastric cancer cell lines SGC7901 and BGC823 were cultured in RPMI1640 and then treated with different concentrations of 5-Aza-CdR (1 × 10^-7, 5 × 10^-7, 1 × 10^-6 and 5 × 10^-6 mol/L). The proliferation of the cells was detected by MTT assay and flow cytometry (FCM). The methylation of Apaf-1 gene in the two kinds of cell lines was detected by methylation-specific-polymerase chain reaction (MSP), and the expression of Apaf-1 was detected by reverse transcription-polymerase chain reaction (RT-PCR) and Westen blot analysis.

RESULTS: 5-Aza-CdR displayed a growth inhibitory effect on SGC7901 and BGC823 cells in a dose- and time-dependent manner after exposure to 5-Aza-CdR at different concentrations (1 × 10^-7, 5 × 10^-7, 1 × 10^-6, 5 × 10^-6 mol/L) for 24, 48 and 72 hours. FCM analysis showed that the apoptosis rates in SGC7901 cells (2.53% ± 1.19%, 5.93% ± 0.86%, 10.14% ± 1.51%) and BGC823 cells (1.57% ± 0.26%, 4.64% ± 1.05%, 8.21% ± 1.46%) were increased significantly after exposure to 5-Aza-CdR (5 × 10^-7, 1 × 10^-6, 5 × 10^-6 mol/L) for 72 hours as compared with 0.12% ± 0.03% and 0.57% ± 0.03% in the control cells (P < 0.05). The methylation and loss of Apaf-1 mRNA and protein expression were detected in SGC7901 and BGC823 cells before 5-Aza-CdR treatment. However, the methylation was reversed and Apaf-1 was re-expressed after 5-Aza-CdR treatment.

CONCLUSION: 5-Aza-CdR can inhibit the proliferation of SGC7901 and BGC823 cells through blocking cell cycles and inducing cell apoptosis, during which the reversion of Apaf-1 gene methylation plays an important role.