Analysis of gene induction in human fibroblasts and bladder cancer cells exposed to the methylation inhibitor 5-aza-2'-deoxycytidine

Hypermethylation of the promoters of cancer-related genes is often associated with their inactivation during tumorigenesis. Several preclinical and clinical trials have been developed to use DNA methylation inhibitors, such as 5-aza-2'-deoxycytidine (5-Aza-CdR) in attempts to reactivate silenced genes in human cancers. We used high-density oligonucleotide gene expression microarrays to examine the effects of 5-Aza-CdR treatment on human fibroblast cells (LD419) and a human bladder tumor cell line (T24). Data obtained 8 days after recovery from 5-Aza-CdR treatment showed that more genes were induced in tumorigenic cells (61 genes induced; >or=4-fold) than nontumorigenic cells (34 genes induced; >or= 4-fold). Approximately 60% of induced genes did not have CpG islands within their 5' regions, suggesting that some genes activated by 5-Aza-CdR may not result from the direct inhibition of promoter methylation. Interestingly, a high percentage of genes activated in both cell types belonged to the IFN signaling pathway, confirming data from other tumor cell types.     

5-Aza-2'-deoxycytidine induces p21WAF expression by demethylation of p73 leading to p53-independent apoptosis in myeloid leukemia

The DNA methylation inhibitor 5-Aza-2'-deoxycytidine (5-Aza-CdR) has significant therapeutic value for the treatment of patients with myelodysplastic syndrome (MDS), acute myeloid leukemia (AML) and chronic myeloid leukemia (CML). The demethylating effect of 5-Aza-CdR has been well characterized. In contrast, less is known about the molecular events downstream of the methylation inhibition. Here, 5-Aza-CdR induced apoptosis in AML cells (both p53 mutant and wild-type) but not in epithelial or normal PBMCs. Cell death was accompanied by activation of the mitochondrial apoptosis pathway, as shown by release of cytochrome c and AIF and loss of mitochondrial membrane potential (DeltaPsim). Activation of caspase-3 (but not -6 and -8) was detectable using Western blot analysis and measurement of caspase enzymatic activity. 5-Aza-CdR treatment resulted in the induction of p21, which correlated with the arrest of AML cells in the G1 cell cycle phase. Induction of p21 expression was independent of its promoter methylation status but mediated by 5-Aza-CdR-induced reexpression of the tumor-suppressor p73, a known upstream regulator of p21. The p73 promoter was hypermethylated in AML cell lines and in primary AML cells but not in epithelial cells, which were resistant toward 5-Aza-CdR. Therefore, 5-Aza-CdR-mediated specific killing of myeloid cells might be dependent on its ability to revert p73 promoter methylation and to reexpress p73 mRNA. In addition, exogenous expression of p73 rendered epithelial cells sensitive to apoptosis induced by 5-Aza-CdR or other cytostatic drugs. We therefore conclude that p73 is a relevant target for methylation-dependent efficacy of 5-Aza-CdR in AML cells.     

Aberrant methylation of the RIZ1 gene in myelodysplastic syndrome and acute myeloid leukemia

We performed methylation specific PCR analysis on the RIZ1 promoter in MDS and AML. Methylation was detected in 17 of 34 MDS (50%) and 22 of 72 AML (31%) (p = 0.053). Methylation was detected in eleven of 17 secondary AML from MDS (65%), and eleven of 55 de novo AML (20%) (p = 0.0005). Bisulfite sequence revealed methylation at many CpG sites in the promoter. Decreased RIZ1 expression was accompanied by methylation in six of nine samples examined, while it was also observed in seven of 13 without methylation. Treatment of AML cells, that have RIZ1 methylation, with 5-Aza-dC, induced growth suppression with RIZ1 restoration. Our results suggest that the RIZ1 gene is inactivated in MDS and AML in part by methylation, whereas another mechanism should be involved in others.     

5-氮杂-2'-脱氧胞苷对肺癌细胞H460生物学行为及抑癌基因RASSF1A表达的影响

 目的　观察5-氮杂-2'-脱氧胞苷（5-Aza-CdR）对肺癌细胞H460的生物学行为及RASSF1A mRNA表达的影响。方法　5-Aza-CdR处理H460细胞,通过MTT方法、平板克隆试验观察细胞生长活性的变化,PCR检测RASSF1A甲基化状态,Western blotting法检测RASSF1A的蛋白表达,流式细胞术进行细胞周期分析。结果　H460细胞经5-Aza-CdR处理后,与未处理组相比,生长速度出现不同程度减慢,克隆形成率明显降低,RASSF1A甲基化程度降低,延缓H460细胞周期G1／S进程,使细胞阻滞于G1期。结论　在肺癌细胞系中,RASSF1A基因甲基化可能导致其表达缺失,而5-Aza-CdR能够恢复RASSF1A基因的表达,为肺癌的去甲基化治疗提供理论依据。     

High-risk myelodysplastic syndromes and hypermethylation of the p15Ink4B gene

Recent studies have elucidated that not only genetic alterations but also epigenetic changes may play an important role in carcinogenesis. In particular, de novo methylation of CpG islands within the promoter region associated with the inactivation of tumor suppressor genes (TSGs) has been demonstrated in various malignancies. Since de novo acute myelogenous leukemia shows frequent inactivation of the p15INK4B gene through the promoter methylation only, we investigated the methylation status of the p15INK4B gene in myelodysplastic syndrome (MDS). In MDS, the p15INK4B gene is also frequently hypermethylated at the promoter region located at the 5'-CpG island of exon 1. Association of frequent and strong methylation with high-risk MDS suggested that promoter methylation of the p15INK4B gene plays an important role as a late event during MDS progression. Since several TSGs and growth regulatory genes, including the p15INK4B gene, may be inactivated through promoter hypermethylation in hematological malignancies, modulation of the methylation status may be considered as a novel treatment modality in MDS.     

Methylation of secreted frizzled related protein gene in acute leukemia patients in China

Background: DNA methylation of CpG islands within the promoters of specific genes may play roles in tumor initiation and progression. It has been suggested such events may serve as critical check points. Methods:The present study analyzed the methylation status of CpG islands within the promoters of secreted frizzled-related proteins (SFRPs) in 87 acute leukemia (AL) patients, 20 normal controls, and four AL cell lines. 5-aza-2’-deoxycytidine (5-Aza-CdR), an inhibitor of DNA methylation, was employed to determine its effect on SFRP expression. Result: Methylation of at least one SFRP promoter was observed in 69% of the AL patients analyzed. In addition, methylation of all four SFRP promoters was observed in Molt-4, Jurkat, HL60 and NB4 cells. In Jurkat cells, methylation levels of four SFRP promoters decreased in a dose-dependent manner upon treatment with 5-Aza-CdR, which coincided with increased mRNA expression. With increasing 5-Aza-CdR concentrations, the expression of DNA methyltransferases, DNMT3A and DNMT3B, significantly decreased in a dose-dependent manner. Conclusion: The present study demonstrated that SFRP gene methylation may be involved in AL progression, with a possible epigenetic mechanism influencing Wnt signaling.     

RIL, a LIM gene on 5q31, is silenced by methylation in cancer and sensitizes cancer cells to apoptosis

Gene silencing associated with promoter methylation can inactivate tumor suppressor genes (TSG) in cancer. We identified RIL, a LIM domain gene mapping to 5q31, a region frequently deleted in acute myelogenous leukemia (AML) and myelodysplastic syndrome (MDS), as methylated in 55 of 79 (70%) of cancer cell lines tested. In a variety of primary tumors, we found RIL methylation in 55 of 92 (60%) cases, with highest methylation in AML and colon cancer, and in 30 of 83 (36%) MDS samples, whereas normal tissues showed either absence or substantially lower levels of methylation, which correlates with age. RIL is ubiquitously expressed but silenced in methylated cancers and could be reactivated by the hypomethylating agent 5-aza-2'-deoxycytidine. Restoring RIL expression in colon cancer cells by stable transfection resulted in reduced cell growth and clonogenicity and an approximately 2.0-fold increase in apoptosis following UV exposure. In MDS, RIL methylation is a marker of adverse prognosis independent of chromosome 5 and 7 deletions. Our data suggest that RIL is a good candidate TSG silenced by hypermethylation in cancer.     

Elevation of breast carcinoma Nm23-H1 metastasis suppressor gene expression and reduced motility by DNA methylation inhibition

We hypothesize that elevation of Nm23-H1 expression in micrometastatic breast cancer cells may inhibit their metastatic colonization and further invasion, and induce differentiation, thus resulting in a clinical benefit. The current study investigated the possible contribution of DNA methylation to the regulation of Nm23-H1 expression, based on the observation that two CpG islands are present in its promoter. 5-Aza-2'-deoxycytidine (5-Aza-CdR), a DNA methylation inhibitor, increased the Nm23-H1 expression of 5 of 11 human breast carcinoma cell lines in vitro, including 3 of 3 metastatically competent lines. Increased Nm23-H1 expression was accompanied by a reduction in motility in vitro, with minimal effect on proliferation. Both increased Nm23-H1 expression and decreased motility were observed using low (75 nM) concentrations of 5-Aza-CdR. Array analysis of MDA-MB-231 breast carcinoma cells treated with 5-Aza-CdR confirmed the elevation of nm23-H1 mRNA, whereas relatively few other genes exhibited altered expression. Bisulfite sequencing of the two CpG islands in a panel of cell lines and in 20 infiltrating ductal carcinomas revealed that one island (-3090 bp to -3922 bp) exhibited infrequent differential methylation. The data indicate that DNA methylation inhibitors can directly or indirectly cause both elevation of Nm23-H1 expression and decreased function in one aspect of metastasis, motility.     

Comparative analysis of hypermethylation of cell cycle control and DNA-mismatch repair genes in low-density and CD34+ bone marrow cells from patients with myelodysplastic syndrome

Hypermethylation of CpG islands within the promoter region is one of the mechanisms by which genes are inactivated and may be one of the reason for silencing of cell cycle control or DNA-mismatch repair genes in myelodysplastic syndrome (MDS). Since the function of cell cycle control genes including the cyclin-dependent kinase inhibitors known as p15(INK4b) and p16(INK4a), as well as p14(ARF) which blocks MDM-2 (an inhibitor of p53), the retinoblastoma (RB1) protein and the mismatch repair gene MGMT is critical for hematopoietic proliferation and differentiation, we performed methylation specific polymerase chain reaction (MSP) in low-density, non-adherent bone marrow cells from 49 patients with MDS. In addition, expression of p15(INK4b) and RB1 was analysed by quantitative real-time PCR. From selected patients, we analyzed the methylation pattern of cell cycle control genes in CD34+ bone marrow cells. Thirty-nine of 49 cases (80%) had at least one of five genes methylated in our MDS samples by analysing low-density non-adherent bone marrow cells. The frequency of p15(INK4b) methylation was 34 of 49 samples (69%). The incidence of methylation of both p14(ARF) and p16(INK4a) was four of 49 (8%). RB1 gene was methylated in seven samples (14%) and each patient had RA. Interestingly, none of these genes were methylated in the purified CD34+ hematopoietic stem cells from the MDS patients. Furthermore, all our RARS patients had a methylated p15(INK4b) promoter correlating with non-detectable expression of this gene in bone marrow cells from those patients. These results indicate that hypermethylation of cell cycle control genes in MDS may occur late during the differentiation of myelodysplastic stem cells.     

DNA methylation of coding and non-coding regions of the human H-RAS gene in normal and tumor tissues.

To study a possible role of DNA methylation in the regulation of expression of the human H-RAS gene in vivo, 41 samples of different normal tissues and 33 tumors of various histotypes were analysed for DNA methylation. In a subset of normal tissues the RNA expression was also examined. The promoter region of the gene showed the features of a CpG island being CpG rich and unmethylated in all the normal tissues and tumors. The coding region displayed an intermediate level of methylation in the majority of normal and tumor tissues. Among the normal tissues only thymus DNA was found to be hypermethylated, while testes and sperm cells DNAs were hypomethylated. The 3' region was found to be completely methylated only in sperm cells and was never completely demethylated. The majority of the tissues showed an intermediate level of methylation, and a certain tissue specificity emerged by comparing tissues of the same and different histotypes. However, the overall methylation of both coding and 3' regions did not correlate with the levels of tissue-specific RNA expression. In heterozygous individuals, allelic methylation of the 3' region showed either perfectly balanced or slightly unbalanced methylation of the two alleles in normal tissues, while an allele-specific methylation was found in 5 out of 12 fresh tumor samples.     

Effect of promoter methylation of the p16 gene on phosphorylation of retinoblastoma gene product and growth of hepatocellular carcinoma cells.

The biological significance of hypermethylation of p16 gene promoter in human hepatocellular carcinoma (HCC) cells remains to resolved. In order to clarify the significance of methylation of p16 gene promoter, we examined the methylation status of p16 gene in association with phosphorylation of retinoblastoma gene product (pRb) and cell growth in human HCC cell lines. The presence of methylation was examined by methylation-specific PCR. Expression and phosphorylation of p16 and pRb were examined by Western blot analysis. Genetic changes were analyzed by multiplex PCR and DNA sequencing. The effect of demethylation of p16 was assessed by cell growth. p16 gene promoter was methylated in HuH7 and HLF cells. The demethylating agent, 5-aza-2-deoxycytidine (5-Aza-CdR), upregulated p16 mRNA in HuH6 and HuH7 cells. 5-Aza-CdR increased p16 protein expression in HuH6, HuH7, and HLF cells, and it clearly decreased the phosphorylation level of pRb in HuH6, HuH7 and PLC/PRF/5 cells. Treatment with 5-Aza-CdR inhibited the growth of HuH7 cells. Homozygous deletion and significant mutations were absent. Methylation in the p16 promoter region is biologically significant, being associated with phosphorylation of pRb and cell growth in human HCC cells.     

DNA methylation and histone deacetylation associated with silencing DAP kinase gene expression in colorectal and gastric cancers

Death-associated protein kinase is a positive regulator of programmed cell death induced by interferon gamma. To investigate the role of epigenetic inactivation of death-associated protein kinase in gastrointestinal cancer, we examined the methylation status of the 5' CpG island of the death-associated protein kinase gene. Methylation of the 5' CpG island was detected in 3 of 9 colorectal and 3 of 17 gastric cancer cell lines, while among primary tumours, it was detected in 4 of 28 (14%) colorectal and 4 of 27 (15%) gastric cancers. By contrast, methylation of the edge of the CpG island was detected in virtually every sample examined. Death-associated protein kinase expression was diminished in four cell lines that showed dense methylation of the 5' CpG island, and treatment with 5-aza-2'-deoxycitidine, a methyltransferase inhibitor, restored gene expression. Acetylation of histones H3 and H4 in the 5' region of the gene was assessed by chromatin immunoprecipitation and was found to correlate directly with gene expression and inversely with DNA methylation. Thus, aberrant DNA methylation and histone deacetylation of the 5' CpG island, but not the edge of the CpG island, appears to play a key role in silencing death-associated protein kinase expression in gastrointestinal malignancies.     

肺腺癌细胞DR4基因启动子甲基化与TRAIL敏感性的相关性研究

目的 探讨DR4基因启动子甲基化水平与肺腺癌细胞株对肿瘤坏死因子相关凋亡诱导配体（TRAIL）敏感性之间的相关性。方法 选取未经5-氮杂-2'-脱氧胞苷（5-Aza-CdR）处理和10 μmol/L 5-Aza-CdR处理3 d后的肺腺癌细胞A549、LTEP-α-2,采用CCK-8法检测细胞增殖抑制率,倒置显微镜下观察细胞形态学改变,流式细胞仪检测细胞凋亡率;采用RT-PCR法、免疫印迹法和甲基化特异性PCR（MSP）法分别检测肺腺癌细胞株（A549、LTEP-α-2）DR4基因mRNA、蛋白表达和启动子区甲基化状态。结果 肺腺癌细胞（A549、LTEP-α-2）对低浓度TRAIL高度耐受,提高TRAIL浓度（15.625、31.25、62.5、125、250、500 μg／ml）作用细胞24、48 h后,细胞生长受到不同程度抑制,且呈剂量和时间依赖性;经5-Aza-CdR处理后,TRAIL对肺腺癌细胞的增殖抑制作用均较处理前显著增强（P＜0.05）,倒置显微镜下细胞形态表现出变圆、皱缩甚至脱落等特征。应用5-Aza-CdR处理后,125 μg／ml TRAIL诱导肺腺癌细胞的凋亡率较处理前明显升高（P＜0.05）。A549、LTEP-α-2细胞存在DR4 mRNA及蛋白的低表达,其基因启动子处于甲基化状态;经5-Aza-CdR处理后,肺腺癌细胞中DR4 mRNA及蛋白的表达均显著升高（P＜0.05）,其基因启动子处于非甲基化状态。结论 5-Aza-CdR可以逆转DR4基因启动子甲基化状态,上调基因表达,增强TRAIL诱导肺腺癌细胞凋亡的能力,从而逆转TRAIL耐药。5-Aza-CdR联合TRAIL可能是治疗肺腺癌的一种新策略。