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.     

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.     

Induction of gene expression by 5-Aza-2'-deoxycytidine in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) but not epithelial cells by DNA-methylation-dependent and -independent mechanisms.

The methylation inhibitor 5-Aza-2'-deoxycytidine (5-Aza-CdR, decitabine) has therapeutic efficacy in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Using microarray analysis, we investigated global changes in gene expression after 5-Aza-CdR treatment in AML. In the AML cell line OCI-AML2, Aza-CdR induced the expression of 81 out of 22 000 genes; 96 genes were downregulated (> or =2-fold change in expression). RT-PCR analysis of 10 randomly selected genes confirmed the changes of expression in AML cells. Similar results were obtained with primary AML and MDS cells after treatment with 5-Aza-CdR ex vivo and in vivo, respectively. In contrast, significantly fewer changes in gene expression and cytotoxicity were detected in normal peripheral blood mononuclear and bone marrow cells or transformed epithelial cells treated with 5-Aza-CdR. Interestingly, only 50.6% of the induced genes contain putative CpG islands in the 5' region. To further investigate the significance of promoter methylation in the induced genes, we analyzed the actual methylation status of randomly selected 5-Aza-CdR-inducible genes. We detected hypermethylation exclusively in the 5' region of the myeloperoxidase (MPO) gene. DNA methylation inversely correlated with MPO expression in newly diagnosed untreated AML patients (P< or =0.004). In contrast, all other analyzed 5-Aza-CdR-inducible genes revealed no CpG methylation in the promoter region, suggesting a methylation-independent effect of 5-Aza-CdR.     

5 Aza CdR通过DNMT1调控卵巢癌细胞ERCC1基因甲基化及其表达

目的:研究5-氮杂-2'-脱氧胞苷(5-Aza-CdR)在卵巢癌细胞系SKOV3中对核苷酸切除交叉修复互补基因1(exeision repair cross complementation group 1,ERCC1)表达的影响及可能的机制.方法:设计特异性针对DNA甲基转移酶1(DNAmethyhransferase 1,DNMT1)基因的shRNA转染人人卵巢癌细胞系SKOV3细胞中,Western blotting检测SKOV3细胞DNMT1以及ERCC1的表达变化;利用不同浓度5-Aza-CdR于不同时间点处理卵巢癌SKOV3细胞,Western blotting检测DNMTI和ERCC1蛋白在处理前后的变化,利用亚硫酸氢钠法检测ERCC1基因启动子区域甲基化水平.结果:0.5、1.0、2.0、4.0μmol/L的5-Aza-CdR作用于SKOV3细胞后,DNMT1表达水平呈浓度依赖性降低,而ERCC1表达水平呈浓度依赖性升高;使用终浓度为1.0 μmol/L的5-Aza-CdR处理SKOV3细胞12、24、36 h后,DNMT1表达水平呈时间依赖性降低,而ERCC1表达水平呈时间依赖性升高,亚硫酸氢钠法检测示药物处理前ERCC1启动子区域处于高甲基化水平,在用1.0μmol/L的5-Aza-CdR处理后,其启动子发生了去甲基化.结论:5-Aza-CdR通过DNMT1调控卵巢癌SKOV3细胞中ERCC1基因的甲基化及其表达水平.     

CpG island methylation and expression of the secreted frizzled-related protein gene family in chronic lymphocytic leukemia

B-cell chronic lymphocytic leukemia (CLL) is characterized by a clonal accumulation of mature neoplastic B cells indicating disruption of apoptosis. Restriction Landmark Genome Scanning was done to identify novel target genes silenced by CpG island methylation in CLL. Secreted frizzled-related protein 4 (SFRP4), a negative regulator of the Wnt signaling pathway, was found to be frequently methylated in CLL samples. Wnt signaling has been shown to control normal apoptotic behavior and is required for normal B-cell development whereas aberrant activation of this pathway has been observed in CLL. We show aberrant DNA methylation and silencing of SFRP4, as well as of additional SFRP family members, in primary CLL samples. Induction of their expression in a dose-dependent manner following treatment with a demethylating agent, 5-aza-2'-deoxycytidine, was shown. Of the five SFRP family members studied in detail, SFRP1 was hypermethylated and down-regulated in all CLL patient samples studied, suggesting that this epigenetic event is a critical step during leukemogenesis. Our results suggest that silencing of SFRPs by CpG island methylation is one possible mechanism contributing to aberrant activation of Wnt signaling pathway in CLL.     

Identification of differentially methylated CpG islands in prostate cancer

Epigenetic change such as DNA methylation is one important mechanism for regulating gene expression as genetic change, such as mutation or loss of heterozygosity. Methylation of cancer-related genes has been shown to play an important role in carcinogenesis and tumor progression. Using methylated CpG island amplification (MCA)/representational difference analysis (RDA), we identified four CpG islands in neurotrophin tyrosine kinase receptor type 2 (NTRK2), Protocadherine Flamingo1 and MFPC (Methylated Fragments in Prostate Cancer) 7 and 8. Bisulfite sequencing revealed that 2 regions of NTRK2 as well as MFPC7 and MFPC8 were aberrantly methylated in prostate cancer cell lines, and COBRA showed that 48 (76.24%), 37 (58.7%) and 14 (22.2%) of 63 prostate cancer tissues were methylated, respectively, for these sites. On the other hand, none of 13 benign prostate samples were methylated, except for 1 (7.7%) with NTRK2. For NTRK2, mRNA expression was negative in prostate cancer cell lines (LNCaP and DU145) but was recovered on a methyltransferase inhibitor (5-Aza-CdR) treatment. The role of NTRK2 within NTRK remains unclear. Our results suggest that these 3 hypermethylated DNA fragments also may be markers of prostate cancer detection.     

Epigenetic inactivation of the candidate tumor suppressor gene HOXB13 in human renal cell carcinoma

Epigenetic alterations like DNA methylation and the resulting inactivation of cancer-related genes often contribute to the development of various cancers. To identify the genes that are silenced by aberrant methylation in renal cell carcinoma (RCC), we subjected two RCC lines to methylated CpG island amplification/representational difference analysis. This identified 27 CpG islands. Combined bisulfite restriction analysis of these CpG islands in primary RCC cases revealed that four were methylated in a tumor-specific manner. One of these was identified as the human homeo-box gene B13 (HOXB13) gene, but the remaining three CpG islands were not associated with known genes. The methylation frequencies of HOXB13 in primary RCC samples and lines were 30 and 73%, respectively. The methylation status of HOXB13 correlated with the loss of its expression both in RCC lines and primary tumors, and methyltransferase inhibitor treatment induced the recovery of its expression. Exogenous expression of HOXB13 in RCC cells that lacked endogenous HOXB13 expression suppressed colony formation and induced apoptotic features. Furthermore, HOXB13 methylation correlated positively with tumor grade and microvessel invasion. These results suggest that HOXB13 is a novel candidate tumor suppressor gene in RCC and that its inactivation may play an important role in both RCC tumorigenesis and progression.     

Hypermethylation and Clinicopathological Significance of RASAL1 Gene in Gastric Cancer

Background: Recent studies have suggested that expression of the RAS protein activator like-1 gene (RASAL1)is decreased in gastric carcinoma tissues and cell lines, indicated a role in tumorigenesis and development ofgastric cancer. Reduced expression of RASAL1 could result in aberrant increase of activity of RAS signalingpathways in cancer cells. However, the exact mechanism which induces down-regulation of the RASAL1 generemains unclear. This study aimed to determine the methylation status and regulation of RASAL1 in gastric cancer.Materials and Methods: Using the methylation-specific polymerase chain reaction (MSP), the methylation statusof CpG islands in the RASAL1 promoter in gastric cancers and paired adjacent non-cancerous tissues from 40patients was assessed and its clinicopathological significance was analyzed. The methylation status of RASAL1 ingastric cancer lines MKN-28, SGC-790l, BGC-823, as well as in normal gastric epithelial cell line GES-l was alsodetermined after treatment with a DNA methyltransferase inhibitor, 5-aza-2’-doexycytidine (5-Aza-CdR). RASactivity (GAS-GTP) was assessed through a pull-down method, while protein levels of ERK1/2, a downstreammolecule of RAS signaling pathways, were determined by Western blotting. Results: The frequencies of RASAL1promoter methylation in gastric cancer and paired adjacent non-cancerous tissues were 70% (28/40) and 30%(12/40) respectively (P<0.05). There were significantly correlations between RASAL1 promoter methylation withtumor differentiation, tumor size, invasive depth and lymph node metastasis in patients with gastric cancer(all P<0.05), but no correlation was found for age or gender. Promoter hypermethylation of the RASAL1 genewas detected in MKN-28, SGC-790l and BGC-823 cancer cells, but not in the normal gastric epithelial cell lineGES-1. Elevated expression of the RASAL1 protein, a decreased RAS-GTP and p-ERK1/2 protein were detectedin three gastric cancer cell lines after treatment with 5-Aza-CdR. Conclusions: Aberrant hypermethylation ofthe RASAL1 gene promoter frequently occurs in gastric cancer tissues and cells. In addition, the demethylatingagent 5-Aza-CdR can reverse the hypermethylation of RASAL1 gene and up-regulate the expression of RASAL1significantly in gastric cancer cells in vivo. Our study suggests that RASAL1 promoter methylation may have acertain relationship with the reduced RASAL1 expression in gastric cancer.     

Genome‐wide DNA methylation analysis of neuroblastic tumors reveals clinically relevant epigenetic events and large‐scale epigenomic alterations localized to telomeric regions

The downregulation of specific genes through DNA hypermethylation is a major hallmark of cancer, although the extent and genomic distribution of hypermethylation occurring within cancer genomes is poorly understood. We report on the first genome‐wide analysis of DNA methylation alterations in different neuroblastic tumor subtypes and cell lines, revealing higher order organization and clinically relevant alterations of the epigenome. The methylation status of 33,485 discrete loci representing all annotated CpG islands and RefSeq gene promoters was assessed in primary neuroblastic tumors and cell lines. A comparison of genes that were hypermethylated exclusively in the clinically favorable ganglioneuroma/ganglioneuroblastoma tumors revealed that nine genes were associated with poor clinical outcome when overexpressed in the unfavorable neuroblastoma (NB) tumors. Moreover, an integrated DNA methylation and copy number analysis identified 80 genes that were recurrently concomitantly deleted and hypermethylated in NB, with 37 reactivated by 5‐aza‐deoxycytidine. Lower expression of four of these genes was correlated with poor clinical outcome, further implicating their inactivation in aggressive disease pathogenesis. Analysis of genome‐wide hypermethylation patterns revealed 70 recurrent large‐scale blocks of contiguously hypermethylated promoters/CpG islands, up to 590 kb in length, with a distribution bias toward telomeric regions. Genome‐wide hypermethylation events in neuroblastic tumors are extensive and frequently occur in large‐scale blocks with a significant bias toward telomeric regions, indicating that some methylation alterations have occurred in a coordinated manner. Our results indicate that methylation contributes toward the clinicopathological features of neuroblastic tumors, revealing numerous genes associated with poor patient survival in NB.     

Cell type-specific methylation of an intronic CpG island controls expression of the MCJ gene

Over 50% of human genes are associated with CpG islands and DNA methylation within such CpG islands has been clearly correlated with inhibition of expression. Whereas changes in DNA methylation play a key role in a number of human diseases, in particular cancer, in normal DNA CpG islands are nearly always methylation free, regardless of the expression status of the associated gene. Only limited evidence supports a role for DNA methylation in controlling tissue-specific expression in adult somatic tissue. Loss of expression of the MCJ gene has previously been linked to increased chemotherapeutic drug resistance in ovarian cancer. We report that loss of expression of MCJ in drug-resistant ovarian cancer cell lines depends on methylation of a CpG island within its first exon, but is independent of methylation within the promoter region. Furthermore, cell type-specific expression of the MCJ gene in normal cells also depends on the methylation status of the CpG island within its first exon. The MCJ CpG island is methylated and the gene is not expressed in cells of epithelial origin, but unmethylated and expressed in cells of lymphocyte or fibroblast origin. Chromatin immunoprecipitation assays determined that MCJ CpG island methylation was associated with loss of histone acetylation in ovarian epithelial cells compared with unmethylated fibroblast cells. Reduced acetylation was observed not only within the CpG island, but also within the promoter region, suggesting that CpG island methylation may direct alterations in chromatin structure within the promoter region, leading to gene inactivation.     

Silencing of bidirectional promoters by DNA methylation in tumorigenesis

CpG island methylation within promoters is known to silence individual genes in cancer. The involvement of this process in silencing gene pairs controlled by bidirectional promoters is unclear. In a screen for hypermethylated CpG islands in cancer, bidirectional promoters constituted 25.2% of all identified promoters, which matches with the genomic representation of bidirectional promoters. From the screen, we selected three bidirectional gene pairs for detailed analysis, WNT9A/CD558500, CTDSPL/BC040563, and KCNK15/BF195580. Levels of mRNA of all three pairs of genes were inversely correlated with the degree of promoter methylation in multiple cancer cell lines. Hypomethylation of these promoters induced by 5-aza-2'-deoxycytidine treatment reactivated or enhanced gene expression bidirectionally. The bidirectional nature of the WNT9A/CD558500 promoter was confirmed by luciferase assays, and hypermethylation down-regulated expression of both genes in the pair. Methylation of WNT9A/CD558500 and CTDSPL/BC040563 promoters occurs frequently in primary colon cancers and acute lymphoid leukemias (ALL), respectively, and methylation was correlated with decreased gene expression in ALL patient samples. Our study shows that hypermethylation of bidirectional promoter-associated CpG island silences two genes simultaneously, a property that should be taken into account when studying the functional consequences of hypermethylation in cancer.     

微阵列定量检测急性白血病患者E-cadherin基因启动子区的甲基化

目的利用微阵列定量检测急性白血病患者E-cadherin基因启动子区CpG岛的甲基化改变,初步探讨基因芯片在肿瘤甲基化检测中的作用。方法用亚硫酸氢盐处理基因组DNA,并以此为模板进行PCR扩增。目的序列中未甲基化的CpG位点被翻转成TpG,而甲基化的CpG位点保持不变。设计5组探针构建一种检测急性白血病E-cadherin基因甲基化改变的微阵列。通过绘制标准曲线,定量检测样本的甲基化改变。结果利用微阵列定量检测了5例急性白血病患者的样本E-cadherin基因的甲基化改变,5个检测区域不同程度发生了甲基化,且发生高甲基化的区域一致。检测结果经过基因测序验证。结论基因芯片能够作为一种定量检测基因甲基化改变的有效工具,可用于白血病甲基化的定量研究。其较基因测序省时省力,且能实现定量和高通量检测。     

5-氮杂-2'-脱氧胞苷对伯基特淋巴瘤NAMALWA细胞株增殖及阳性调控区锌指蛋白1α基因表达的影响

 【摘要】　目的　探讨DNA甲基化抑制剂5-氮杂-2'-脱氧胞苷（5-Aza-CdR）对伯基特淋巴瘤NAMALWA细胞株增殖及抑癌基因阳性调控区锌指蛋白1α（PRDM1α）表达的影响。方法　四甲基偶氮唑蓝（MTT）法检测5-Aza-CdR对NAMALWA细胞株增殖的影响,SYBR Green 相对定量反转录聚合酶链反应方法检测PRDM1α基因表达水平。结果　5-Aza-CdR可抑制NAMALWA细胞的增殖,且表现为浓度依赖性,在终浓度为0.01、0.0625、0.1、0.125、0.25、0.5、1、2和4 μmol／L时对NAMALWA细胞株的抑制率分别为21.93 %、39.23 %、47.69 %、50.37 %、53.54 %、57.72 %、62.31 %、65.68 %和67.87 %,且不同药物浓度间吸光度值比较,差异有统计学意义（均P＜0.01）。同时,5-Aza-CdR能使NAMALWA细胞株中PRDM1α重新表达,0.5、1、2 μmol／L加药组与对照组比较,ΔCt之间差异有统计学意义（P＜0.05）。结论　DNA甲基化抑制剂5-Aza-CdR能显著抑制伯基特淋巴瘤NAMALWA细胞株增殖,可能与其诱导的PRDM1α基因的去甲基化和PRDM1α的再表达有关。     

Array-based profiling of the differential methylation status of CpG islands in hepatocellular carcinoma cell lines

Alterations in the DNA methylation status particularly in CpG islands are involved in the initiation and progression of many types of human cancer. A number of DNA methylation alterations have been reported in hepatocellular carcinoma (HCC). However, a systematic analysis is required to elucidate the relationship between differential DNA methylation status and the characteristics and progression of HCC. In the present study, a global analysis of DNA methylation using a human CpG-island 12K array was performed on a number of HCC cell lines of different origin and metastatic potential. Based on a standard methylation alteration ratio of ≥2 or ≤0.5, 58 CpG island sites and 66 tumor-related genes upstream, downstream or within were identified. This study showed a series of CpG island methylation alterations in the HCC cell lines. The expression of various oncogenes, tumor suppressor genes and other key genes were up- or downregulated, respectively, resulting in CpG island hypomethylation or hypermethylation accordingly. To conclude, a foundation has been provided for screening CpG island methylation profiles as HCC biological markers.     

5-氮-2'-脱氧胞嘧啶对U266细胞系P16基因去甲基化作用研究

  目的 探讨5-氮-2'-脱氧胞嘧啶（5-Aza-CdR）诱导骨髓瘤细胞系U266 p16基因 DNA 5′CpG岛去甲基化作用及对U266细胞增生的影响。方法 采用巢式甲基特异性PCR法（n-MSP）、DNA序列分析、RT-PCR、细胞生长曲线、流式细胞仪DNA含量分析法检测5-Aza-CdR对U266细胞 p16基因去甲基化作用及其对U266细胞的生长、增生及细胞周期的影响。结果 （1）5-Aza-CdR能够逆转U266细胞 p16 基因异常甲基化；（2）5-Aza-CdR能激活p16基因沉默的再转录；（3）5-Aza-CdR能下调U266细胞甲基转移酶DNMT1、DNMT3A、DNMT3B 的表达并呈浓度依赖性；（4）5-Aza-CdR作用的U266细胞被阻滞于G0 ~ G1期。结论 5-Aza-CdR可能通过抑制甲基转移酶直接对p16 基因去甲基化，逆转U266 细胞DNA 异常甲基化，并有效地激活因高甲基化所致p16基因沉默的再转录