Histone modifications and silencing prior to DNA methylation of a tumor suppressor gene

We attempted to answer two central questions about epigenetic silencing of the tumor suppressor gene p16(INK4a) in this study: (1) whether the maintenance of associated histone modifications is dependent on DNA methylation and (2) whether such histone modifications can occur prior to DNA methylation. By coupling chromatin immunoprecipitation with gene targeting and the analysis of specific alleles, we found that elimination of DNA methylation from a p16(INK4a) allele resulted in profound changes in surrounding histones. After continued passage of such cells, methylation of histone H3 lysine-9 occurred in conjunction with re-silencing in the absence of DNA methylation. These results have important implications for understanding the biochemical events underlying the silencing of tumor suppressor genes and the resultant growth suppression.     

DNA甲基化和E-cadherin基因甲基化与胃癌关系研究进展

目的：总结DNA甲基化和E-cadherin基因甲基化与胃癌关系的研究现状。方法：应用PubMed及万方数据知识服务平台检索系统,以“胃癌、DNA甲基化、Eu钙黏蛋白基因和CpG岛”等为关键词,检索1979-01-2013-05的相关文献,共检索到英文文献2093篇,中文文献672篇。纳入标准：1）关键词包括胃癌及DNA甲基化;2）文中包括E-钙黏蛋白基因启动子区CpG岛甲基化。剔除标准：1）非E-钙黏蛋白基因启动子区CpG岛的甲基化;2）关键词有E-钙黏蛋白但文中无甲基化描述。符合纳入标准的中文文献56篇,英文文献43篇,根据剔除标准剔除中文文献46篇,英文文献23篇,最后纳入分析30篇文献。结果：DNA甲基化在基因表达、调控过程中发挥重要作用,其功能紊乱在恶性肿瘤形成过程中具有重要作用,与胃癌的发生密切相关。E-cadherin基因能抑制肿瘤细胞的浸润和转移,E-cadherin基因启动子区CpG岛甲基化是胃肠道肿瘤E-cadherin基因失活的主要原因,可引起E-cadherin表达下降或缺失,与胃癌的发生、浸润、转移和预后密切相关。结论：DNA甲基化和E-cadherin基因甲基化与胃癌的形成、浸润和转移等关系密切,但其要成为胃癌防治的靶点仍需进一步研究。     

DNA methylation and cancer

Tumor suppressor genes can be silenced by DNA methylation during cancer development. Aberrant DNA methylation is closely associated with histone deacetylases and histone methyltransferases that can modify histone amino-terminal lysines and develop specific histone codes, resulting in inactive chromatin formation. These processes change epigenetic information that builds up abnormal chromatin structure, and creates the unique features of cancer cells. It is well known that thousands of genes are deregulated in cancer cells. Epigenetic alterations involving aberrant DNA methylation is a possible mechanism that can explain the genome-wide abnormality of gene expression. The mechanism responsible for the aberrant DNA methylation is unclear now, however it seems that de novo DNA methyltransferases (DNMTs) play an important role in the process. DNMT3 A and DNMT3B are thought to be de novo DNMTs in human. A nucleoside analogue of cytidine induces demethylation of DNA in cancer cells by inhibiting the function of DNMTs. It is significant to elucidate precise mechanisms of aberrant DNA methylation and develop small molecules that can inhibit methylation.     

DNA methylation and cancer

There is tremendous ferment in the field of epigenetics as the relationships between chromatin structure and DNA methylation patterns become clearer. Central to this activity is the realization that the 'histone code', which involves the post-translational modification of histones and which has important ramifications for chromatin structure, may be linked to the DNA cytosine methylation pattern. New discoveries have suggested that histone lysine 9 methylation is implicated in the spread of heterochromatin in Drosophila and other organisms. Very recently it has been found that histone lysine 9 methylation is also necessary for some DNA methylation in Neurospora and plants. There is therefore the possibility that these two processes are closely linked, suggesting ways in which DNA methylation patterns may be established during normal development. Understanding these processes is fundamental to understanding what goes awry during the process of aging and carcinogenesis where DNA methylation patterns become substantially altered and contribute to the malignant phenotype.     

DNA methylation and cancer

The main thrusts of the arguments that aberrant DNA methylation is involved in the generation of tumor heterogeneity and progression can be summarized as follows. The methylation of specific cytosine residues in DNA is certainly an important component in multilevel gene control in eukaryotes. The discovery of CpG clusters in the flanking regions of genes and their under-methylation on housekeeping genes, except those located on inactive X-chromosomes, strongly suggests a controlling function for modification in these regions. Since methylation plays an important role in controlling normal cellular development, it follows that aberrations within this mechanism may be implicated in the abnormal gene control which characterizes cancer. Methylation patterns are not copied rigorously in rapidly dividing cells. This may be because there is normally a close coordination between DNA synthesis, DNA methylation, and DNA packaging, and changes in the timing of these processes could conceivably result in hypomethylation at some sites and de novo methylation at others. Since the greatest variability of methylation patterns is seen in nonexpressed genes, it is possible that there is a tendency for cells to activate genes when dividing in an inappropriate growth environment. The constant evolution and shuffling of methylation patterns which occur during division might play a role in the development of new phenotypes within cell populations. One might predict that selective pressures within the host would select for those cells with specific new methylation patterns allowing for the expression of genes necessary for survival in a particular environment. Many experiments have in fact shown that methylation levels and patterns and indeed methyltransferase levels (57) are altered in cancer cells. Thus, there is considerable heterogeneity within tumor populations with regard to this fundamental biological control mechanism. The fact that direct intervention by the use of 5-aza-Cyd can result in dramatic alterations in malignant potential allows this hypothesis to be tested more critically. Hopefully, the use of 5-aza-Cyd in defined systems will allow us to isolate genes which might become activated by drug treatment and which might contribute to metastatic potential. An understanding of the fundamental aspects of the enzymology and control of DNA methylation might therefore allow us to make significant inroads into understanding how heterogeneity is generated and what we might do about it.     

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.     

MGMT germline polymorphism is associated with somatic MGMT promoter methylation and gene silencing in colorectal cancer

O-6-methylguanine-DNA methyltransferase (MGMT) repairs inappropriately methylated guanine residues in DNA. MGMT promoter methylation and gene silencing are common events in colorectal cancer, and may or may not co-exist with the CpG island methylator phenotype (CIMP). To date, no study has examined the relationship between MGMT promoter methylation and common MGMT single nucleotide polymorphisms (SNPs), which have been associated with colorectal cancer risk. Utilizing real-time polymerase chain reaction (MethyLight technology), we quantified DNA methylation in MGMT and eight other markers (a CIMP diagnostic panel including CACNA1G, CDKN2A, CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1 in 182 colorectal cancers collected from two prospective cohorts, the Nurses' Health Study and the Health Professionals Follow-up Study. We genotyped four MGMT germline SNPs in normal DNA and assessed microsatellite instability (MSI), 18q loss of heterozygosity and KRAS and BRAF status in tumors. The presence of a common MGMT promoter SNP (NM_002412.2:c.-56C>T) (rs16906252) was strongly associated with MGMT methylation (multivariate odds ratio 18.0; 95% confidence interval, 6.2-52.1, P < 0.0001). The presence of the c.-56C>T SNP was also associated with loss of MGMT expression in tumors (assessed by immunohistochemistry) (P = 0.009). This promoter SNP was not correlated with KRAS, BRAF, CIMP or MSI status. None of the other three non-promoter SNPs was significantly associated with any molecular changes tested. In conclusion, we have found a strong association between the germline polymorphism (c.-56C>T) of the MGMT promoter and promoter methylation/silencing of MGMT in colorectal cancer. Our data provide compelling evidence for common susceptibility for MGMT promoter CpG island methylation.     

NPTX2基因DNA甲基化与胰腺癌的研究进展

神经元正五聚蛋白Ⅱ（NPTX2)属于神经元正五聚体蛋白家族(NPs)的成员之一,参与细胞周期调控、细胞增殖、凋亡和致癌等生物学过程。近年来研究发现,在胰腺癌中DNA甲基化普遍存在,导致一些抑癌基因高甲基化而失活,NPTX2作为胰腺癌的一种抑癌基因,在胰腺癌癌前病变阶段就出现明显高甲基化。DNA甲基化可能是导致胰腺癌中NPTX2蛋白功能失活,表达沉默的机制之一。而DNA 甲基化是肿瘤的早期、多发、可逆事件,有望作为胰腺癌早期诊断的潜在标志物以及治疗靶点。文章对NPTX2 的 DNA 甲基化在胰腺癌中的最新研究进展做一综述。     

Targeting DNA methylation in cancer

Cancer growth and metastasis require the coordinate change in gene expression of different sets of genes. While genetic alterations can account for some of these changes, many of the changes in gene expression observed in cancer are caused by epigenetic modifications. The epigenome consists of the chromatin and its modifications, the "histone code" as well as the pattern of distribution of covalent modifications of cytosines residing in the dinucleotide sequence CG by methylation. The normal pattern of distribution of DNA methylation is altered in cancer. A number of genes are regionally hypermethylated but many parts of the genome are hypomethylated. Hypermethylation of tumor suppressor genes is involved in silencing of strategic genes. DNA hypermethylation has received much attention and a number of clinical trials are underway with different inhibitors of DNA methylating enzymes. It is now becoming clear however that hypomethylation also plays a role in cancer by activating genes required for invasion and metastasis. The potential therapeutic implications of targeting DNA methylation in cancer are discussed.     

乳腺癌相关DNA甲基化生物标记的研究进展

乳腺癌是常见的女性恶性肿瘤。据估计2002年全球每年新发病例115万（占所有新发癌症病例数的23％）,已成为除肺癌外最常见的恶性肿瘤。表观遗传改变被证明在乳腺癌的发生、发展中起着至关重要的作用心,其留下的可以被检测的表观遗传痕迹（尤其是DNA的甲基化）为乳腺癌的早期诊断和临床治疗反应及预后评价带来有价值的应用前景。