DNA低甲基化与肿瘤的关系

DNA甲基化异常包括全基因组的低甲基化和局部基因的高甲基化。在肿瘤的发生、发展过程中,DNA低甲基化比高甲基化更为常见。DNA甲基化且与肿瘤类型、肿瘤分期及肿瘤侵袭的顺序中表现出相当的特异性。DNA低甲基化对肿瘤的早期诊断和预防有重要意义。     

High-resolution mapping of DNA hypermethylation and hypomethylation in lung cancer

Changes in DNA methylation patterns are an important characteristic of human cancer. Tumors have reduced levels of genomic DNA methylation and contain hypermethylated CpG islands, but the full extent and sequence context of DNA hypomethylation and hypermethylation is unknown. Here, we used methylated CpG island recovery assay-assisted high-resolution genomic tiling and CpG island arrays to analyze methylation patterns in lung squamous cell carcinomas and matched normal lung tissue. Normal tissues from different individuals showed overall very similar DNA methylation patterns. Each tumor contained several hundred hypermethylated CpG islands. We identified and confirmed 11 CpG islands that were methylated in 80-100% of the SCC tumors, and many hold promise as effective biomarkers for early detection of lung cancer. In addition, we find that extensive DNA hypomethylation in tumors occurs specifically at repetitive sequences, including short and long interspersed nuclear elements and LTR elements, segmental duplications, and subtelomeric regions, but single-copy sequences rarely become demethylated. The results are consistent with a specific defect in methylation of repetitive DNA sequences in human cancer.     

乳头状甲状腺癌与相关基因DNA甲基化

DNA甲基化是重要的表观遗传修饰方式之一,在肿瘤的发病、诊断及预后判断中有重要的临床意义.近年的研究发现甲状腺特异基因[促甲状腺激素受体(TSHR)、钠-碘转运体(NIS)]与肿瘤抑制基因(RASSF1A、P16、ECAD、ATM、SLC5A8、Rap1 GAP、TIMP3、DAPK、RARβ2、PTEN、MLH1)等的DNA甲基化在乳头状甲状腺癌的发生及发展过程中起重要作用,并与BRAF突变、RET/PTC重排及RAS/RAF/丝裂原活化蛋白激酶激酶/细胞外信号调节激酶/丝裂原活化蛋白激酶(RAS/RAF/MEK/ERK/MAPK)通路等密切相关.临床上,对乳头状甲状腺癌相关基因的DNA甲基化进行检测,可提供一种新的诊断及判断预后的方法,有望成为精确诊断肿瘤的早期指标,并从表观遗传学角度提供治疗疾病的新方法.     

CG gene body DNA methylation changes and evolution of duplicated genes in cassava

DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.DNA methylation plays an important role in the regulation of the expression of genes and the maintenance of transposable element (TE) silencing. In contrast to animals, in which methylation is often restricted to the CG context, plants exhibit robust methylation in every possible context CG, CHG (H is A, T, or C), and CHH. Previous research has identified different pathways responsible for the maintenance and establishment of DNA methylation patterns. In Arabidopsis thaliana, METHYLTRANSFERASE1 (MET1), a homolog of mammalian Dnmt1, mainly maintains methylation at the CG context, whereas CHROMOMETHYLASE3 (CMT3) mainly maintains CHG methylation. DOMAINS REARRANGED METHYLTRANSFERASE2 (DRM2) and CHROMOMETHYLASE2 (CMT2) maintain CHH methylation in the chromosome arms and pericentromeric regions, respectively (1–3). On the other hand, establishment of DNA methylation is performed by DRM2 through a complex pathway termed RNA-directed DNA methylation (RdDM) (4).To date, the majority of our knowledge about DNA methylation is derived from the model plant Arabidopsis. These studies have allowed the identification of different components involved in different methylation pathways, the genome-wide identification of methylation patterns, and the study of effects of DNA methylation on gene expression. The knowledge acquired from Arabidopsis can now be used as the basis for investigations of methylation in agronomically important plants. However, thus far very few crop species have been subjected to detailed DNA methylation studies (5). Cassava (Manihot esculenta) is cultivated for its starch-rich tuberous roots and is one of the world’s most important staple crops, especially in tropical America, Africa, and Asia (6). Cassava is a source of carbohydrates for nearly a billion people, but it is especially important for a large portion of Africa, where it serves as a subsistence crop because of its ability to tolerate drought and grow on poor soils, conditions unsuitable for rice and maize (6, 7). The genome sequence of cassava has been described recently with an estimated genome size of roughly 760 million base pairs (7). We have used bisulfite sequencing (BS-seq) to examine DNA methylation in cassava at single-base pair resolution. Broadly, the pattern of DNA methylation of both protein-coding genes and TEs is similar to other plants, although DNA methylation levels in cassava are higher than those in Arabidopsis. LTR retrotransposons, such as GYPSY and COPIA, tend to be more heavily methylated than other TEs. Interestingly, differentially expressed gene pairs derived from the last genome duplication tend to show differential gene body methylation, with the highly expressed paralogs displaying significantly higher gene body methylation. We also find that the most differentially gene body-methylated paralogs have distinct biological functions compared with genes that have maintained similar gene body methylation patterns.     

Studies on the hypomethylation of c-myc, c-Ha-ras oncogenes and histopathological changes in human gastric carcinoma

In order to study the status of DNA methylation of specific oncogenes and the relationship between them and the pathological changes in gastric carcinoma, we analysed the methylated status of c-myc, c-Ha-ras oncogenes by Southern blot hybridization. Genomic DNA from cancerous, paracancerous and non-cancerous areas of surgically resected specimens were examined in 22 cases of advanced human gastric carcinoma. Specimens were digested by the restriction endonucleases MspI/HpaII, which are able to cleave between methylated and non-methylated cytosine at their nucleotide recognition site the DNA 5′-CCGG sequence, and were hybridized with c-myc, c-Ha-ras oncogene probes. Moreover, the corresponding pathological changes in gastric carcinoma were observed. The results showed that c-myc, c-Ha-ras oncogenes from cancerous (10/22, 5/10) and paracancerous areas (13/22, 4/10) were hypomethylated and that there was no significant relationship between them and the histopathological changes.     

Effects of Sirt1 on DNA methylation and expression of genes affected by dietary restriction

Changes in DNA methylation across the life course may contribute to the ageing process. We hypothesised that some effects of dietary restriction to extend lifespan and/or mitigate against features of ageing result from changes in DNA methylation, so we determined if genes that respond to dietary restriction also show age-related changes in DNA methylation. In support of our hypothesis, the intersection of lists of genes compiled from published sources that (1) were differentially expressed in response to dietary restriction and (2) showed altered methylation with increased age was greater than expected. We also hypothesised that some effects of Sirt1, which may play a pivotal role in beneficial effects of dietary restriction, are mediated through DNA methylation. We thus measured effects of Sirt1 overexpression and knockdown in a human cell line on DNA methylation and expression of a panel of eight genes that respond to dietary restriction and show altered methylation with age. Six genes were affected at the level of DNA methylation, and for six expressions were affected. In further support of our hypothesis, we observed by DNA microarray analysis that genes showing differential expression in response to Sirt1 knockdown were over-represented in the complied list of genes that respond to dietary restriction. The findings reveal that Sirt1 has effects on DNA methylation across the genome and affects, in particular, the expression of genes that respond to dietary restriction. Sirt1-mediated effects on DNA methylation and, consequently, gene expression may thus be one of the mechanisms underlying the response to dietary restriction.

Electronic supplementary material

The online version of this article (doi:10.1007/s11357-012-9485-8) contains supplementary material, which is available to authorized users.     

人原发性肝细胞癌中总基因组DNA甲基化变化的研究

目的：研究原发性肝细胞癌组织中总基因组DNA甲基化水平及其与病理学及生物学行为的关系。方法：以甲基化酶温育3H-腺苷甲硫氨酸掺入、液闪计数法分析33例中晚期肝癌手术标本的癌灶和癌旁组织细胞内总基因组DNA甲基化水乎，并以10例正常肝组织作对照比较。结果：肝癌灶内的DNA甲基化水平显著低于癌旁组织（P＜0．05）和正常对照肝组织（P＜0．01），其甲基化水平降低程度与肿瘤的大体形态（多发性或单灶性．结节型或区块型）有关，而与组织学改变（Edmondson分级）、门脉癌栓有否及血清AFP水平无明显关系。结论：人原发性肝细胞癌组织中DNA的甲基化水平有显著降低，值得进一步研究肝细胞癌组织个别癌基因片段甲基化及mRNA表达状况。     

DNA甲基化与动脉粥样硬化

动脉粥样硬化是多基因遗传与环境因素相互作用的结果,是受表观遗传规律控制的重要疾病之一.DNA甲基化是最早发现和研究最为成熟的表观遗传分子机制.检测DNA甲基化的方法 很多,各有其优缺点.基因组DNA全面低甲基化和相关候选基因的异常甲基化修饰与动脉粥样硬化的发生发展密切相关.文章对相关方面的研究进展进行了综述.     

Age-dependent decreases in DNA methyltransferase levels and low transmethylation micronutrient levels synergize to promote overexpression of genes implicated in autoimmunity and acute coronary syndromes

T cell DNA methylation levels decline with age, activating genes such as KIR and TNFSF7 (CD70), implicated in lupus-like autoimmunity and acute coronary syndromes. The mechanisms causing age-dependent DNA demethylation are unclear. Maintenance of DNA methylation depends on DNA methyltransferase 1 (Dnmt1) and intracellular S-adenosylmethionine (SAM) levels, and is inhibited by S-adenosylhomocysteine (SAH). SAM levels depend on dietary micronutrients including folate and methionine. SAH levels depend on serum homocysteine concentrations. T cell Dnmt1 levels also decline with age. We hypothesized that age-dependent Dnmt1 decreases synergize with low folate, low methionine or high homocysteine levels to demethylate and activate methylation-sensitive genes. T cells from healthy adults ages 22–81, stimulated and cultured with low folate, low methionine, or high homocysteine concentrations showed demethylation and overexpression of KIR and CD70 beginning at age ∼50 and increased further with age. The effects were reproduced by Dnmt1 knockdowns in T cells from young subjects. These results indicate that maintenance of T cell DNA methylation patterns is more sensitive to low folate and methionine levels in older than younger individuals, due to low Dnmt1 levels, and that homocysteine further increases aberrant gene expression. Thus, attention to proper nutrition may be particularly important in the elderly.     

DNA甲基化修饰在心血管疾病中的研究进展

DNA甲基化是广泛存在于真核生物中的基因修饰机制,对细胞分化过程和基因转录发挥着重要的调节功能。DNA甲基化能够遗传并且受到环境、饮食、衰老和疾病的影响。近年来很多研究发现,DNA甲基化在心血管疾病（如动脉粥样硬化、高血压和心力衰竭等）的发生发展中发挥重要作用。