DNA甲基化与食管癌的发生和发展

 食管癌是全球第8位常见恶性肿瘤,且死亡率居第6位［1］。食管癌的主要组织类型分为食管鳞状细胞癌（食管鳞癌）和食管腺癌［2］。在西方国家食管腺癌发病率逐渐增高;亚洲食管癌的主要类型是食管鳞癌,约占食管癌的90%。食管癌的分布呈现地域性［3, 4］。尽管多种治疗方案的联合治疗可改善食管癌的治疗效果,但其预后仍然很差［2］。食管癌的发生发展与遗传学（基因突变、杂合子缺失和染色体重塑等）及表观遗传学（DNA甲基化、组蛋白修饰和非编码RNA等）的改变相关［1, 5］。DNA甲基化是表观遗传学的主要形式,并与食管癌发生发展密切相关［6 8］。为此,笔者主要对食管癌的发生发展过程中,肿瘤抑制基因甲基化的改变进行综述。     

DNA甲基化与大肠癌发生关系的研究

DNA的甲基化参与基因的表达调控它的异常与肿瘤等疾病的发生有关,抑癌基因启动子区的异常甲基化和癌基因的去甲基化均影响肿瘤发生发展。在大肠癌的发生发展过程中,也伴随着DNA的异常甲基化。本文对目前常见的基因甲基化及其对大肠癌的作用和影响以及在治疗和预后所起的作用作一综述。     

DNA甲基化及其在癌症中的作用研究进展

DNA甲基化作为一种重要的表观遗传机制，在癌症发生发展中起了重要的作用。是分子生物学的研究热点，引起各国科学家的关注。针对DNA甲基化以及DNA甲基化异常的机制进行概述。     

应用DNA芯片技术结合核技术对辐射致癌分子机制的研究

DNA芯片技术是新近出现的新的基因分析方法,它是将成千上万个寡核苷酸固定在约厘米大小的硅片上,将待测材料用荧光素或同位素标记,在DNA芯片上与探针杂交,通过激光共聚焦显微镜对芯片进行扫描获取杂交探针的荧光信号,该技术可用于DNA测序,转录情况分析,基因诊断与基因药物设计,突变及多肽性检测遗传作图等方面的研究。     

应用DNA芯片技术结合核技术对辐射致癌分子机制的研究

DNA芯片技术是新近出现的新的基因分析方法。它是将成千上万个寡核苷酸固定在约厘米大小的硅片上,将待测材料用荧光素或同位素标记,在DNA芯片上与探针杂交,通过激光共聚焦显微镜对芯片进行扫描获取杂交探针的荧光信号。该技术可用于DNA测序,转录情况分析,基因诊断与基因药物设计,突变及多肽性检测遗传作图等方面的研究。     

snoRNA在电离辐射诱导的DNA损伤中的作用及研究进展

核仁小RNA (small nucleolus RNA,snoRNA)是一类在真核生物中普遍存在的非编码RNA,根据其结构特征,可分为两大类:box C/D snoRNA和box H/ACA snoRNA,分别介导RNA 2''-O-甲基化和假尿嘧啶化修饰。近期研究发现,snoRNA还影响mRNA前体(pre-mRNA)的可变剪接,能够通过生成miRNA来介导基因沉默,并通过与蛋白质相互作用调节其功能活性。在电离辐射的生物效应中,DNA损伤与修复过程是至关重要的生物学基础。然而,目前关于snoRNA在电离辐射引起的DNA损伤中的作用的研究还相当有限。本综述旨在概述snoRNA的生物学功能及其在电离辐射诱导的DNA损伤修复中可能的调控角色,以期为探究snoRNA的功能及机制提供新思路。     

小剂量辐射对小鼠全基因组DNA甲基化的影响

目的 探讨小剂量辐射(LDR)对小鼠全血基因组DNA甲基化的影响,以及DNMT1、MBD2在外周血单个核细胞(PBMC)及各组织中的表达变化。方法 SPF级BALB/c雄性小鼠30只按随机数字表法均分为3组:对照组、单次0.5 Gy照射组和分次0.5 Gy(0.05 Gy/d×10 d)照射组。照射组均行6 MV X射线全身照射。其中分析早期效应的15只小鼠(5只/组)在末次照射后2 h,每组10只处死,分析延迟效应的另外15只小鼠末次照射后30 d处死。收集PBMC、肾脏、肝脏、脾脏、脑及肺组织。采用整体甲基化定量试剂盒和高效液相色谱法(HPLC)分析全血DNA甲基化水平,RT-PCR法检测小鼠PBMC及各组织DNMT1和MBD2 mRNA的表达。结果 末次照射后2 h,与对照组比较,分次照射组全血DNA甲基化水平降低(两种检测方法,t =10.19和8.93,P<0.05),DNMT1和MBD2 mRNA在小鼠PBMC、肾脏和肝脏中表达均降低(t =5.06、3.01、3.97、12.25、3.50和3.73,P<0.05),MBD2 mRNA表达在脾脏中降低(t =3.03,P<0.05);而单次照射组均无明显改变。末次照射后1个月,单次、分次照射组的全血甲基化水平较对照组差异均无统计学意义,仅分次照射组小鼠PBMC和脑组织MBD2 mRNA水平降低(t =3.52和2.85,P<0.05)。结论 分次LDR可引起全基因组低甲基化,这种效应具有组织特异性,可能与DNMT1、MBD2的表达降低有关。     

辐射致癌危险模型及人群危险转移研究概况

对日本原子弹爆炸幸存者队列的流行病学研究,是各国进行辐射危害评价及赔偿的主要依据。依据流行病学数据建立模型,定量计算辐射危险,使该结果的应用更加明确。近年来随着日本原子弹爆炸幸存者队列数据资料的进一步搜集、方法学的不断完善,模型的研究也取得了新的进展。该文对迄今为止各个主要致力于辐射致癌研究的机构给出的辐射致癌模型及人群危险转移进行综述,简要介绍建立模型及转移时考虑的因素,以期为我国辐射致癌赔偿相关应用提供参照。     

基于随机森林的电离辐射诱导DNA双链断裂分类模型的构建与应用

目的 构建预测电离辐射诱导DNA双链断裂（DSB）水平的随机森林分类模型,初步研究DSB在基因组中的分布规律。方法 将GRCh38参考基因组分为50 kb的片段,根据MCF-7细胞的测序数据把片段分为电离辐射诱导的DSB低水平和高水平区域,以8种表观遗传学特征作为输入,随机将数据集的2/3列为训练集,1/3列为测试集,构建含100棵决策树的随机森林分类模型。分析分类模型中表观遗传学的特征重要性,展示这些标记在不同DSB水平区域的富集差异。结果 随机森林分类模型在测试集上预测的准确率为99.4%,精准率为98.9%,召回率为99.9%,受试者操作特征曲线下面积为0.994。8个特征中H3K36me3和DNase标记的重要性最高,富集分析表明DSB高水平区域的这两类标记明显高于DSB低水平区域。结论 以表观遗传学数据作为特征输入,随机森林分类模型可在50 kb基因组区域上准确预测电离辐射诱导的DSB水平,分析表明这些DSB可能主要分布在基因组中转录活跃的部位。     

DNA甲基化修饰与代谢相关疾病的关系及运动干预展望

<正>随着社会的发展和人民生活水平的不断提高,人们的饮食与生活习惯都发生了巨大的变化。伴随发生的是人群肥胖、高脂血症和2型糖尿病(T2DM)等代谢性疾病的发病率迅速上升且患病人群年轻化,严重威胁着人类的健康和生活质量[1]。最新研究显示,代谢性疾病的发生及发展不仅受遗传因素控制,还受环境因素导致的表观遗传修饰改变的影响。     

Effects of ionizing radiation on DNA methylation: from experimental biology to clinical applications

Purpose: Ionizing radiation (IR) is a ubiquitous environmental stressor with genotoxic and epigenotoxic capabilities. Terrestrial IR, predominantly a low-linear energy transfer (LET) radiation, is being widely utilized in medicine, as well as in multiple industrial applications. Additionally, an interest in understanding the effects of high-LET irradiation is emerging due to the potential of exposure during space missions and the growing utilization of high-LET radiation in medicine.

Conclusions: In this review, we summarize the current knowledge of the effects of IR on DNA methylation, a key epigenetic mechanism regulating the expression of genetic information. We discuss global, repetitive elements and gene-specific DNA methylation in light of exposure to high and low doses of high- or low-LET IR, fractionated IR exposure, and bystander effects. Finally, we describe the mechanisms of IR-induced alterations to DNA methylation and discuss ways in which that understanding can be applied clinically, including utilization of DNA methylation as a predictor of response to radiotherapy and in the manipulation of DNA methylation patterns for tumor radiosensitization.     

Radiation-induced molecular changes in rat mammary tissue: Possible implications for radiation-induced carcinogenesis

Purpose:?Ionizing radiation is a potent mammary gland carcinogen, yet the exact molecular etiology of radiation-induced breast cancer remains unknown.

Materials and methods:?Our study utilized a rat model of breast carcinogenesis to analyse the molecular and epigenetic changes induced in mammary gland tissue upon exposure to ionizing radiation (IR). Using a methylation-sensitive cytosine extension assay we studied the IR-induced changes in DNA methylation. In parallel, we analysed the expression of proteins involved in DNA methylation, DNA repair and cell proliferation control. Molecular changes were related to cellular proliferation and apoptosis.

Results:?We found that IR led to a loss of genomic cytosine methylation in the exposed mammary tissue. Global DNA hypomethylation was paralleled by reduction in the levels of maintenance (DNMT1) and de novo (DNMT3a and 3b) DNA methyltransferases and methyl-binding protein MeCP2. The observed DNA hypomethylation was linked, at least in part, to activation of DNA repair processes. Concurrently, we observed increased levels of phosphorylated extracellular signal-regulated kinase (p-ERK1/2), phosphorylated AKT kinase (p-AKT), cyclin D1 and proliferating cells nuclear antigen (PCNA) proteins, suggesting IR alters intra-cellular signaling and cell cycle control mechanisms in mammary tissue. We also noted a significant induction of apoptosis in the exposed tissue 6 hours after irradiation. The observed apoptosis levels were paralleled by the slight elevation of cellular proliferation.

Conclusions:?We have demonstrated that a single exposure to 5 Gy of X rays leads to noticeable epigenetic changes in the rat mammary gland that occurred in the context of activation of DNA damage repair and alterations in the pro-survival growth-stimulatory cellular signaling pathways. The possible cellular repercussions of the observed changes in relationship to breast carcinogenesis are discussed.     

LINE-1 DNA methylation: A potential forensic marker for discriminating monozygotic twins

Discriminating individuals within a pair of monozygotic (MZ) twins using genetic markers remains unresolved. This inability causes problems in criminal or paternity cases involving MZ twins as suspects or alleged fathers. Our previous study showed DNA methylation differences in interspersed repeat sequences such as Alu and LINE-1 within pairs of newborn MZ twins. To further evaluate the possible value of LINE-1 DNA methylation for discriminating MZ twins, this study investigated the LINE-1 DNA methylation of a large number of twins. We collected blood samples and buccal cell samples from 119 pairs of MZ and 57 pairs of dizygotic (DZ) twins. Genomic DNA was extracted and LINE-1 methylation level was detected using bisulfite pyrosequencing. The mean methylation level of the three CpG sites in the blood sample among the 176 unrelated individuals was 76.60% and 70.08% in buccal samples. This difference was significant, indicating the tissue specificity of LINE-1 DNA methylation. Among 119 pairs of MZ twins, 15 pairs could be discriminated according to the difference of CpG methylation level between them, which accounted for 12.61% of total number of MZ pairs. As for DZ twins, 10 pairs had significant differences between two individuals, which accounted for 17.54% of the total 57 DZ pairs. In conclusion, there are global DNA methylation differences within some healthy concordant monozygotic (MZ) twin pairs. LINE-1 DNA methylation might be a potential marker for helping to discriminate individuals within MZ twin pairs, and the tissue specificity must be considered in practice.     

Age determination through DNA methylation patterns in fingernails and toenails

Over the past decade, age prediction based on DNA methylation has become a vastly investigated topic; many age prediction models have been developed based on different DNAm markers and using various tissues. However, the potential of using nails to this end has not yet been explored. Their inherent resistance to decay and ease of sampling would offer an advantage in cases where post-mortem degradation poses challenges concerning sample collection and DNA-extraction. In the current study, clippings from both fingernails and toenails were collected from 108 living test subjects (age range: 0–96 years). The methylation status of 15 CpGs located in 4 previously established age-related markers (ASPA, EDARADD, PDE4C, ELOVL2) was investigated through pyrosequencing of bisulphite converted DNA. Significant dissimilarities in methylation levels were observed between all four limbs, hence both limb-specific age prediction models and prediction models combining multiple sampling locations were developed. When applied to their respective test sets, these models yielded a mean absolute deviation between predicted and chronological age ranging from 5.48 to 9.36 years when using ordinary least squares regression. In addition, the assay was tested on methylation data derived from 5 nail samples collected from deceased individuals, demonstrating its feasibility for application in post-mortem cases. In conclusion, this study provides the first proof that chronological age can be assessed through DNA methylation patterns in nails.     

Assessment of DNA methylation markers for forensic applications

ABSTRACT

DNA methylation displays promise in a variety of forensic applications, including chronological age estimation and identical twin differentiation. Knowledge of the age of a body fluid donor would offer intelligence information, as well as provide context to physical characteristic markers. Differentiation of identical twins would also be of considerable benefit as the DNA profile of identical twins cannot be distinguished when a correspondence between DNA profiles recovered from crime scene samples and a person is identified. Our research investigates and develops a methodology for DNA methylation analysis that could be implemented into forensic casework. Our results show that the differentiation of identical twins and chronological age prediction are both possible, with similar accuracies to other international research. Targeted multiplexing of bisulphite converted DNA in combination with massively parallel sequencing is demonstrated as a viable alternative to traditional methylation analysis techniques.     

Radiation-induced DNA Damage and Its Repair

Summary

Application of modern methods of organic chemistry and recombinant DNA technologies has provided new insights in the field of DNA radiation damage and its repair. An overview of the chemical nature of the lesions inflicted on DNA by ionizing radiation is presented. The structures of 29 different DNA modified base or sugar residues are shown in comprehensive formation schemes.

A fraction of radiation-induced modified bases is spontaneously released from the DNA chain during irradiation. Another part remains attached to the DNA chain backbone and for its characterization mild formic acid or enzymatic hydrolysis have been used. Starting from the chemical formulae of the altered base residues, the specific repair enzymes and their modes of action are discussed. Various glycosylases and endonucleases have been purified to homogeneity, and in some cases the gene which encodes the protein cloned. Using methods derived from Maxam and Gilbert sequencing procedures and DNA fragment ³²P-labelled at one end, it has been shown that the alkali—labile sites in DNA induced by radiation are strongly dependent on the DNA base sequence. Enzymatic methods have been used to analyse the DNA base defects produced by gamma-irradiation of cells under in vivo conditions. Structures of modified bases were the same as those observed when DNA was irradiated in aqueous solution.     

A forensic case study for body fluid identification using DNA methylation analysis

Recently, a method of identifying body fluids using DNA methylation has been developed (Frumkin et al., 2011). An existing multiplex assay using 9 CpG markers could differentiate 5 body fluids: semen, blood, saliva, menstrual blood, and vaginal fluid. To validate this technique, we evaluated the previously described body fluid identification method by means of single base extension (SBE). DNA methylation was applied to 22 samples in 18 forensic cases; seven of these were semen, three were blood, eight were saliva, three were vaginal fluid, and one was menstrual blood. Total of 18 samples were tested, the DNA methylation profiles were coincident from preliminary tests (acid phosphatase (AP), leucomalachite green (LMG, Sigma Aldrich, St Louis, MO, USA) and SALIgAE®) except one sample which displayed an all-negative result. After applying the DNA methylation method to forensic samples, we determined that it could be very useful for differentiating vaginal secretions from menstrual blood, for which there is no conventional preliminary testing method.     

Development of a forensically useful age prediction method based on DNA methylation analysis

Forensic DNA phenotyping needs to be supplemented with age prediction to become a relevant source of information on human appearance. Recent progress in analysis of the human methylome has enabled selection of multiple candidate loci showing linear correlation with chronological age. Practical application in forensic science depends on successful validation of these potential age predictors. In this study, eight DNA methylation candidate loci were analysed using convenient and reliable pyrosequencing technology. A total number of 41 CpG sites was investigated in 420 samples collected from men and women aged from 2 to 75 years. The study confirmed correlation of all the investigated markers with human age. The five most significantly correlated CpG sites in ELOVL2 on 6p24.2, C1orf132 on 1q32.2, TRIM59 on 3q25.33, KLF14 on 7q32.3 and FHL2 on 2q12.2 were chosen to build a prediction model. This restriction allowed the technical analysis to be simplified without lowering the prediction accuracy significantly. Model parameters for a discovery set of 300 samples were R² = 0.94 and the standard error of the estimate = 4.5 years. An independent set of 120 samples was used to test the model performance. Mean absolute deviation for this testing set was 3.9 years. The number of correct predictions ±5 years achieved a very high level of 86.7% in the age category 2–19 and gradually decreased to 50% in the age category 60–75. The prediction model was deterministic for individuals belonging to these two extreme age categories. The developed method was implemented in a freely available online age prediction calculator.     

DNA修复基因hOGG1的寡核苷酸多态性与癌症遗传易感性的关系

该文从基因结构、生物学功能和基因寡核苷酸多态性与疾病发生等方面探讨人源8-羟基鸟嘌呤DNA糖苷酶(hOGG1)基因在DNA损伤修复中的作用及其基因寡核苷酸多态性与癌症的遗传易感性的关系；综述hOGG1基因与癌症遗传易感性的分子流行病学研究；探讨hOGG1基因寡核苷酸多态性与辐射致癌的关系；指出hOGG1基因作为癌症易感人群诊断和预防标志物的价值.