A comparison of methylation levels in HPV18, HPV31 and HPV33 genomes reveals similar associations with cervical precancers

BackgroundHigh risk human papillomavirus (HR-HPV) infection is common and only a small minority of infections become persistent and lead to cervical cancers. Women positive for HR-HPV usually require a second test to avoid unnecessary colposcopies and over treatment. Elevated DNA methylation of HR-HPV L1 and L2 genes in high grade disease has emerged as a promising molecular triage tool.ObjectivesOur aim was to accurately measure methylation levels at selected CpG positions in the HPV18, HPV31 and HPV33 genomes. We focused on the L2, L1, URR and E6 regions because these were previously shown to be interesting areas for study.Study designPyrosequencing was used to measure methylation in 208 HPV18, 207 HPV31, and 126 HPV33 positive women selected from a London colposcopy referral population.ResultsAfter adjustment for multiple testing, at FDR 5%, elevated methylation was significantly associated with cervical intraepithelial neoplasia grades 2 or worse (CIN2+) in all investigated CpGs in HPV18 L2 and L1. Two of 6 L2 and 12 of 15 L1 sites in HPV31 and 6 of 8 L2 and 3 of 13 L1 sites in HPV33 showed significantly elevated methylation in CIN2+. Methylation of CpG sites in the URR and E6 region of the HPV types was low and most differences were not significant.ConclusionElevated methylation of CpG sites in the L1 and L2 regions of HPV18, HPV31 and HPV33 is associated with CIN2+ and a panel test may be useful for triage of women with HR-HPV infections.     

超重孕妇低生糖负荷膳食干预对新生儿DNA甲基化影响的探索性研究

目的通过对超重孕妇实施低血糖生成指数(GI)膳食的干预,探讨胎盘组织和脐血中与体重增长有关基因的甲基化的改变。 方法采用随机化单盲对照干预试验设计,研究对象为初次产检孕周≤12周且体重超重的孕妇。以研究对象纳入的顺序号为随机序列号,采用简单随机化的方法随机分为干预组和对照组。干预组在中国孕妇保健规范的基础上结合国家对孕妇的膳食和体力活动规范实施低GI膳食指导干预 ,对照组仅按照国家规范给予指导,不给予低GI膳食的指导。两组分别在孕早期、中期和晚期干预3次。 干预组和对照组各纳入25例。孕妇分娩时收集胎盘组织和脐血,提取DNA,采用Illumina甲基化芯片进行两步法全基因组甲基化测定。 结果孕妇孕期相关暴露因素在干预组与对照组差异无统计学意义;胎儿出生体重干预组高于对照组［（3.7±0.5） vs (3.5±0.4) kg］,但差异无统计学意义(P=0.248)。本研究结果结合生物信息数据库分析,筛选出19个基因位点,所属18个基因,其中5个基因位于1号染色体,2个基因位于7号染色体,其余基因分布分散。比较干预组与对照组甲基化的改变,发现脐血中2个差异的甲基化CpG位点,分别位于TEKT5和MIR378C基因上,胎盘组织中1个差异的甲基化CpG位点,所属PGBD5基因。 结论通过对超重孕妇采取低GI膳食干预,胎盘组织和脐血中基因的甲基化可以发生改变,为中国超重、肥胖孕妇疾病的预防提供新的方法,对子代的健康成长有重要的意义。     

Cancer-related changes and low-to-moderate exposure to welding fumes: A longitudinal study

ObjectiveThis study tested for an association between early cancer-related biomarkers and low-to-moderate exposure to fumes from welding mild steel.MethodsMale, non-smoking participants from southern Sweden were recruited and examined (N=338, 171 welders and 167 controls); of these, 78 welders and 96 controls were examined on two occasions six years apart. Exposure to welding fumes was evaluated by measuring respirable dust, welding years, and cumulative exposure. DNA methylation of CpG sites within the cancer-related genes AHRR, F2RL3, and B3GNTL1 was measured by pyrosequencing and relative mitochondrial DNA copy number and telomere length were measured by qPCR in whole-blood samples. Multivariate models were used for longitudinal analysis.ResultsMedian exposure to respirable dust was 0.7 mg/m³ at both timepoints, adjusted for use of personal protective equipment. Compared with controls, welders showed a significant decrease over time in DNA methylation of B3GNTL1 CpG1 and CpG4 [adjusted for age, body mass index, and smoking: β=-0.66, standard error (SE)=0.28; β=-0.48, SE=0.24, respectively]. In addition, exposure to respirable dust and cumulative exposure was associated with a decrease in methylation of F2RL3 CpG2 among all welders (adjusted β=-0.67, SE=0.23 and β=-0.03, SE=0.02, respectively). No significant associations were found for AHRR, mitochondrial DNA copy number, or telomere length.ConclusionLow-to-moderate exposure to welding fumes was associated with a small effect on selected early epigenetic biomarkers of cancer. The direction of the methylation pattern (lower methylation of specific CpG sites) indicates early lung cancer-related changes associated with mild steel welding.     

DNA甲基化年龄预测研究进展

衰老是生物体多个器官、组织和细胞功能下降的一个过程,与衰老相关的疾病会在衰老过程中逐渐出现,同时伴随着表观遗传学机制的变化。相关领域的研究也表明,表观遗传学机制的变化过程与生物学年龄的增长密切相关。随着全球老龄化现象的加剧,抗衰老逐渐成为一个备受关注的研究方向,然而衰老过程的表观遗传学表征、机理和定量分析方式仍然需要深入研究。该文对当前基于DNA甲基化的衰老与年龄预测的领域研究进展进行梳理,介绍表观遗传时钟、生物时钟和DNA甲基化的基本原理,以及相应表观遗传时钟的典型研究方法和有效样本资源,并深入讨论该领域研究存在的挑战及发展趋势,旨在为研究者提供全面的参考,促进抗衰老相关临床实践和大健康应用的发展。     

表遗传学与肿瘤

通常认为遗传学上的基因突变是肿瘤发病机制中的关键事件,尤其是抑癌基因的体细胞突变与肿瘤的发生有着密切的关系。但是,近年来随着对肿瘤认识的深入,人们发现DNA序列以外的调控机制异常在肿瘤的发生、发展过程中更为普遍,也更为重要。这种调控机制被称为表观遗传学（Epigenetics）,研究没有DNA序列变化的,可遗传的表达改变。例如基因启动子区CpG岛甲基化模式的异常与许多肿瘤的发生有着密切的关系。除了DNA甲基化调控形式外,表观遗传学还包括基因组印迹、染色质组蛋白修饰、隔离蛋白以及非编码RNA（包括microRNA）等DNA序列本身以外的各种调控方式。本文将就表观遗传学调控机制与肿瘤发生的关系作一简要综述。     

胃癌组织中PDCD4基因的表达和甲基化水平及其临床意义

目的 观察胃癌组织中抑癌基因PDCD4启动子区甲基化状态及其对PDCD4表达水平的影响并探讨其临床意义。方法 通过免疫组织化学、Western blot法检测胃癌组织中PDCD4蛋白的表达;RT-PCR法检测PDCD4 mRNA的表达;甲基化特异性PCR（MSP）法检测PDCD4启动子区甲基化水平。分析PDCD4表达水平以及启动子甲基化水平与胃癌患者临床病理特征之间的相关性。结果 胃癌组织中PDCD4蛋白及mRNA表达水平均显著降低（P<0.05）,甲基化作用显著增强（P<0.05）。PDCD4蛋白表达缺失与胃癌的分化、临床分期以及淋巴结转移密切相关（P<0.05）;PDCD4高甲基化与胃癌的淋巴结转移、临床分期密切相关（P<0.05）。PDCD4甲基化水平与PDCD4蛋白以及mRNA表达水平均呈负相关（P<0.05）。结论 胃癌组织中PDCD4表达水平显著降低,并与胃癌发展相关,启动子区高甲基化可能是PDCD4表达缺失的原因。     

肺癌miR-146a表达及其对细胞增殖、侵袭及迁移的影响

目的探讨微小RNA-146a(miR-146a)在肺癌组织和细胞中的表达和甲基化状态,及其对A549细胞增殖、侵袭、迁移的影响及可能机制。方法收集2018年1月至2019年4月在我院行根治性手术的非小细胞肺癌组织和对应癌旁组织,实时荧光定量PCR(QPCR)和甲基化特异性PCR(MSP)检测miR-146a的表达水平和甲基化状态,并分析甲基化状态与肺癌临床病理特征的关系。采用5-氮杂-2’-脱氧胞苷(5-AZA-2’-dC)处理A549细胞(处理组),MTT、Transwell实验和划痕实验检测处理组细胞增殖、侵袭和迁移活性。采用Western blotting检测Notch1和发状分裂相关增强子1(Hes-1)蛋白表达。结果肺癌组织和A549细胞中miR-146a表达量分别为0.63±0.28、0.85±0.11,均低于癌旁正常组织和BEAS-2B细胞(P<0.05)。MSP检测显示肺癌组织miR-146a甲基化率为62.5%(50/80),高于癌旁组织(P<0.05);miR-146a甲基化状态与肿瘤直径、TNM分期、淋巴结转移有关(P<0.05)。处理组细胞miR-146a表达水平为2.15±0.48,高于空白对照组(P<0.05);处理组细胞增殖、侵袭和迁移活性均低于空白对照组(P<0.05)。处理组Notch1蛋白和Hes-1蛋白表达水平分别为0.24±0.05和0.22±0.06,均低于空白对照组(P<0.05)。结论启动子异常甲基化导致在肺癌组织和细胞中miR-146a表达量降低,可能通过减弱对Notch1/Hes-1信号通路的抑制作用,促进肺癌细胞增殖、侵袭和转移,miR-146a有望成为肺癌新的生物治疗靶点。     

Aberrantly Methylated cfDNA in Body Fluids as a Promising Diagnostic Tool for Early Detection of Breast Cancer

Breast malignancies are the leading type of cancer among women. Its prevention and early detection, particularly in young women, remains challenging. To this end, cell-free DNA (cfDNA) detected in body fluids demonstrates great potential for early detection of tissue transformation and altered molecular setup, such as epigenetic profiles. Aberrantly methylated cfDNA in body fluids could therefore serve as a potential diagnostic and prognostic tool in breast cancer management. Abnormal methylation may lead to both an activation of oncogenes via hypomethylation and an inactivation of tumor suppressor genes by hypermethylation. We update the state of the art in the area of aberrant cfDNA methylation analyses as a diagnostic and prognostic tool in breast cancer, report on the main technological challenges, and provide an outlook for advancing the overall management of breast malignancies based on cfDNA as a target for diagnosis and tailored therapies.     

lncRNA MIR4435-2HG的表达水平及甲基化状态与脑胶质瘤病理分级的关系

目的 探讨长链非编码RNA MIR4435-2HG的表达水平及甲基化状态与脑胶质瘤病理分级的关系.方法 选取2019年1～12月手术切除的脑胶质瘤组织110例和颅脑损伤内减压术中切除正常脑组织20例(对照组).采用实时荧光定量PCR和甲基化特异性PCR检测组织和血清MIR4435-2HG水平及甲基化状态.结果 110例...