CpG island methylation in gastroenterologic neoplasia: a maturing field

Fifteen years after the first demonstration of epigenetic tumor-suppressor gene inactivation associated with promoter methylation, the field has reached a level of understanding that threatens a re-writing of established biologic concepts. In gastrointestinal malignancies, epigenetic analysis has led to novel hypotheses regarding the etiology of age-associated cancer susceptibility and the interactions between environmental exposures and neoplasia. Methylation profiling has uncovered a distinct pathway to colorectal neoplasia that may arise from a hitherto underestimated precursor lesion, the proximal hyperplastic polyp-serrated adenoma pathway. Epigenetic information has shown promise in clarifying susceptibility to cancer and defining poor prognosis groups in gastrointestinal cancers. Finally, the field has engendered renewed interest in therapeutic targeting of epigenetic regulatory molecules, and several such drugs are currently in clinical trials. It is likely that epigenetic pathways will be integrated in the routine management of gastrointestinal malignancies over the next decade.     

肝癌细胞p15基因CpG岛甲基化研究

目的通过检测肝癌细胞株HepG2的抑癌基因p15基因启动子区CpG岛的甲基化状态,探讨其与肿瘤发生的可能相关性。方法应用甲基化特异性PCR(MSP)技术,对人肝癌细胞株HepG2的p15基因启动子区域CpG岛的甲基化状态进行检测,以人淋巴瘤细胞株Raji为阳性对照,以正常人外周血单核细胞(PBMC)和肝细胞为阴性对照。结果肝癌细胞HepG2中p15基因启动子区域CpG岛甲基化和非甲基化检测均呈阳性,正常人外周血单核细胞和肝细胞甲基化检测阴性。结论肝癌细胞株HepG2抑癌基因p15基因CpG岛存在高度甲基化,可能与肝癌的发生相关。     

Quantitative profiling of CpG island methylation in human stool for colorectal cancer detection

Purpose

The aims of this study were to investigate the use of quantitative CGI methylation data from stool DNA to classify colon cancer patients and to relate stool CGI methylation levels to those found in corresponding tissue samples.

Methods

We applied a quantitative methylation-specific PCR assay to determine CGI methylation levels of six genes, previously shown to be aberrantly methylated during colorectal carcinogenesis. Assays were performed on DNA from biopsies of “normal” mucosa and stool samples from 57 patients classified as disease-free, adenoma, or cancer by endoscopy, and in tumour tissue from cancer patients. Additionally, CGI methylation was analysed in stool DNA from an asymptomatic population of individuals covering a broad age range (mean?=?47?±?24 years)

Results

CGI methylation levels in stool DNA were significantly higher than in DNA from macroscopically normal mucosa, and a significant correlation between stool and mucosa was observed for ESR1 only. Multivariate statistical analyses using the methylation levels of each CGI in stool DNA as a continuous variable revealed a highly significant (p?=?0.003) classification of cancer vs. non-cancer (adenoma + disease-free) patients (sensitivity?=?65 %, specificity?=?81 %).

Conclusion

CGI methylation profiling of stool DNA successfully identified patients with cancer despite the methylation status of CGIs in stool DNA not generally reflecting those in DNA from the colonic mucosa.     

核转录因子E2相关因子2启动子CpG岛甲基化对其蛋白表达及COPD的影响

核转录因子E2相关因子2 (nuclear factor erythroid-2-related factor 2,Nrf2)在人体氧化与抗氧化平衡过程中起了重要的作用.氧化与抗氧化失衡是COPD的重要发病机制之一.近来有研究发现 Nrf2启动子CpG岛甲基化能够影响 Nrf2蛋白的表达,从而影响抗氧化防御过程.明确 Nrf2启动子CpG岛甲基化与 Nrf2蛋白表达及COPD的关系,对今后临床上治疗 COPD寻找新途径具有重要意义.     

Transcriptional silencing of Dickkopf gene family by CpG island hypermethylation in human gastrointestinal cancer

AIM： To clarify alterations of Dickkopfs （Dkks） and Kremen2 （Krm2） in gastrointestinal cancer.
METHODS： We investigated the expression profiles and epigenetic alterations of Dkks and Krm2 genes in gastrointestinal cancer using RT-PCR, tissue microarray analysis, and methylation specific PCR （MSP）. Cancer cells were treated with the demethylating agent and/or histone deacetylase inhibitor. WST-8 assays and/n y/tro invasion assays after treatment with specific siRNA for those genes were performed.
RESULTS： Dkks and Krm2 expression levels were reduced in a certain subset of the gastrointestinal cancer cell lines and cancer tissues. This was correlated with promoter hypermethylation. There were significant correlations between Dkks over-expression levels and beta-catenin over-expression in colorectal cancer. In colorectal cancers with beta-catenin over-expression, Dkk-1 expression levels were significantly lower in those with lymph node metastases than in those without. Down-regulation of Dkks expression by siRNA resulted in a significant increase in cancer cell growth and invasiveness in vitro.
CONCLUSION： Down-regulation of the Dkks associated to promoter hypermethylation appears to be frequently involved in gastrointestinal tumorigenesis.     

人胃癌Runx3基因CpG岛甲基化的关键位点和演进

目的:研究人胃癌Runx3基因CpG岛甲基化的关键位点和演进.方法:应用MSP法和Western blot法分别检测26例人胃癌和相应的癌旁正常组织标本Runx3基因CpG岛从5'区向转录起始点方向连续6个位点的甲基化状态和Runx3蛋白的表达.结果:根据MSP的结果计算出上述连续6个位点的甲基化阳性率,结果随着向转录起始点方向的演进,各位点甲基化的阳性率逐渐降低,胃癌组和癌旁组从第3位点开始出现差异,至第5和第6位点差异显著(P＜0.05);按照胃癌分化程度分组,低分化组与高分化组在3-6位点差异显著(P＜0.05).胃癌组与癌旁组Runx3蛋白表达水平(0.499±0.106 vs 0.721±0.080)以及低分化组与高分化组(0.437±0.053 vs 0.617±0.073)Runx3蛋白表达水平均存在显著差异(P＜0.01).结论:人胃癌Runx3基因CpG岛的甲基化从5'区向转录起始点方向演进,甲基化的演进与肿瘤的分化程度有关;转录起始点部位可能为Runx3基因甲基化的关键位点.     

CpG island methylation as an early event during adenoma progression in carcinogenesis of sporadic colorectal cancer

BACKGROUND AND AIMS: CpG island methylation is present in various tumors, including colorectal carcinomas, and is thought to be an important mechanism in carcinogenesis. We evaluated the methylation status of primary colorectal tumors to determine its role in the adenoma to carcinoma sequence. METHODS: The methylation status of APC, THBS1, MGMT, hMLH1 and GSTP1, as determined by methylation specific PCR (MSP), and microsatellite instability (MSI) using three mononucleotide markers were assessed in 40 colorectal adenomas and 36 adenocarcinomas. The correlations of methylation status and MSI with the clinicopathologic parameters of the tumors were determined. RESULTS: Of the 40 adenomas, 24 (60%) were methylated at one or more loci, and 12 (30%) at two or more loci (CpG island methylation phenotype-high, CIMP-H). Of 36 carcinomas, 27 (75%) were methylated at one or more loci and 11 (30.5%) at two or more loci (CIMP-H). THBSI was the most frequently methylated locus in both adenomas (n = 19, 47.5%) and carcinomas (n = 16, 44.4%). Overall, methylation status of adenomas and carcinomas did not differ significantly (P = 0.53), nor did the methylation status of individual genes. For adenomas, size (P = 0.049) and histologic classification of the villous components (P = 0.018) were each associated with methylation status. For carcinomas, however, no clinicopathologic variable was related to methylation status. MSI was detected in three adenomas (7.5%) and five carcinomas (13.9%), and was closely correlated with hMLH1 methylation (P < 0.001). CONCLUSIONS: In colorectal tumors, CpG island methylation of tumor suppressor genes appears to be common and may be involved in the progression of adenomas.     

CpG island methylator phenotype (CIMP) of colorectal cancer is best characterised by quantitative DNA methylation analysis and prospective cohort studies

BACKGROUND: The concept of CpG island methylator phenotype (CIMP) is not universally accepted. Even if specific clinicopathological features have been associated with CIMP, investigators often failed to demonstrate a bimodal distribution of the number of methylated markers, which would suggest CIMP as a distinct subtype of colorectal cancer. Previous studies primarily used methylation specific polymerase chain reaction which might detect biologically insignificant low levels of methylation. AIM: To demonstrate a distinct genetic profile of CIMP colorectal cancer using quantitative DNA methylation analysis that can distinguish high from low levels of DNA methylation. MATERIALS AND METHODS: We developed quantitative real time polymerase chain reaction (MethyLight) assays and measured DNA methylation (percentage of methylated reference) of five carefully selected loci (promoters of CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 460 colorectal cancers from large prospective cohorts. RESULTS: There was a clear bimodal distribution of 80 microsatellite instability-high (MSI-H) tumours according to the number of methylated promoters, with no tumours showing 3/5 methylated loci. Thus we defined CIMP as having >or=4/5 methylated loci, and 17% (78) of the 460 tumours were classified as CIMP. CIMP was significantly associated with female sex, MSI, BRAF mutations, and wild-type KRAS. Both CIMP MSI-H tumours and CIMP microsatellite stable (MSS) tumours showed much higher frequencies of BRAF mutations (63% and 54%) than non-CIMP counterparts (non-CIMP MSI-H (0%, p<10(-5)) and non-CIMP MSS tumours (6.6%, p<10(-4)), respectively). CONCLUSION: CIMP is best characterised by quantitative DNA methylation analysis. CIMP is a distinct epigenotype of colorectal cancer and may be less frequent than previously reported.     

Molecular correlates with MGMT promoter methylation and silencing support CpG island methylator phenotype-low (CIMP-low) in colorectal cancer

Background

The CpG island methylator phenotype (CIMP or CIMP‐high) with widespread promoter methylation is a distinct epigenetic phenotype in colorectal cancer. In contrast, a phenotype with less widespread promoter methylation (CIMP‐low) has not been well characterised. O‐6‐methylguanine‐DNA methyltransferase (MGMT) promoter methylation and silencing have been associated with G>A mutations and microsatellite instability‐low (MSI‐low).

Aim

To examine molecular correlates with MGMT methylation/silencing in colorectal cancer.

Methods

Utilising MethyLight technology, we quantified DNA methylation in MGMT and eight other markers (a CIMP‐diagnostic panel; CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) in 920 population‐based colorectal cancers.

Results

Tumours with both MGMT methylation and loss were correlated positively with MSI‐low (p = 0.02), CIMP‐high (⩾6/8 methylated CIMP markers, p = 0.005), CIMP‐low (1/8–5/8 methylated CIMP markers, p = 0.002, compared to CIMP‐0 with 0/8 methylated markers), KRAS G>A mutation (p = 0.02), and inversely with 18q loss of heterozygosity (p = 0.0002). Tumours were classified into nine MSI/CIMP subtypes. Among the CIMP‐low group, tumours with both MGMT methylation and loss were far more frequent in MSI‐low tumours (67%, 12/18) than MSI‐high tumours (5.6%, 1/18; p = 0.0003) and microsatellite stable (MSS) tumours (33%, 52/160; p = 0.008). However, no such relationship was observed among the CIMP‐high or CIMP‐0 groups.

Conclusion

The relationship between MGMT methylation/silencing and MSI‐low is limited to only CIMP‐low tumours, supporting the suggestion that CIMP‐low in colorectal cancer may be a different molecular phenotype from CIMP‐high and CIMP‐0. Our data support a molecular difference between MSI‐low and MSS in colorectal cancer, and a possible link between CIMP‐low, MSI‐low, MGMT methylation/loss and KRAS mutation.     

EMs患者在位子宫内膜hMLH1蛋白表达变化及其基因启动子CpG岛甲基化观察

目的观察子宫内膜异位症（EM s）患者在位子宫内膜组织中hMLH1蛋白的表达变化及hMLH1基因启动子CpG岛甲基化情况。方法采用免疫组化法分别检测52例（Ⅰ、Ⅱ、Ⅲ、Ⅳ期分别为9、16、12、15例）EM s患者及30例健康志原者（对照组）在位子宫内膜中的hMLH1,采用甲基化特异性聚合酶链反应（MSP）法检测两组在位子宫内膜hMLH1启动子CpG岛甲基化情况。分离hMLH1启动子CpG岛甲基化异常者在位内膜中的腺细胞和间质细胞,采用MSP志愿分别检测两种细胞hMLH1启动子CpG岛甲基化情况。结果 EM s组中hMLH1蛋白表达减弱共6例,其中Ⅰ、Ⅱ、Ⅲ、Ⅳ期分别为0、0、1、5例,其余样本hMLH1蛋白表达均呈阳性;对照组30例无hMLH1蛋白表达减弱者,hMLH1蛋白表达均表现为阳性。EM s组中hMLH1启动子CpG岛部分甲基化3例,其中Ⅰ、Ⅱ、Ⅲ、Ⅳ期分别为0、0、0、3例,余均表现为非甲基化;对照组30例均表现为hMLH1启动子CpG岛非甲基化。EM s组Ⅳ期患者与Ⅰ、Ⅱ、Ⅲ期患者及对照组相比,P均〈0.05。3例hMLH1启动子CpG岛表现为部分甲基化者子宫内膜组织中hMLH1蛋白表达均减弱,其腺细胞中hMLH1启动子区表现为半甲基化,间质细胞hMLH1启动子区未见明显甲基化条带。结论 EM s患者在位子宫内膜组织中存在hMLH1表达减弱及hMLH1启动子CpG岛部分甲基化,主要集中在腺细胞,hMLH1异常与严重EM s的发病有关。     

CpG island methylation of the hTERT promoter is associated with lower telomerase activity in B-cell lymphocytic leukemia

OBJECTIVE: Expression of the catalytic subunit of the telomerase enzyme hTERT is essential for prolonging the replicative lifespan and is the rate-limiting step in cellular immortalization and carcinogenesis. Because hTERT expression is positively correlated with telomerase activity, its regulation is suggested as the major determinant of enzymatic activity. The hTERT promoter region contains two CpG islands, which are known to be target sites for de novo DNA methylation. To elucidate the impact of this epigenetic mechanism on telomerase activity, we analyzed the degree of hTERT promoter methylation in 30 patients with B-cell chronic lymphocytic leukemia. MATERIALS AND METHODS: hTERT promoter methylation was assessed using a methylation-specific competitive polymerase chain reaction assay. The assay is based on digestion of genomic DNA with a methylation-sensitive restriction enzyme before amplification with an internal standard. RESULTS: Patients exhibiting high telomerase activity showed significantly less methylation of the hTERT promoter core domain than patients with low enzyme activity. In addition, telomerase activity was significantly associated with telomere length and overall survival. CONCLUSIONS: Our data show that the degree of CpG island methylation of the hTERT promoter exhibits an impact on telomerase activity in a subgroup of patients with B-cell chronic lymphocytic leukemia and therefore is assumed to play a role in regulating hTERT gene expression in these patients.     

Isolation of DNA fragments associated with methylated CpG islands in human adenocarcinomas of the lung using a methylated DNA binding column and denaturing gradient gel electrophoresis

We have constructed a library of DNA fragments heavily methylated in human adenocarcinomas of the lung to permit the comprehensive isolation of methylated CpG islands in cancer. Heavily methylated genomic DNA fragments from tumors of nine male patients were enriched using a methylated DNA binding column and used for construction of the library. From this library, DNA fragments having properties of CpG islands were isolated on the basis of their reduced rate of strand dissociation during denaturing gradient gel electrophoresis. Approximately 1,000 clones, corresponding to 0.3% of the library were analyzed, and nine DNA fragments were identified as being associated with CpG islands that were methylated in tumor DNA. One CpG island was methylated specifically in tumor DNA, whereas the remaining eight CpG islands were methylated both in normal and tumor DNA derived from the same patients. Our results suggest that the number of CpG islands methylated specifically in tumors is not large. The library, which contains DNA fragments from methylated CpG islands comprehensively, is expected to be valuable when elucidating epigenetic processes involved in carcinogenesis.     

胰腺癌细胞系BxPC3及胰腺癌组织Ras相关区域家族1A启动子CpG岛的甲基化状态

目的 检测Ras相关区域家族1A(Ras association domain family 1A,RASSF1A)在胰腺癌细胞株BxPC3及胰腺癌组织中的甲基化状态,探讨其启动子异常甲基化在胰腺癌发病机制中的可能作用.方法 采用结合重亚硫酸盐的限制性内切酶法(combined bisulfite restriction analysis,COBRA)检测胰腺癌细胞株BxPC3、5例正常胰腺组织、13对胰腺癌及相应癌旁正常胰腺组织中RASSF1A启动子CpG岛的甲基化状态,计算其甲基化率.以甲基化酶抑制剂5-Aza-dC(5-Aza-2-deoxycitydine)处理BxPC3,观察处理前后甲基化率变化情况及RASSF1A mRNA表达变化.结果 在BxPC3细胞株中,RASSF1A启动子的CpG岛甲基化率为62.90%;正常胰腺、癌旁及癌组织中平均分别为9.14%、53.79%和55.82%.与正常胰腺组织相比,胰腺癌旁及癌组织的RASSF1A启动子甲基化率明显增高(P值<0.01),而癌旁及癌组织之间无明显差异(P>0.05).BxPC3经5-Aza-dC处理后,RASSF1A的CpG岛甲基化率显著下降至42.50%(P<0.05),同时RASSF1A mRNA表达增强.结论 RASSF1A启动子CpG岛异常甲基化是胰腺癌发生发展中的早期事件,可能参与胰腺癌的发病过程.     

Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer

BACKGROUND & AIMS: The concept of a CpG island methylator phenotype (CIMP), especially in microsatellite stable colon cancer, is not accepted universally. We therefore evaluated a large population-based sample of individuals with colon cancer and used univariate and multivariate analyses of CIMP with clinicopathologic variables and tumor mutations to determine the biologic relevance of this phenotype. METHODS: A total of 864 tumors from individuals with colon cancer from Utah and Northern California were evaluated by methylation-specific polymerase chain reaction of CpG islands in hMLH1, methylated in tumors (MINT) 1, MINT 2, MINT 31, and CDKN2A (p16). CIMP high was defined as methylation at 2 or more of these loci. The BRAF V600E mutation was determined by sequencing. Microsatellite instability had been determined previously. RESULTS: In a multivariate analysis of microsatellite stable tumors, CIMP high was related significantly to the V600E BRAF mutation (odds ratio, 39.52; 95% confidence interval, 11.44-136.56), KRAS2 mutations (odds ratio, 2.22; 95% confidence interval, 1.48-3.34), older age (P trend = .03), and increased stage (P trend = .03), and these tumors were less likely to be located in the distal colon (odds ratio, .42; 95% confidence interval, .27-.65). CIMP-high unstable tumors also were more likely to have the V600E BRAF mutation, be located proximally, and occur in older individuals (in univariate analyses). However, CIMP-high unstable tumors were significantly more likely than their stable counterparts to be KRAS2 wild type, TP53 wild type, poorly differentiated, proximally located, occur at lower stages, and have the BRAF V600E mutation (64.1% vs 17.6%). CONCLUSIONS: The evaluation of a large, population-based sample strongly supports the biologic relevance of CIMP in colon cancer. However, the presence or absence of microsatellite instability has a major effect on the expression of this phenotype.     

甲基化特异性聚合酶链反应检测粪便ppENK基因甲基化对胰腺癌诊断的可行性

目的 评价甲基化特异性聚合酶链反应(MSP)检测粪便ppENK基因高甲基化用于诊断胰腺癌的可行性.方法 收集胰腺癌患者24例和对照6例的新鲜粪便标本.采用MSP检测全部粪便标本中ppENK的甲基化状态;采用PCR检测全部粪便标本中野生型ppENK的阳性率.采用PCR-限制性片段长度多态性(RFLP)检测粪便K-ras的突变情况.将胰腺癌细胞PC3单细胞悬液加入同一健康者粪便标本,MSP法检测ppENK甲基化阳性,计算甲基化阳性时需掺入的胰腺癌细胞的最少数量.结果 30份粪便标本的甲基化检出率为0(0/30),非甲基化检出率为10％(3/30),野生型ppENK检出率为6.7％ (2/30);PCR-RFLP可检测出所选10份野生型ppENK阴性的胰腺癌标本中的8份,其中7份有K- ras第12位密码子突变.MSP方法能够检测到粪便中ppENK甲基化条带所需胰腺癌细胞的数量至少为50个/ml.结论 采用MSP方法检测胰腺癌患者粪便标本的ppENK基因甲基化状态,尚不能成为筛查和诊断胰腺癌的方法.