Left-Sided microsatellite unstable colorectal cancers show less frequent methylation of hMLH1 and CpG island methylator phenotype than right-sided ones

CONDENSED ABSTRACT: We compared the methylation status of several loci between right-sided and left-sided colorectal cancers (CRCs). To the best of our knowledge, this is the first to report that left-sided CRCs show significantly less frequent methylation at several loci and CpG island methylator phenotype (CIMP) than right-sided ones. BACKGROUND AND OBJECTIVES: MSI CRC occurs in 10-20% of unselected series of patients with CRC. Somatic hMLH1 promoter methylation is reported to cause MSI in sporadic cases. Many researchers report that MSI CRCs are more frequently located in the right-side colon than MSS CRCs. Though the number is very small, some MSI CRCs are located in the left-side colorectum. We focused on the existence of left-sided MSI CRCs and investigated whether they arise through hMLH1 methylation as they do in right-sided ones. METHODS: Thirty-eight sporadic MSI CRCs were included in the study. The methylation status of the promoter of hMLH1, p16, MINT1, 2 and 31 were examined and the proportions of methylated samples for each locus were compared. RESULTS: The left-sided group showed significantly less frequent methylation in hMLH1, p16, MINT1, 2 and 31. The frequency of CIMP+ samples in the left-sided group was significantly lower than the right-sided group. CONCLUSIONS: Left-sided MSI CRCs show significantly less frequent methylation of hMLH1. They also showed significantly less frequent occurrence of CIMP+ than right-sided ones. It is possible that left-sided MSI CRCs differ from the right-sided ones in the way of acquiring MSI.     

Prognostic implication of the CpG island methylator phenotype in colorectal cancers depends on tumour location

Background:

Colorectal cancer (CRC) is usually categorised as proximal or distal CRC. Recently, many researchers have tried to determine the molecular heterogeneity of CRCs along bowel subsites. However, the differential effects of the CpG island methylator phenotype (CIMP) and microsatellite instability (MSI) on the clinical outcome according to tumour location are not well-known.

Methods:

We analysed clinicopathologic and molecular characteristics, including CIMP, MSI, KRAS and BRAF mutations, in 734 CRCs according to bowel subsites. And the prognostic value of CIMP and MSI was analysed according to tumour location.

Results:

We found a linear increase of female predominance, T, N category, stage, differentiation, absence of luminal necrosis, tumour -infiltrating lymphocytes, Crohn''s-like lymphoid reaction, serration and mucin production from the rectum to caecum. CpG island methylator phenotype -high and MSI-high gradually increased from the rectum to caecum. CpG island methylator phenotype is a poor prognostic factor of overall survival (hazard ratio (HR): 4.13, 95% confidence interval (CI): 1.27–13.46) and disease-free survival (HR: 2.90, 95% CI: 1.04–8.08) in rectal cancers.

Conclusion:

Clinicopathologic and molecular profiles of CRCs gradually change along bowel subsites, and the prognostic implication of CIMP is different according to tumour location.     

APC gene methylation is inversely correlated with features of the CpG island methylator phenotype in colorectal cancer

The notion of a CpG island methylator phenotype (CIMP) was proposed to describe a subset of colorectal cancers (CRC) displaying frequent and concordant methylation of CpG islands located within gene promoter regions. Some workers have failed to observe associations between CIMP and specific clinicopathological features of CRC, possibly because of the choice of genes used to define this phenotype. The aim of the current study was to determine whether the aberrant methylation of 6 genes implicated in CRC development was associated with the same phenotypic features of this tumour type. The MethyLight assay was used to provide quantitative estimates of MLH1, P16, TIMP3, P14, DAPK and APC methylation levels in 199 unselected colorectal tumours. The methylation of MLH1, P16, TIMP3 and P14 was highly concordant (p < 0.0001 for each pair) but that of DAPK and APC was not. An inverse association was observed between the methylation of APC and TIMP3 (p = 0.004). Methylation of the MLH1, P16, TIMP3 and P14 genes was associated with tumour infiltrating lymphocytes (p < 0.05), microsatellite instability (p < 0.001), BRAF mutation (p < 0.0001) and elevated concentrations of the methyl group carriers tetrahydrofolate (THF) and 5,10-methylene THF (p < 0.05). In contrast, APC methylation was associated with wildtype BRAF (p = 0.003) and with lower concentrations of methyl group carriers (p < 0.05). These findings highlight the importance of gene selection in studies that aim to characterize the biological features and clinical behaviour of CIMP+ tumours.     

CpG island methylation status of miRNAs in esophageal squamous cell carcinoma

Previous studies on esophageal squamous cell carcinoma (ESCC) indicated that it contains much dysregulation of microRNAs (miRNAs). DNA hypermethylation in the miRNA 5' regulatory region is a mechanism that can account for the downregulation of miRNA in tumors (Esteller, N Engl J Med 2008;358:1148-59). Among those dysregulated miRNAs, miR-203, miR-34b/c, miR-424 and miR-129-2 are embedded in CpG islands, as is the promoter of miR-34a. We investigated their methylation status in ESCC by bisulfite sequencing PCR (BSP) and methylation specific PCR (MSP). The methylation frequency of miR-203 and miR-424 is the same in carcinoma and in the corresponding non-tumor tissues. The methylation ratio of miR-34a, miR-34b/c and miR-129-2 is 66.7% (36/54), 40.7% (22/54) and 96.3% (52/54), respectively in ESCC, which are significantly higher than that in the corresponding non-tumor tissues(p < 0.01). Quantitative RT-PCR analysis in clinical samples suggested that CpG island methylation is significantly correlated with their low expression in ESCC, 5-aza-2'-deoxycytidine (DAC) treatment partly recovered their expression in EC9706 cell line. We conclude that CpG island methylation of miR-34a, miR-34b/c and miR-129-2 are frequent events and important mechanism for their low expression in ESCC. DNA methylation changes have been reported to occur early in carcinogenesis and are potentially good early indicators of carcinoma (Laird, Nat Rev Cancer 2003;3:253-66). The high methylation ratio of miR-129-2 indicated its potential as a methylation biomarker in early diagnosis of ESCC.     

BRAF mutation, CpG island methylator phenotype and microsatellite instability occur more frequently and concordantly in mucinous than non-mucinous colorectal cancer

Mucinous colorectal cancer (CRC) has been reported to have distinct clinicopathological and genetic characteristics. However, the incidence and the relationship among microsatellite instability (MSI), CpG island methylator phenotype (CIMP) and BRAF and KRAS mutations in mucinous and non-mucinous CRC are not known. Activating mutations of BRAF and KRAS and their relationship with MSI and CIMP were examined in 83 sporadic CRC specimens (26 mucinous and 57 non-mucinous CRC). MSI, CIMP, BRAF and KRAS mutation were observed in 17, 24, 25 and 36% of the tumors, respectively. BRAF mutation was highly correlated with MSI (p < 0.001) and CIMP (p < 0.001). A higher incidence of MSI (27% vs. 12%), CIMP (38% vs. 18%, p < 0.05) and BRAF mutation (46% vs. 16%, p < 0.01) was observed in mucinous CRC. KRAS mutation (27% vs. 40%) was observed more frequently in non-mucinous CRC. Significantly higher percentages of mucinous CRC (54%, p < 0.05) had MSI or CIMP or BRAF mutations. Concordant occurrence of 2 or more of these alterations was observed in 39% of mucinous CRC and only 11% of non-mucinous CRC (p < 0.01). The more frequent occurrence and closer association among MSI, CIMP and BRAF mutation in mucinous CRC observed in our study further supports the idea that its pathogenesis may involve distinct genetic and epigenetic changes.     

应用CpG岛芯片技术分析人肝癌细胞株CpG岛甲基化差异基因

目的 在全基因组水平研究与肝细胞癌发生及转移相关的cpc岛甲基化谱型改变.方法 采用加拿大University Health Network芯片中心的12K人CpG岛芯片,对多系列人肝癌细胞株HepB、HepG2、PLC/RPF/5/RPF/5、SMMC-7721、BEL-7402、MHCC97-H、MHCC97-L、HCCLM3和HCCLM6进行全基因组CpG岛甲基化差异扫描,以Chang's liver细胞株为对照.其中MHCC97系列细胞株(MHCC97-H、HCCLM3、HCCLM6)均以低转移潜能细胞株MHCC97-L作为对照,筛选转移潜能相关差异基因.对数据进行归一化处理及聚类分析,筛选出具有甲基化差异的基因,并随机选取2个基因进行甲基化特异性PCR(MSP)验证.结果 以Cy5/cy3≥2或者≤0.5为差异显著性标准,筛选出9个肝癌细胞株中差异表达趋势一致的CpG岛差异甲摹化位点58个,其上下游肿瘤相关基因66个,包括抑癌基因及其配体基因、凋亡基因及抗凋亡基因、细胞增殖分化基因、细胞周期相关基因、细胞信号通路关键基因等.MHCC97系列高转移潜能细胞株MHCC97-H、HCCLM3和HCCLM6筛选出转移潜能相关CpG岛甲基化差异位点分别为16、13和6个,肿瘤相关基因分别为24、16和6个.MSP验证与芯片结果相符.结论 在肝癌的发生、发展过程中,存在一系列关键基因CpG岛甲基化改变.在肝癌细胞株中,抑癌基因及相关信号通路关键基因可能由于其启动子区CpG岛高甲基化而表达下调,而促癌基因及相关信号通路关键基因可能由于其启动子区CpG岛低甲基化而上调表达.     

Profiling CpG island field methylation in both morphologically normal and neoplastic human colonic mucosa

Aberrant CpG island (CGI) methylation occurs early in colorectal neoplasia. Quantitative methylation-specific PCR profiling applied to biopsies was used to quantify low levels of CGI methylation of 18 genes in the morphologically normal colonic mucosa of neoplasia-free subjects, adenomatous polyp patients, cancer patients and their tumours. Multivariate statistical analyses distinguished tumour from mucosa with a sensitivity of 78.9% and a specificity of 100% (P=3 x 10(-7)). In morphologically normal mucosa, age-dependent CGI methylation was observed for APC, AXIN2, DKK1, HPP1, N33, p16, SFRP1, SFRP2 and SFRP4 genes, and significant differences in CGI methylation levels were detected between groups. Multinomial logistic regression models based on the CGI methylation profiles from normal mucosa correctly identified 78.9% of cancer patients and 87.9% of non-cancer (neoplasia-free+polyp) patients (P=4.93 x 10(-7)) using APC, HPP1, p16, SFRP4, WIF1 and ESR1 methylation as the most informative variables. Similarly, CGI methylation of SFRP4, SFRP5 and WIF1 correctly identified 61.5% of polyp patients and 78.9% of neoplasia-free subjects (P=0.0167). The apparently normal mucosal field of patients presenting with neoplasia has evidently undergone significant epigenetic modification. Methylation of the genes selected by the models may play a role in the earliest stages of the development of colorectal neoplasia.     

DNA methylation patterns in adenomas from FAP, multiple adenoma and sporadic colorectal carcinoma patients

Colorectal adenomas have traditionally been regarded as homogeneous. The aim of our study was to identify molecular features that may differentiate sporadic adenomas from familial adenomas such as Familial Adenomatous Polyposis (FAP) and Multiple Adenoma patients. DNA methylation was tested at Methylated IN Tumor (MINT) loci (1,2,12,31) and the CpG promoter region of genes MLH1, HPP1, MGMT, p14ARF and p16INK4a in FAP-associated adenomas (33) from 5 patients with a known APC mutation (Group 1, FAP), adenomas (29) from 4 Multiple Adenoma patients (Group 2 Multiple), adenomas (14) from 3 patients with sporadic colorectal cancers showing high microsatellite instability (Group 3, MSI-H) and adenomas (16) from 7 patients, with sporadic colorectal cancers showing microsatellite stable or low level instability (Group 4, MSS/MSI-L). Aberrant Crypt Foci (ACFs), Hyperplastic Polyps (HPs) and cancers were also examined for methylation status as well as K-ras mutation. Multiple Adenoma patients were examined for germline polymorphisms in the base excision repair gene, MYH. The familial syndrome, FAP -associated adenomas showed a significantly low frequency of MINT methylation (15.5%,) compared to sporadic MSS/MSI-L-associated adenomas (35.5%). Group 3 (MSI-H) adenomas were different in that many showed serration and a high level of methylation (57.1%). Group 2, Multiple Adenoma cases, resembled sporadic MSS/MSI-L-associated adenomas. However the promoter regions of key genes, MGMT, p14ARF and p16INK4a were methylated to a greater extent than MINTs in both sporadic and familial adenomas. Genetic profiling of adenomas supports the concept that adenomas belonging to familial syndromes pursue a different pathway to tumorigenesis than their sporadic counterpar/ts from their earliest formation.     

Promoter methylation of Wnt5a is associated with microsatellite instability and BRAF V600E mutation in two large populations of colorectal cancer patients

Background:

In colorectal cancer (CRC), tumour microsatellite instability (MSI) status and CpG island methylator phenotype (CIMP) status are indicators of patient outcome, but the molecular events that give rise to these outcomes remain largely unknown. Wnt5a is a critical regulator of non-canonical Wnt activity and promoter hypermethylation of this gene has emerging prognostic roles in CRC; however the frequency and prognostic significance of this epigenetic event have not been explored in the context of colorectal tumour subtype. Consequently, we investigated the frequency and prognostic significance of Wnt5a methylation in a large cohort of MSI-stratified CRCs.

Methods:

Methylation was quantified in a large cohort of 1232 colorectal carcinomas from two clinically distinct populations from Canada. Associations were examined between methylation status and clinicopathlogical features, including tumour MSI status, BRAF V600E mutation, and patient survival.

Results:

In Ontario, Wnt5a methylation was strongly associated with MSI tumours after adjustment for age, sex, and tumour location (odds ratio (OR)=4.2, 95% confidence interval (CI)=2.4–7.4, P<10⁻⁶) and with BRAF V600E mutation, a marker of CIMP (OR=12.3, 95% CI=6.9–21.7, P<10⁻¹⁷), but was not associated with patient survival. Concordant results were obtained in Newfoundland.

Conclusion:

Methylation of Wnt5a is associated with distinct tumour subtypes, strengthening the evidence of an epigenetic-mediated Wnt bias in CRC.     

Distinct CpG island methylation profiles and BRAF mutation status in serrated and adenomatous colorectal polyps

A subset of colorectal cancers with CpG island methylator phenotype-high (CIMP-H) is frequently associated with MSI and BRAF V600E mutation. Since limited data are available on different histological types of colorectal polyps, we compared the pattern and the frequency of promoter methylation, CIMP-H, MSI, KRAS and BRAF V600E mutations and the relationship among these molecular parameters and the clinicopathologic characteristics in 110 serrated polyps (48 hyperplastic polyps, 32 sessile serrated adenomas and 30 serrated adenomas) and 32 tubular adenomas using 7 commonly used tumor-associated gene loci. No significant difference in the frequency of overall methylation frequency (86% vs. 100%) and CIMP-H (39% vs. 28%) between serrated polyps and tubular adenomas was observed, but proximally located serrated polyps showed more frequent methylation at 5 of 7 loci examined, and were more likely to be CIMP-H (62% vs. 22%). MGMT methylation was more common in tubular adenomas while MLH1 and HIC1 were more frequently methylated in serrated polyps. BRAF mutation was frequently present in all types of serrated polyps (80%), but was absent in tubular adenomas and was not associated with CIMP or MSI status. These results show comparable frequencies of promoter methylation of tumor-associated genes and CIMP-H, but distinct differences in gene-specific or colonic site-specific methylation profiles occur in serrated polyps and tubular adenomas. BRAF mutation occurs independently of CIMP and MSI in all types of serrated polyps and may serve as a marker of serrated pathway of colorectal carcinogenesis.     

四种肿瘤细胞p16基因CpG岛甲基化的检测

目的:检测4种肿瘤细胞系中p16基因CpG岛甲基化的状况。方法:利用甲基化特异性PCR(MSP)检测了4种肿瘤细胞(SPC-A1、BIU-87、T24、Hep-G2)的甲基化状况。结果:除BIU-87外,其它3种肿瘤细胞p16基因都有不同程度的甲基化。结论:p16基因CpG岛的甲基化与肿瘤的发生、发展关系密切。     

A distinct DNA methylation profile associated with microsatellite and chromosomal stable sporadic colorectal cancers

Aberrant DNA methylation, microsatellite instability (MSI) and chromosomal instability (CIN) are well-characterised molecular features of sporadic colorectal cancers (CRCs). In addition to CpG island methylator phenotype (CIMP) associated with MSI, an intermediate methylation subgroup is also a feature of non-MSI cancers. A large proportion of CRCs have no evidence of either MSI or CIN, here called Microsatellite and Chromosomal Stable (MACS), and require their methylation profile to be established. The clinical and molecular features of 170 sporadic CRC patients were investigated and stratified into MSI, CIN and MACS groups. MACS were most often found in the left colon and had a significantly lower BRAF mutation frequency (p < 0.001) compared with MSI. MACS had better survival [hazard ratio (HR) = 0.244, p = 0.017] compared with CIN, but were similar to MSI. The methylation status of 1,505 CpG loci from cancer-related genes was analysed in a subset of CRCs (n = 44 normal-tumour pairs) and compared with CIN, MSI and MACS status. Using two-way hierarchical clustering, three subgroups were identified, which associated with CIN, MSI and MACS status. Using significance analysis of microarray, 16 CpG loci demonstrating methylation changes associated with MACS were identified. A combination of six loci identified MACS with 81% sensitivity and 93% specificity. This result now requires independent validation. Hypomethylation of a CpG locus within the sonic hedgehog (SHH) promoter correlated with increased gene expression and was associated significantly with MACS cancers. In conclusion, we propose that MACS have distinct clinicopathological features and can be distinguished from other CRCs by a specific set of methylation loci.     

CpG岛甲基化表型及OPCML基因甲基化与肝细胞癌发生的关系

背景与目的：CpG岛甲基化表型（CpG island methylator phenotype,CIMP）涉及到多个基因启动子同时甲基化,具有肿瘤特异性,与多种肿瘤的发生或预后相关。但有关肝癌CPG岛甲基化表型的研究罕见报道。OPCML（opioid-binding protein／cell adhesion molecule—like）基因目前多为针对上皮性卵巢癌的研究．被认为是卵巢癌的候选抑癌基因。本研究旨在探讨CIMP及OPCML基因与肝癌的发生是否有关。方法：运用甲基化特异性PCR方法检测50例肝细胞癌组织及48例癌旁组织中OPCML、p15、SOCS-1、GST-P、RAR．b、p16、p73、p14、MGMT和hMLHl基因的甲基化状况。结果：肝癌组织甲基化率普遍比相应癌旁组织甲基化率高：OPCML（70．0％VS．64．6％）、p15（58．0％VS．50．0％）、SOCS-1（78．0％VS．50．0％）、GST—P（56．0％VS．27．1％）、RAR-b（30．0％vs．6．3％）、p16（26．0％vs．14．6％）、p73（16．0％vs．0％）、p14（36．0％vs．27．1％）、MGMT（16．0％vs．10．4％）和hMLH1（18．O％VS．4．2％）。SOCS-1,GST-p,RAR-b,p16和p73基因甲基化率在肝癌组与癌旁组差异有显著性（P〈0．05）,其它基因两组之间的甲基化率差异无显著性。CIMP阳性组（同时具有≥3个位点甲基化）复发时间较早,1年无瘤生存率为18．2％,而CIMP阴性组（具有〈3个位点甲基化）复发时间较晚,1年无瘤生存率为75．0％（P〈0．05）。结论：肝癌中存在着CpG岛甲基化表型（CIMP）。CIMP可作为肝癌患者预后判断的指标之一：OPCML基因甲基化可能在肝癌的发生中发挥重要的作用。     

基因启动子区甲基化与结直肠癌研究进展

近年来研究表明,表观遗传修饰的ＤＮＡ甲基化在结直肠癌的发生发展中具有重要的作用。在结直肠癌中普遍存在ＤＮＡ甲基化,对于肿瘤的早期诊断具有重要的指导意义。因为ＤＮＡ甲基化的可逆性,可能为肿瘤的治疗提供靶点。从ＤＮＡ甲基化方面寻找预测结直肠癌药物疗效的分子标志物,有可能成为推动结直肠癌个体化治疗的新方向。     

Effects of Helicobacter pylori infection on genetic instability,the aberrant CpG island methylation status and the cellular phenotype in Barrett's esophagus in a Japanese population

Genetic or epigenetic alterations in Barrett's esophagus (BE) with/without Helicobacter pylori (H. pylori) infection remain unclear. We examined the effects of H. pylori infection on genetic instability (GIN), the CpG island methylation status and a biomarker related to BE carcinogenesis. We analyzed 113 Japanese individuals with endoscopically suspected BE. The patients included, Group CLE (n = 25): no specialized intestinal metaplasia (SIM) in a columnar lined epithelium (control); Group BE (n = 88): all had SIM. Microsatellite instability and a loss of heterozygosity as GIN, the methylation status at hMLH1, E‐cadherin, p16 and APC, and immunoreactivity using a monoclonal antibody (mAb) Das‐1, which specifically reacts with BE, were evaluated. Nine additional patients with BE were prospectively followed up for 2 years after successful H. pylori eradication. The frequency of GIN, methylation at E‐cadherin and APC, and mAb Das‐1 reactivity in Group BE was significantly higher than that in Group CLE (p < 0.0001, p < 0.0001 and p < 0.005, and p < 0.0001, respectively). Furthermore, GIN, E‐cadherin methylation and mAb Das‐1 reactivity showed a significantly higher incidence in patients with H.pylori infection than in those without H. pylori infection (p < 0.01, p < 0.005, and p < 0.01, respectively). Interestingly, the patients from Group BE were observed to change to a stable state of molecular alterations in 60% for GIN, 42.9% for E‐cadherin methylation and 55.6% for APC methylation, or a reduction of mAb Das‐1 reactivity was noted in 25% following eradication. H. pylori infection may therefore affect these molecular alterations associated with the pathogenesis of BE, to some degree, in the Japanese population. © 2008 Wiley‐Liss, Inc.     

CpG island methylator phenotype (CIMP) in cancer: causes and implications

Strong evidence exists for a subgroup of tumours, from a variety of tissue types, exhibiting concordant tumour specific DNA methylation: the "CpG island methylator phenotype" (CIMP). Occurrence of CIMP is associated with a range of genetic and environmental factors, although the molecular causes are not well-understood. Both increased expression and aberrant targeting of DNA methyltransferases (DNMTs) could contribute to the occurrence of CIMP. One under-explored area is the possibility that DNA damage may induce or select for CIMP during carcinogenesis or treatment of tumours with chemotherapy. DNA damaging agents can induce DNA damage at guanine rich regions throughout the genome, including CpG islands. This DNA damage can result in stalled DNA synthesis, which will lead to localised increased DNMT1 concentration and therefore potentially increased DNA methylation at these sites. Chemotherapy can select for cells which have increased tolerance to DNA damage due to increased lesion bypass, in some cases by mechanisms which involve inactivation of genes by CpG island methylation. CIMP has been associated with worse patient prognosis, probably due to increased epigenetic plasticity. Therefore, further clinical testing of the diagnostic and prognostic value of the current CIMP markers, as well as increasing our understanding of the molecular causes underlying CIMP are required.