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Genetics supersedes epigenetics in colon cancer phenotype
Abstract
A CpG island DNA methylator phenotype has been postulated to explain silencing of the hMLH1 DNA mismatch repair gene in cancer of the microsatellite mutator phenotype. To evaluate this model, we analyzed methylation in CpG islands from six mutator and suppressor genes, and thirty random genomic sites, in a panel of colorectal cancers. Tumor-specific somatic hypermethylation was a widespread age-dependent process that followed a normal Gaussian distribution. Because there was no discontinuity in methylation rate, our results challenge the methylator phenotype hypothesis and its hypothetical pathological underlying defect. We also show that the mutator phenotype dominates over the gradual accumulation of DNA hypermethylation in determining the genotypic features that govern the phenotypic peculiarities of colon cancer of the mutator pathway.
... I 2 = 78.7%)] [24,41,44,53,55,62,64,69,74,78,83,100,105,113,[119][120][121][122][123] and KRAS mutation [OR = 0.71 (95% CI = 0.55-0.93, I 2 = 81%)] [16,19,21,[23][24][25][26]31,33,[37][38][39][40]43,47,48,52,53,55,59,60,62,67,[69][70][71][72]74,[76][77][78]83,84,105,107,110,111,113,121,124,125]. ...
... [24,41,44,53,55,62,64,69,74,78,83,100,105,113,[119][120][121][122][123] and KRAS mutation [OR = 0.71 (95% CI = 0.55-0.93, I 2 = 81%)] [16,19,21,[23][24][25][26]31,33,[37][38][39][40]43,47,48,52,53,55,59,60,62,67,[69][70][71][72]74,[76][77][78]83,84,105,107,110,111,113,121,124,125]. No associations were observed with APC mutation [OR = 0.56 (95% CI = 0.16-1.84, ...
... We also confirmed previously reported association of CIMP-H with microsatellite instability (MSI-H) status [OR = 10.95 (95% CI = 8.49-14.13, I 2 = 83%)] among CRC patients [16,17,19,20,23,25,28,33,34,36,[38][39][40][41]43,44,47,48,50,55,[58][59][60][64][65][66][67][68]70,72,74,77,[80][81][82]84,95,107,[109][110][111][112][127][128][129][130][131][132][133][134][135][136][137][138]. Finally, we also observed a positive association of CIMP-H tumors with presence of high levels of fusobacterium nucleatum [OR = 2.99 (95% CI = 2.01-4.43, ...
Background:
CpG island methylator phenotype (CIMP) tumors, comprising 20% of colorectal cancers, are associated with female sex, age, right-sided location, and BRAF mutations. However, other factors potentially associated with CIMP have not been robustly examined. This meta-analysis provides a comprehensive assessment of the clinical, pathologic, and molecular characteristics that define CIMP tumors.
Methods:
We conducted a comprehensive search of the literature from January 1999 through April 2018 and identified 122 articles, on which comprehensive data abstraction was performed on the clinical, pathologic, molecular, and mutational characteristics of CIMP subgroups, classified based on the extent of DNA methylation of tumor suppressor genes assessed using a variety of laboratory methods. Associations of CIMP with outcome parameters were estimated using pooled odds ratio or standardized mean differences using random-effects model.
Results:
We confirmed prior associations including female sex, older age, right-sided tumor location, poor differentiation, and microsatellite instability. In addition to the recognized association with BRAF mutations, CIMP was also associated with PIK3CA mutations and lack of mutations in KRAS and TP53. Evidence of an activated immune response was seen with high rates of tumor-infiltrating lymphocytes (but not peritumoral lymphocytes), Crohn-like infiltrates, and infiltration with Fusobacterium nucleatum bacteria. Additionally, CIMP tumors were associated with advance T-stage and presence of perineural and lymphovascular invasion.
Conclusion:
The meta-analysis highlights key features distinguishing CIMP in colorectal cancer, including molecular characteristics of an active immune response. Improved understanding of this unique molecular subtype of colorectal cancer may provide insights into prevention and treatment.
... In this chapter we describe the MS-AFLP array [1,2], a microarraybased methodology to analyze changes in DNA methylation patterns in human samples. This platform is based on the methylationsensitive amplified length polymorphism technique (MS-AFLP) [3,4], previously employed to study somatic DNA methylation alterations in human cancers [5,6]. ...
... Any hit with more than 90% identity over 50 bp was considered positive. According to this criterion, most of the NotI sites are in unique sequences or in low-repetitive sequences MS-AFLP we showed the lack of evidence for a methylator phenotype when focusing on hypermethylation alterations [5], and the association between DNA hypomethylation changes with aging and genomic damage [6]. ...
... Thanks to its ability to detect both hypermethylation and hypomethylation alterations, MS-AFLP was instrumental to discover that these two types of alterations correlated between them, accumulated in a gradual fashion [5,6], and correlated with patient age in gastrointestinal cancers [6]. These findings strongly suggested that the many of the DNA methylation alterations detected in tumors actually took place in the cancer cell-of-origin during normal aging and before, or shortly after its clonal expansion [6]. ...
Somatic, and in a minor scale also germ line, epigenetic aberrations are fundamental to carcinogenesis, cancer progression, and tumor phenotype. DNA methylation is the most extensively studied and arguably the best understood epigenetic mechanisms that become altered in cancer. Both somatic loss of methylation (hypomethylation) and gain of methylation (hypermethylation) are found in the genome of malignant cells. In general, the cancer cell epigenome is globally hypomethylated, while some regions-typically gene-associated CpG islands-become hypermethylated. Given the profound impact that DNA methylation exerts on the transcriptional profile and genomic stability of cancer cells, its characterization is essential to fully understand the complexity of cancer biology, improve tumor classification, and ultimately advance cancer patient management and treatment. A plethora of methods have been devised to analyze and quantify DNA methylation alterations. Several of the early-developed methods relied on the use of methylation-sensitive restriction enzymes, whose activity depends on the methylation status of their recognition sequences. Among these techniques, methylation-sensitive amplification length polymorphism (MS-AFLP) was developed in the early 2000s, and successfully adapted from its original gel electrophoresis fingerprinting format to a microarray format that notably increased its throughput and allowed the quantification of the methylation changes. This array-based platform interrogates over 9500 independent loci putatively amplified by the MS-AFLP technique, corresponding to the NotI sites mapped throughout the human genome.
... According to this model, MAFG activation would lead to a higher rate of methylation of its target genes, including hMLH1. Once hMLH1 is epigenetically silenced, the MSI mutator phenotype is triggered ultimately driving cancer genotype and phenotype (Yamashita et al., 2003). ...
... A particular consideration is targeting methylation in tumors with epigenetic silencing of hMLH1 (encompassing most of the CIMP-high CRCs). Once unleashed the mutator phenotype, numerous mutations accumulate in MSI-target cancer genes largely dictating tumor phenotype (Yamashita et al., 2003). Re-expression of hMLH1 will not correct the mutations already present in cancer driver genes, but nevertheless it might be beneficial because it could increase sensitivity to cytotoxic V. Vymetalkova, et al. ...
Colorectal carcinogenesis is a multistep process involving the accumulation of genetic alterations over time that ultimately leads to disease progression and metastasis. Binding of transcription factors to gene promoter regions alone cannot explain the complex regulation pattern of gene expression during this process. It is the chromatin structure that allows for a high grade of regulatory flexibility for gene expression. Posttranslational modifications on histone proteins such as acetylation, methylation, or phosphorylation determine the accessibility of transcription factors to DNA. DNA methylation, a chemical modification of DNA that modulates chromatin structure and gene transcription acts in concert with these chromatin conformation alterations. Another epigenetic mechanism regulating gene expression is represented by small non-coding RNAs. Only very recently epigenetic alterations have been included in molecular subtype classification of colorectal cancer (CRC). In this chapter, we will provide examples of the different epigenetic players, focus on their role for epithelial-mesenchymal transition and metastatic processes and discuss their prognostic value in CRC.
... Methylation of the DNA mismatch repair gene, MLH1, had previously been determined to lead to MSI [3], and CIMP correlated with the presence of MSI as well as proximal cancer location [46]. However, it was observed that methylation events accumulated more across a progressive continuum that may have been more related to age-dependent changes [48]. In addition, corresponding clinical and molecular parameters were found to be more attributable to the mutator or MSI phenotype rather than an epigenetic phenotype [48,49]. ...
... However, it was observed that methylation events accumulated more across a progressive continuum that may have been more related to age-dependent changes [48]. In addition, corresponding clinical and molecular parameters were found to be more attributable to the mutator or MSI phenotype rather than an epigenetic phenotype [48,49]. A subsequent panel of methylated markers devised from interrogating almost 200 CpG sites across 300 colorectal cancers and using a sensitively quantitative MethyLight technology was able to detect a bimodal distribution of the methylator phenotype which was specific for BRAF-mutated cancers reliably segregating with CIMP-high [50]. ...
The BRAF oncogene is an integral component of the MAP kinase pathway, and an activating V600E mutation occurs in 15% of sporadic colorectal cancer. This is an early event in serrated pathway tumourigenesis, and the BRAF V600E has been commonly associated with the CpG island methylator phenotype, microsatellite instability (MSI), and a consistent clinical presentation including a proximal location and predilection for elderly females. A proportion of the BRAF mutant lesions remain as microsatellite stable (MSS), and in contrast to the MSI cancers, they have an aggressive phenotype and correlate with poor patient outcomes. Recent studies have found that they have clinical and molecular features of both the BRAF mutant/MSI and the conventional BRAF wild-type cancers and comprise a distinct colorectal cancer subgroup. This review highlights the importance of the BRAF mutation occurring in colorectal cancer stratified for molecular background and discusses its prognostic and clinical significance.
... They also demonstrated that this loss of methylation was combined by hypermethylation and inactivation of tumor suppressor or DNA repair genes [21] . This epigenetic modification has recently been associated with the normal mucosaaberrant crypt focus (ACF)-adenoma-carcinoma sequence, playing an important role in CRC development [22] . Consequently, DNA methylation appears to be one of the cornerstones of carcinogenesis because it occurs at the first steps of CRC process; involves CIMP pathway with MSI, as hypermethylation of MMR genes results in MSI sporadic CRC; through CIMP, it has been linked with CIN in colon malignancy (promoter methylation of GATA4, GATA5, p16 resulted in chromosomal loss or gain); and finally it is implicated in each of these paths through many abnormally methylated genes as recently studies have revealed [23][24][25][26][27][28] (Figure 2). ...
... As it has been already highlighted, the critical role of abnormal DNA methylation to specific steps in the CRC carcinogenesis has been expressed since 1983 from Feinberg and Vogelstein [20] . Since then and during the recent years, many studies have revealed that this epigenetic modification has been associated with the normal mucosa-ACF-adenoma-carcinoma sequence, playing an important role in CRC development, mainly, at early stages [22][23][24][25][26][27] . It is known that during DNA methylation, DNA methyl transferases (DNMTS) catalyze the addition of a methyl group (CH3) to the fifth carbon position on cytosines within CpG dinucleotides. ...
Colorectal cancer (CRC) is one of the most prevalent malignancies in the world. CRC-associated morbidity and mortality is continuously increasing, in part due to a lack of early detection. The existing screening tools such as colonoscopy, are invasive and yet high cost, affecting the willingness of patients to participate in screening programs. In recent years, evidence is accumulating that the interaction of aberrant genetic and epigenetic modifications is the cornerstone for the CRC development and progression by alternating the function of tumor suppressor genes, DNA repair genes and oncogenes of colonic cells. Apart from the understanding of the underlying mechanism(s) of carcinogenesis, the aforementioned interaction has also allowed identification of clinical biomarkers, especially epigenetic, for the early detection and prognosis of cancer patients. One of the ways to detect these epigenetic biomarkers is the cell-free circulating DNA (circDNA), a blood-based cancer diagnostic test, mainly focusing in the molecular alterations found in tumor cells, such as DNA mutations and DNA methylation. In this brief review, we epitomize the current knowledge on the research in circDNA biomarkers - mainly focusing on DNA methylation - as potential blood-based tests for early detection of colorectal cancer and the challenges for validation and globally implementation of this emergent technology.
... An even weaker correlation was observed if the indices were computed by restricting to loci with only significant Z scores ("Materials and methods"; Figure S2 in Additional file 1). The lack of a strong correlation between the two DNAm indices, across so many cancer types, is consistent with studies suggesting that cancer hyper-and hypomethylation constitute independent processes in tumor progression [41][42][43]. ...
... Thus, local correlations between these indices should translate to some level of correlation at the global scale. However, the relatively low R 2 values also suggest that cancer hyper-and hypomethylation constitute independent processes in tumor progression, consistent with other reports [41][42][43]. We can reconcile all of these observations by noting that most studies did not consider the degree of quantitative change across different tumors. ...
One of the most important recent findings in cancer genomics is the identification of novel driver mutations which often target genes that regulate genome-wide chromatin and DNA methylation marks. Little is known, however, as to whether these genes exhibit patterns of epigenomic deregulation that transcend cancer types.
Here we conduct an integrative pan-cancer-wide analysis of matched RNA-Seq and DNA methylation data across ten different cancer types. We identify seven tumor suppressor and eleven oncogenic epigenetic enzymes which display patterns of deregulation and association with genome-wide cancer DNA methylation patterns, which are largely independent of cancer type. In doing so, we provide evidence that genome-wide cancer hyper- and hypo- DNA methylation patterns are independent processes, controlled by distinct sets of epigenetic enzyme genes. Using causal network modeling, we predict a number of candidate drivers of cancer DNA hypermethylation and hypomethylation. Finally, we show that the genomic loci whose DNA methylation levels associate most strongly with expression of these putative drivers are highly consistent across cancer types.
This study demonstrates that there exist universal patterns of epigenomic deregulation that transcend cancer types, and that intra-tumor levels of genome-wide DNA hypomethylation and hypermethylation are controlled by distinct processes.
... We also did not find the reported correlations between hypermethylation and right localization, MSI and K-ras mutations (22,24,25). The significance of this classification should be revised under the light of recent studies (26,27), whose conclusions are supported by our results. ...
... Besides these evidences, the relationship between genome-wide hypomethylation and chromosomal instability has not been addressed form a quantitative point of view. This is critical taking into account the wide variation in the levels of the cumulated genetic (14)(15)(16)(17)(18) and epigenetic (19) (reviewed in (24)(25)(26)). Analysis of MSI was performed as previously described (27). ...
... In other words, tumor-specific aberrant methylation in promoter CGIs may assemble itself in CIMP-H and randomly occur in remaining CRCs. Although this bimodal distribution in tumors has been demonstrated using several gene marker panels (5,14), Yamashita et al (20) doubted the presence of CIMP, claiming that tumor-specific somatic hypermethylation of six genes (MLH1, p16, p14, MGMT, APC and CDH1) was an age-dependent feature and that the distribution of the number of tumors harboring their markers was normal (20). This inconsistency could have been due to the different marker panels used in each study. ...
... In other words, tumor-specific aberrant methylation in promoter CGIs may assemble itself in CIMP-H and randomly occur in remaining CRCs. Although this bimodal distribution in tumors has been demonstrated using several gene marker panels (5,14), Yamashita et al (20) doubted the presence of CIMP, claiming that tumor-specific somatic hypermethylation of six genes (MLH1, p16, p14, MGMT, APC and CDH1) was an age-dependent feature and that the distribution of the number of tumors harboring their markers was normal (20). This inconsistency could have been due to the different marker panels used in each study. ...
A subset of colorectal cancers (CRCs) harbor the CpG island methylator phenotype (CIMP), with concurrent multiple promoter hypermethylation of tumor-related genes. A serrated pathway in which CIMP is developed from serrated polyps is proposed. The present study characterized CIMP and morphologically examined precursor lesions of CIMP. In total, 104 CRCs treated between January 1996 and December 2004 were examined. Aberrant promoter methylation of 15 cancer-related genes was analyzed. CIMP status was classified according to the number of methylated genes and was correlated with the clinicopathological features, including the concomitant polyps in and around the tumors. The frequency of aberrant methylation in each CRC showed a bimodal pattern, and the CRCs were classified as CIMP-high (CIMP-H), CIMP-low (CIMP-L) and CIMP-negative (CIMP-N). CIMP-H was associated with aberrant methylation of MLH1 (P=0.005) and with an improved recurrence-free survival (RFS) rate following curative resection compared with CIMP-L/N (five-year RFS rate, 93.8 vs. 67.1%; P=0.044), while CIMP-N tumors were associated with frequent distant metastases at diagnosis (P=0.023). No concomitant serrated lesions were present in the tumors, whereas conventional adenoma was contiguous with 11 (10.6%) of 104 CRCs, including four CIMP-H CRCs. CIMP-H was classified in CRCs by a novel CIMP marker panel and the presence of concomitant tumors revealed that certain CIMP-H CRCs may have arisen from conventional adenomas.
... The CIMP hypothesis has been questioned by several groups who found that CRCs could not be clearly categorized into CIMP-positive and CIMP-negative groups [38,39]. Yamashita et al. reported that the numbers of methylated CGIs vary discontinuously from the high-methylation group to the low-methylation group, which is in sharp contrast to the bimodal distribution of microsatellite mutations found in MSI and microsatellite stable (MSS) cancers [38]. ...
... The CIMP hypothesis has been questioned by several groups who found that CRCs could not be clearly categorized into CIMP-positive and CIMP-negative groups [38,39]. Yamashita et al. reported that the numbers of methylated CGIs vary discontinuously from the high-methylation group to the low-methylation group, which is in sharp contrast to the bimodal distribution of microsatellite mutations found in MSI and microsatellite stable (MSS) cancers [38]. They also showed that many of the hypermethylation events are age-dependent and concluded that the mutator phenotype is dominant with respect to the methylator phenotype. ...
Cancers exhibiting the CpG island methylator phenotype (CIMP) are found among a wide variety of human malignancies and represent a subclass of tumors showing concurrent hypermethylation of multiple CpG islands. These CIMP-positive tumors often exhibit characteristic molecular and clinicopathological features, suggesting CIMP represents a distinct carcinogenic pathway. However, marker genes to define CIMP have been largely inconsistent among studies, which has caused results to vary. Nonetheless, recent advances in genome-wide methylation analysis have enabled the existence of CIMP to be confirmed, and large-scale cancer genome analyses have begun to unravel the previously unknown molecular basis of CIMP tumors. CIMP is strongly associated with clinical outcome, suggesting it may be a predictive biomarker.
... Some investigators conferred distinctive phenotypic and biological properties to the tumors displaying a socalled CpG island methylator phenotype (CIMP), which was viewed as preceding the development of a subset of MSI colon cancers [18,19]. However, no apparent bimodal distribution was seen for the somatic hypermethylation alterations in gastrointestinal cancers [20,21] thus challenging the CIMP hypothesis. Nearly 15 years later, the CIMP concept, despite the publication of many CIMP papers (reviewed in [22]) still awaits for a clear definition, including a stable set of CIMP markers, as well as for identification of the underlying methylator gene(s) [22,23]. ...
... Comparing the intensity of the fingerprint bands from normal and tumor tissue DNA provided an unbiased insight of the complex picture of those epigenetic alterations. Employing this technique for the study of colorectal cancer we demonstrated that the MSI phenotype was dominant over hypermethylation [21] and that some of the tumors without MSI could be rationalized by an age-associated accumulation of DNA hypomethylation [23]. ...
Background
Recent work led to recognize sessile serrated adenomas (SSA) as precursor to many of the sporadic colorectal cancers with microsatellite instability (MSI). However, comprehensive analyses of DNA methylation in SSA and MSI cancer have not been conducted.
Methods
With an array-based methylation sensitive amplified fragment length polymorphism (MS-AFLP) method we analyzed 8 tubular (TA) and 19 serrated (SSA) adenomas, and 14 carcinomas with (MSI) and 12 without (MSS) microsatellite instability. MS-AFLP array can survey relative differences in methylation between normal and tumor tissues of 9,654 DNA fragments containing all NotI sequences in the human genome.
Results
Unsupervised clustering analysis of the genome-wide hypermethylation alterations revealed no major differences between or within these groups of benign and malignant tumors regardless of their location in intergenic, intragenic, promoter, or 3′ end regions. Hypomethylation was less frequent in SSAs compared with MSI or MSS carcinomas. Analysis of variance of DNA methylation between these four subgroups identified 56 probes differentially altered. The hierarchical tree of this subset of probes revealed two distinct clusters: Group 1, mostly composed by TAs and MSS cancers with KRAS mutations; and Group 2 with BRAF mutations, which consisted of cancers with MSI and MLH1 methylation (Group 2A), and SSAs without MLH1 methylation (Group 2B). AXIN2, which cooperates with APC and β-catenin in Wnt signaling, had more methylation alterations in Group 2, and its expression levels negatively correlated with methylation determined by bisulfite sequencing. Within group 2B, low and high AXIN2 expression levels correlated significantly with differences in size (P = 0.01) location (P = 0.05) and crypt architecture (P = 0.01).
Conclusions
Somatic methylation alterations of AXIN2, associated with changes in its expression, stratify SSAs according to some clinico-pathological differences. We conclude that hypermethylation of MLH1, when occurs in an adenoma cell with BRAF oncogenic mutational activation, drives the pathway for MSI cancer by providing the cells with a mutator phenotype. AXIN2 inactivation may contribute to this tumorigenic pathway either by mutator phenotype driven frameshift mutations or by epigenetic deregulation contemporary with the unfolding of the mutator phenotype.
... DNA methylation ensures the precise regulation of gene expression [17]. Hyper-and hypomethylation are relatively independent processes in the cancer genome and in tumor progression [18,19]. Hypermethylated CpG islands in tumors are frequently located in gene promoter regions, in contrast to the overall hypomethylated regions. ...
Epigenetic dysregulation is a common feature of a myriad of human diseases, particularly cancer. Defining the epigenetic defects associated with malignant tumors has become a focus of cancer research resulting in the gradual elucidation of cancer cell epigenetic regulation. In fact, most stages of tumor progression, including tumorigenesis, promotion, progression, and recurrence are accompanied by epigenetic alterations, some of which can be reversed by epigenetic drugs. The main objective of epigenetic therapy in the era of personalized precision medicine is to detect cancer biomarkers to improve risk assessment, diagnosis, and targeted treatment interventions. Rapid technological advancements streamlining the characterization of molecular epigenetic changes associated with cancers have propelled epigenetic drug research and development. This review summarizes the main mechanisms of epigenetic dysregulation and discusses past and present examples of epigenetic inhibitors in cancer diagnosis and treatment, with an emphasis on the development of epigenetic enzyme inhibitors or drugs. In the final part, the prospect of precise diagnosis and treatment is considered based on a better understanding of epigenetic abnormalities in cancer.
... In conjunction with posttranscriptional changes of histones, cytosine methylations are arranged in extensive epigenetic silencing areas (LRES). Genes inside these regions are transcriptionally repressed; for instance, a 4-Mb region on chromosome 3p22 containing the MLH1 gene causes MSI-H CRC (Yamashita et al., 2003). ...
... In approximately 15% of malignant colorectal tumors, a hypermethylator phenotype, called the CpG island methylator phenotype (CIMP), was identified, that is seen predominantly in the elderly [89,90]. CIMP is identified in a subset of CRC that happen through an epigenetic instability pathway and that are contradistinguish by vast hypermethylation of promoter CpG island sites, resulting in the inactivation of several tumor suppressor genes or other tumor-related genes. ...
Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At a molecular level, it is marked by the gradual alterations of biomolecules. Indeed, important changes are observed on the DNA, as well as at a protein level, that are influenced by both genetic and environmental parameters. These molecular changes directly contribute to the development or progression of several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders and others aging-related diseases. Additionally, they increase the risk of mortality. Therefore, deciphering the hallmarks of aging represents a possibility for identifying potential druggable targets to attenuate the aging process, and then the age-related comorbidities. Given the link between aging, genetic, and epigenetic alterations, and given the reversible nature of epigenetic mechanisms, the precisely understanding of these factors may provide a potential therapeutic approach for age-related decline and disease. In this review, we center on epigenetic regulatory mechanisms and their aging-associated changes, highlighting their inferences in age-associated diseases.
... Recent multi-omics analysis has demonstrated that cancer involves a complex regulatory network that harbors both genetic and epigenetic abnormalities, contributing to escape from chemotherapy and host immune surveillance [20,21]. Advances in high-throughput sequencing technologies have led to the identification of individual molecular heterogeneity. ...
Background
Aberrant DNA methylation is an epigenetic marker that has been linked to the pathogenesis of colorectal cancer (CRC). Long noncoding RNAs (lncRNAs) have been increasingly identified to be associated with tumorigenic processes of CRC. Identifying epigenetically dysregulated lncRNAs and characterizing their effects during carcinogenesis are focuses of cancer research.
Methods
Differentially methylated loci and expressed lncRNAs were identified by integrating DNA methylome and transcriptome analyses using The Cancer Genome Atlas database. Bisulfite sequencing PCR (BSP) was performed to analyze LIFR-AS1 promoter methylation status. The functional roles of LIFR-AS1 in CRC were determined by in vitro and in vivo experiments.
Results
We identified a novel hypermethylated lncRNA, LIFR-AS1, that was downregulated and associated with tumorigenesis, metastasis, and poor prognosis in CRC. High methylation burden of LIFR-AS1 indicated a poor survival of CRC patients. Promoter hypermethylation of LIFR-AS1 in tumor tissues was confirmed by BSP. Functional assays revealed that LIFR-AS1 could competitively bind to hsa-miR-29b-3p, and repressed colon cancer cell proliferation, colony formation and invasion. LIFR-AS1 also inhibited tumor growth in a mouse xenograft model of CRC.
Conclusions
Our results showed that the identified DNA methylation-dysregulated lncRNAs may be potential biomarkers and highlighted a role for LIFR-AS1 as a tumor suppressor in CRC.
... Meanwhile, few research groups have questioned the existence of CIMP in CRC due to the arbitrary guidelines used to define it. In 2003, Yamashita et al. observed gradual distribution of methylation of tumour-suppressors that followed Gaussian distribution without a clear cut-off between the CIMP-positive and CIMP-negative tumours [34]. They suggested that methylation accumulation observed in CRC tumours is an age-dependent gradual process rather than non-random cancer-specific aggregation. ...
The CpG island methylator phenotype (CIMP) can be regarded as the most notable emanation of epigenetic instability in cancer. Since its discovery in the late 1990s, CIMP has been extensively studied, mainly in colorectal cancers (CRC) and gliomas. Consequently, knowledge on molecular and pathological characteristics of CIMP in CRC and other tumour types has rapidly expanded. Concordant and widespread hypermethylation of multiple CpG islands observed in CIMP in multiple cancers raised hopes for future epigenetically based diagnostics and treatments of solid tumours. However, studies on CIMP in solid tumours were hampered by a lack of generalisability and reproducibility of epigenetic markers. Moreover, CIMP was not a satisfactory marker in predicting clinical outcomes. The idea of targeting epigenetic abnormalities such as CIMP for cancer therapy has not been implemented for solid tumours, either. Twenty-one years after its discovery, we aim to cover both the fundamental and new aspects of CIMP and its future application as a diagnostic marker and target in anticancer therapies.
... DNA methylation has been linked to tumor suppressor gene silencing [19], including the silencing of hMLH1 MMR gene [20]. In a subset of sporadic CRC, the loss of function of hMLH1 gene led to the accumulation of instability in microsatellite regions of the DNA [11,12]. ...
Background:
Colorectal cancer (CRC) ranks third in terms of incidence and second in mortality worldwide. In CRC, the silencing of mismatch repair genes, including the mutL homolog 1 (hMLH1) has been linked to microsatellite instability (MSI), the lengthening or shortening of microsatellite repeats. Very limited data have been presented so far on the link of hMLH1 methylation and MSI in Southeast Asia populations with sporadic CRC, and on its clinical significance.
Aim:
To investigate the significance of the MSI status and hMLH1 methylation in CRC Filipino patients.
Methods:
Fifty-four sporadic CRC patients with complete clinical data were included in this study. Genomic DNA from CRC tumor biopsies and their normal tissue counterparts were profiled for MSI by high resolution melting (HRM) analysis using the Bethesda Panel of Markers (BAT25, BAT26, D2S123, D5S346, and D17S250). hMLH1 methylation screening was performed using bisulfite conversion and methylation specific polymerase chain reaction. Statistical analysis was conducted to calculate their associations to clinicopathological characteristics and survival relevance (Kaplan-Meier curves and the log-rank test).
Results:
hMLH1 methylation was observed in 9% and 35% of CRC and normal samples, respectively. Higher incidence of consistently methylated hMLH1 found in both normal and CRC was noticed for relation to location of tumor (P < 0.05). As for MSI status, D2S123 the most common unstable microsatellite and MSI-high (MSI-H) was the most common MSI profile, counted for 46% and 50% of normal and CRC tissues, respectively. The presence of MSI-low (MSI-L) and microsatellite stable (MSS) was 43% and 11% for normal, and 31% and 19% for CRC samples. The mean month of patients' survival was shorter in patients whose normal and tumor tissues had methylated compared to those with unmethylated hMLH1 and with MSI-H compared to those with MSI-L/MSS (P < 0.05). This was supported by significant difference in Kaplan-Meier with log-rank analysis. This data indicated that hMLH1 methylation and high MSI status have prognostic value.
Conclusion:
This study showed the clinical significance of hMLH1 methylation and MSI status in sporadic CRC Filipino patients, especially in the normal part of the tumor.
... Special attention is focused on methylation in tumors with epigenetic silencing of hMLH1 (involving in most of the CIMP-high CRCs). When the mutator phenotype is released, numerous mutations might accumulate in MSI-target cancer genes, which largely influence the tumor phenotype [221]. Mutations in the cancer driver genes cannot be repaired by this hMLH1 re-expression; nevertheless, this process could be helpful for increasing the sensitivity to cytotoxic chemotherapy [222]. ...
Colorectal carcinogenesis (CRC) is caused by the gradual long-term accumulation of both genetic and epigenetic changes. Recently, epigenetic alterations have been included in the classification of the CRC molecular subtype, and this points out their prognostic impact. As epigenetic modifications are reversible, they may represent relevant therapeutic targets. DNA methylation, catalyzed by DNA methyltransferases (DNMTs), regulates gene expression. For many years, the deregulation of DNA methylation has been considered to play a substantial part in CRC etiology and evolution. Despite considerable advances in CRC treatment, patient therapy response persists as limited, and their profit from systemic therapies are often hampered by the introduction of chemoresistance. In addition, inter-individual changes in therapy response in CRC patients can arise from their specific (epi)genetic compositions. In this review article, we summarize the options of CRC treatment based on DNA methylation status for their predictive value. This review also includes the therapy outcomes based on the patient’s methylation status in CRC patients. In addition, the current challenge of research is to develop therapeutic inhibitors of DNMT. Based on the essential role of DNA methylation in CRC development, the application of DNMT inhibitors was recently proposed for the treatment of CRC patients, especially in patients with DNA hypermethylation.
... Some cancers even have unique methylomes that define distinct molecular subtype of the cancer. In colorectal cancer, a hypermethylator phenotype called the CpG Island Methylator Phenotype (CIMP) that is seen predominantly in the elderly and in the right colon, can be identified in approximately 15% of cancers (6)(7)(8)(9). Molecular subtypes based on DNA methylation have been identified in many cancer types including gliomas (10,11); gastric cancer (12) and its precursor intestinal metaplasia (13); acute myeloid leukemia (14); and recently in esophageal adenocarcinoma (15). ...
The incidence of cancer, adjusted for secular trends, is directly related to age, and advanced chronological age is one of the most significant risk factors for cancer. Organismal aging is associated with changes at the molecular, cellular and tissue levels and is affected by both genetic and environmental factors. The specific mechanisms through which these age-associated molecular changes contribute to the increased risk of aging-related disease, such as cancer, are incompletely understood. DNA methylation, a prominent epigenetic mark, also changes over a lifetime as part of an 'epigenetic aging' process. Here, we give an update and review of epigenetic aging, in particular the phenomena of epigenetic drift and epigenetic clock, with regard to its implication in cancer etiology. We discuss the discovery of the DNA methylation-based biomarkers for biological tissue age and the construction of various epigenetic age-estimators for human clinical outcomes and health/life span. Recent studies in various types of cancer point to the significance of epigenetic aging in tumorigenesis, and its potential use for cancer risk prediction. Future studies are needed to assess the potential clinical impact of strategies focused on lowering cancer risk by preventing premature aging or promoting healthy aging.
... Using a pharmacological unmasking microarray method, we have identified novel tumor suppressor genes which are epigenetically silenced in a cancer-specific manner [20]. Among them, promoter methylation of HOPX is observed very frequently in a cancer-specific manner, and is correlated with worse long-term prognosis in esophageal squamous cell carcinoma [21], gastric cancer [14], colorectal cancer [12], pancreas cancer [15], and breast cancer [13]. ...
HOPX is involved in multiple organ development and acts as a tumor suppressor in various cancers. Epigenetic silencing of HOPX via its promoter methylation has been shown frequent and cancer-specific in human cancers. The proliferation of thyroid cancer cells and cancer progression are strongly influenced by epigenetic alterations as well as genetic changes. Papillary thyroid cancer (PTC) comprises the vast majority of thyroid cancers and exhibits slow progression. However, ~10% of patients still show disease recurrence and refractoriness to treatment. Accordingly, it is important approach to research epigenetic mechanisms in PTC progression to find useful biomarkers. Here, we aimed to seek into the roles and clinical impact of epigenetic silencing of HOPX in PTC.
The promoter methylation of HOPX was observed in five of six human thyroid cancer cell lines. Down-regulation of HOPX was seen in three cell lines including PTC line K1, and demethylating agents restored HOPX expression. The promoter methylation was observed with high sensitivity and specificity in human PTC tissues. HOPX promoter methylation independently predicted disease recurrence in PTC patients. Epigenetic silencing of HOPX was associated with Ki-67 expression. Of note, HOPX promoter methylation was dramatically associated with worse prognosis especially in patients with stage I PTC. Forced HOPX expression suppressed cell proliferation, invasive activities, and anchorage-independent growth in vitro.
HOPX promoter methylation is frequent and cancer-specific event, leading to aggressive phenotype in PTC. Epigenetic silencing of HOPX may be a clue to tackle cancer progression and have clinical impact as a novel biomarker in PTC.
... Epigenetic changes have recently been associated with the normal mucosa aberrant crypt focus (ACF)-adenoma-carcinoma sequence, which itself plays an important role in CRC development [14]. DNA methylation status, therefore, appears to be a fundamental factor in carcinogenesis of CRC process. ...
Colorectal cancer (CRC) is the third most commonly diagnosed cancer worldwide, representing 13% of all cancers. The role of epigenetics in cancer diagnosis and prognosis is well established. MicroRNAs in particular influence numerous cancer associated processes including apoptosis, proliferation, differentiation, cell-cycle controls, migration/invasion and metabolism. MiRNAs-137 and 342 are exon- and intron-embedded, respectively, acting as tumour-suppressive microRNA via hypermethylation events. Levels of miRNAs 137 and 342 have been investigated here as potential prognostic markers for colorectal cancer patients. The methylation status of miRNA-137 and miRNA-342 was evaluated using methylation-specific (MSP) polymerase chain reaction (PCR) on freshly frozen tissue derived from 51 polyps, 8 tumours and 14 normal colon mucosa specimens. Methylation status of miRNA-137 and miRNA-342 was significantly higher in tumour lesions compared to normal adjacent mucosa. Surprisingly, the methylation frequency of miR-342 (76.3%) among colorectal cancer patients was significantly higher compared to miR-137 (18.6%). Furthermore, normal tissues, adjacent to the lesions (N-Cs), displayed no observable methylation for miRNA-137, whereas 27.2% of these N-Cs showed miRNA-342 hypermethylation. MiRNA-137 hypermethylation was significantly higher in male patients and miR-342 hypermethylation correlated with patient age. Methylation status of miRNA-137 and miRNA-342 has both diagnostic and prognostic value in CRC prediction and prevention.
... The main cause of global hypomethylation followed by hypermethylation of specific genes in tumors is not yet clear. Numerous genes have been shown hypermethylated in various subtypes of cancers (8)(9)(10)(11)(12). In various studies a correlation between tumor and hypermethylation has been demonstrated, such as p15 (INK4B) (13), SOCS1 (suppressor of cytokine signaling 1) (14), Dap kinase (15), ER (estrogen receptor) (16) and researchers have tried to prove a relation between hypermethylation of multiple genes and cancer (10,12,17). ...
... Independent DNA fingerprints were run on acrylamide gels in duplicate or triplicate. Scoring of quantitative changes between normal and tumor DNA was made by visual inspection independently by three researchers, as described previously 14,37 . Somatic alterations were scored on bands with consistent pattern among normal tissues, with clear changes in intensity in tumor samples and called by at least two of the three researchers. ...
VWA2 encodes AMACO, a secreted protein up-regulated in most colorectal carcinomas (CRC), constituting a promising biomarker. The mechanism responsible for its aberrant up-regulation has not been previously described. In this work, we analyzed VWA2 DNA methylation in over 400 primary CRCs. No epigenetic alterations were found in its promoter-associated CpG island. However, the region located downstream of the transcriptional start site was hypomethylated in most CRCs. ChIP-Seq revealed increased levels of the active mark H3K4me3 and reduction of the repressive mark H3K27me3. In contrast, several CRC cell lines exhibited hypermethylation of VWA2. 5-AZA-2-deoxycitidine treatment led to transcriptional activation of VWA2, supporting a functional link between DNA methylation and transcription. VWA2 expression in primary CRCs correlated with that of Myc and Myc-target genes. Transcriptional up-regulation of VWA2 is extremely frequent (78%) and strong (average fold change >15) in CRC, but not in other types of cancer. VWA2 undergoes hypomethylation in the majority of CRCs. This alteration could partly underlie the previously reported over-expression of AMACO. Co-expression profiling suggests that VWA2 might be a constituent of a larger oncogenic transcriptional program regulated by c-Myc. Up-regulation of VWA2 is virtually exclusive of CRC, reinforcing its potential as a specific biomarker.
... It was correlated with mismatch repair deficiency and BRAF mutations in colon cancer (Weisenberger et al., 2006) and many CIMP loci are targets of embryonic Polycomb group proteins (Widschwendter et al., 2007). However, the concept and underlying mechanisms of this coordinated acquisition of CGI hypermethylation are still controversial (Yamashita et al., 2003). Nevertheless, it has been extended to other cancer entities meanwhile, among them glioma and AML (Kelly et al., 2017;Noushmehr et al., 2010). ...
TET enzymes are relatively novel players in the epigenetic regulation of mammalian DNA methylation. They participate in DNA demethylation, but their precise roles in different developmental and disease scenarios are not fully understood. The aim of this work was to investigate the biological roles of TET enzymes in lineage-committed normal and cancer cells. To this end, murine primary cells with genetic deletion of TET enzymes and human cancer cells with recurrent mutations in the cofactor providing isocitrate dehydrogenases (IDH), provoking competitive inhibition of TET enzymes, were analyzed. By characterizing mouse embryonic fibroblasts adipogenic differentiation defects, inefficient activation of genes relevant to adipogenesis and widespread gene deregulation upon TET1/2-deficiency were discovered. Examination of the genome-wide DNA methylation landscape demonstrated the hypermethylation of DNA methylation canyons as a main characteristic of the TET1/2-deficient methylome. Canyons were associated with developmentally important genes and canyon collapse due to hypermethylation coincided with developmental gene deregulation, defective induction of adipogenic markers and the hypermethylation of their promoters. Together, these findings uncovered a novel epigenetic regulatory role in the maintenance of DNA methylation canyons for TET1 and TET2 that is essential for epigenetic programming during differentiation. In the second part of this thesis, published array-based DNA methylation profiles of a large acute myeloid leukemia (AML) patient cohort were used to examine mutant IDH- (mIDH) and TET-dependent DNA methylation changes. This confirmed the known association between mIDH and genome-wide hypermethylation. However, similar global methylation changes were not present in TET2 mutant patients and mIDH carrying patients lacked specific canyon hypermethylation. Intriguingly, neither overexpression of mIDH, nor treatment of a leukemia cell line with D-2-hydroxyglutarate, which is a putative TET inhibitor produced by mIDH, recapitulated the mIDH-associated hypermethylation. Instead, comparison with hematopoietic reference methylomes revealed high similarity between mIDH-associated and myeloid progenitor methylation profiles, suggesting the involvement of differentiation state rather than TET inhibition in the hypermethylation phenotype. These findings implicate a previously unnoted factor in the epigenomic changes of AML cells with mIDH, which may be critical to understand and therapeutically target mIDH-dependent pathogenesis.
... 77 Previous work in our group also identified a prominent hypomethylated sequence in colon cancers by the methylation sensitive amplified fragment polymorphism (MS-AFLP) DNA fingerprinting technique. [82][83][84][85] The sequence was later on identified as SST1/NBL2 86 . In-depth analysis of NBL2 hypomethylation by bisulfite sequencing of an internal 317 bp region, containing a NotI site, showed that SST1/NBL2 was hypomethylated in 22% of colorectal cancers (CRCs), in 15% of gastric cancers, in 20% of ovarian cancers, and in 20% of breast cancers. ...
Abundant repetitive DNA sequences are an enigmatic part of the human genome. Despite increasing evidence on the functionality of DNA repeats, their biological role is still elusive and under frequent debate. Macrosatellites are the largest of the tandem DNA repeats, located on one or multiple chromosomes. The contribution of macrosatellites to genome regulation and human health was demonstrated for the D4Z4 macrosatellite repeat array on chromosome 4q35. Reduced copy number of D4Z4 repeats is associated with local euchromatinization and the onset of facioscapulohumeral muscular dystrophy. Although the role other macrosatellite families may play remains rather obscure, their diverse functionalities within the genome are being gradually revealed. In this review, we will outline structural and functional features of coding and noncoding macrosatellite repeats, and highlight recent findings that bring these sequences into the spotlight of genome organization and disease development.
... The limitations of these early ascertainment methods and lack of extensive overlaps across tumor types, coupled with a variable range of methylation at any given CpG site, fueled a debate over the relevance of CIMP in cancer [44] . The advent of array-based platforms for measuring DNA methylation, such as the Illumina Infinium HumanMethylation27 and HumanMethylation450 arrays [45] , helped end this debate [46] . ...
Over the last two decades, cancer-related alterations in DNA methylation that regulate transcription have been reported for a variety of tumors of the gastrointestinal tract. Due to its relevance for translational research, great emphasis has been placed on the analysis and molecular characterization of the CpG island methylator phenotype (CIMP), defined as widespread hypermethylation of CpG islands in clinically distinct subsets of cancer patients. Here, we present an overview of previous work in this field and also explore some open questions using cross-platform data for esophageal, gastric, and colorectal adenocarcinomas from The Cancer Genome Atlas. We provide a data-driven, pan-gastrointestinal stratification of individual samples based on CIMP status and we investigate correlations with oncogenic alterations, including somatic mutations and epigenetic silencing of tumor suppressor genes. Besides known events in CIMP such as BRAF V600E mutation, CDKN2A silencing or MLH1 inactivation, we discuss the potential role of emerging actors such as Wnt pathway deregulation through truncating mutations in RNF43 and epigenetic silencing of WIF1. Our results highlight the existence of molecular similarities that are superimposed over a larger backbone of tissue-specific features and can be exploited to reduce heterogeneity of response in clinical trials.
... The existence of a distinct CIMP subtype in CRC remained controversial for many years due to the arbitrary definition(s) used to define it. A study by Yamashita et al. [17] challenged the existence of CIMP by reporting a gradual accumulation of methylation in CRC samples. The authors could not identify a clear boundary defining CIMP-positive and CIMP-negative tumors and concluded that age explained the increase in methylation. ...
Epigenetic dysregulation is recognized as a hallmark of cancer. In the last 16 years, a CpG island methylator phenotype (CIMP) has been documented in tumors originating from different tissues. However, a looming question in the field is whether or not CIMP is a pan-cancer phenomenon or a tissue-specific event. Here, we give a synopsis of the history of CIMP and describe the pattern of DNA methylation that defines the CIMP phenotype in different cancer types. We highlight new conceptual approaches of classifying tumors based on CIMP in a cancer type-agnostic way that reveal the presence of distinct CIMP tumors in a multitude of The Cancer Genome Atlas (TCGA) datasets, suggesting that this phenotype may transcend tissue-type specificity. Lastly, we show evidence supporting the clinical relevance of CIMP-positive tumors and suggest that a common CIMP etiology may define new mechanistic targets in cancer treatment.
... In summary, our data suggest that the epigenetic reprogramming at SST1 regions may contribute to genomic instability by facilitating aberrant mitosis and chromosome segregation defects. Because both DNA hypermethylation and hypomethylation seem to precede the somatic genetic alterations in cancer [21,63], the possible use of SST1 methylation as an early detection marker deserves further investigation. The asymmetric association of SST1 demethylation with TP53 mutations is intriguing. ...
DNA hypomethylation at repetitive elements accounts for the genome-wide DNA hypomethylation common in cancer, including colorectal cancer (CRC). We identified a pericentromeric repeat element called SST1 frequently hypomethylated (>5% demethylation compared with matched normal tissue) in several cancers, including 28 of 128 (22%) CRCs. SST1 somatic demethylation associated with genome damage, especially in tumors with wild-type TP53. Seven percent of the 128 CRCs exhibited a higher (" severe ") level of demethylation (≥10%) that co-occurred with TP53 mutations. SST1 demethylation correlated with distinct histone marks in CRC cell lines and primary tumors: demethylated SST1 associated with high levels of the repressive histone 3 lysine 27 trimethylation (H3K27me3) mark and lower levels of histone 3 lysine 9 trimethylation (H3K9me3). Furthermore, induced demethylation of SST1 by 5-aza-dC led to increased H3K27me3 and reduced H3K9me3. Thus, in some CRCs, SST1 demethylation reflects an epigenetic reprogramming associated with changes in chromatin structure that may affect chromosomal integrity. The chromatin remodeler factor, the helicase lymphoid-specific (HELLS) enzyme, called the " epigenetic guardian of repetitive elements " , interacted with SST1 as shown by chromatin immunoprecipitation, and down-regulation of HELLS by shRNA resulted in demethylation of SST1 in vitro. Altogether these results suggest that HELLS contributes to SST1 methylation maintenance. Alterations in HELLS recruitment and function could contribute to the somatic demethylation of SST1 repeat elements undergone before and/or during CRC pathogenesis.
... 55 This pathway has been more controversial, as CIMP is present in nearly all CRCs to varying degrees, and some have argued it does not represent a unique pathogenic mechanism. 56 CpG islands are short DNA sequences rich in CpG dinucleotides found in the 5 0 region of approximately half of human genes. Cytosine methylation results in gene silencing, a process that becomes dysregulated in certain human cancers. ...
Colorectal cancer is a heterogeneous disease with a wide range of long-term outcomes and responses to treatment. Recent advances in the genetic and molecular characterization of tumors has yielded a set of prognostic and predictive biomarkers that aid the identification of patients at higher risk for disease recurrence and progression, and in some cases indicate the likelihood of response to a specific treatment. Increasingly, these biomarkers have become integral to the treatment algorithm for managing patients with colorectal cancer. Prognostic and predictive factors in colorectal cancer can broadly be categorized into treatment impact, clinicopathologic factors, and molecular markers. This review will focus primarily on molecular markers, which are foundational to the paradigmatic shift toward personalized cancer therapy.
... But, in contrast to MSI or other well known phenotypic subtypes of cancers, CIMP still is under controversial discussion and not accepted by the entire scientific society. 142,143 The main reason is that the sites determining CIMP phenotype were not standardized, yet. For the 30 different CpG-islands of the analyzed CIMP positive tumors a variety of different methylation patterns is observable. ...
AREG und EREG sind Liganden des EGFR, deren Expression mit einem positiven EGFR-zielgerichtetem Therapieansprechen in Darmkrebs korreliert. Ziel dieser Arbeit war es, einen epigenetischen Einfluss auf die AREG und EREG Expression zu klären. Es wurde gezeigt, dass AREG und EREG in verschiedenen kolorektalen Krebszelllinien differenziell exprimiert sind, und dass die Expression beider Gene durch epigenetische Inhibitoren erhöht werden kann. Eine Analyse in fünf Zelllinien zeigte jedoch, dass die Promotoren beider Gene hauptsächlich unmethyliert vorlagen. Hingegen wurden kurze Regionen im Gen als differentiell methyliert identifiziert. Im AREG Gen liegt diese Region im Exon 2, was auf einen ungewöhnlichen Regulationsmechanismus hindeutet. Promotorfunktionsanalysen zeigten dann, dass diese Region eine methylierungs- und orientierungsabhängige Promotorfunktion hat, in die das MDB-Protein CTCF involviert sein könnte. Expressionsanalysen wiesen darauf hin, dass auch ZBTB33, ein anderes MDB-Protein, in die AREG Regulation involviert sein könnte. Die ZBTB33 Expression korrelierte negativ mit der AREG Expression in den Zelllinien. Eine ZBTB33-Bindungsstelle konnte ausserdem bioinformatorisch im AREG Exon 2 identifiziert werden. Des weiteren wurde gezeigt, dass die Behandlung der Zelllinie LIM1215 mit HDAC Inhibitoren in vitro zu einer Erhöhung der Sensitivität gegenüber EGFR-zielgerichteten Medikamenten führt, begleitet von einer Erhöhung der AREG und EREG Expression. Im in vivo Versuch konnte die Sensitivität von LIM1215 Zellen durch die Behandlung mit DNMT Inhibitoren erhöht werden. Begleitet wurde dies hier mit einer Verringerung der Methylierung der AREG und EREG intragenischen CpGs. Diese Ergebnisse zeigen auf, dass Patienten, die resistent gegenüber EGFR-zielgerichteten Therapien sind, möglicherweise sensitiv gemacht werden können. In dem Fall könnten AREG und EREG als prädiktive Marker eingesetzt werden, um den Effekt der epigenetischen Inhibitoren zu evaluieren.
... Auch in unserer Arbeit korrelierte CIMP(+) mit . Andere Autoren behaupten, dass CIMP(+) keine einheitliche Gruppe von CRC zusammenfasst, sondern nur eine bestimmte Eigenschaft ist (Yamashita et al., 2003). ...
... CpG island hypermethylation occurring at promoter regions is frequently associated with transcriptional repression and loss of gene function (7). The significance of altered global CpG island methylation patterns in colonic carcinogenesis is under investigation (8,9). It is possible that hypermethylation-mediated silencing of a subset of tumor-related genes contributes to the unique molecular phenotype of MSI-H cancers. ...
Gene silencing through CpG island hypermethylation has been associated with genesis or progression of frequent microsatellite instability (MSI-H) cancers. To identify novel methylation sites unique to MSI-H colon cancers in an unbiased fashion, we conducted a global expression profiling-based methylation target search. We identified 81 genes selectively down-regulated in MSI-H cancers using cDNA microarray analysis of 41 primary colon cancers. Forty six of these 81 genes contained CpG islands overlapping their 5′untranslated regions. Initial screening of six genes in 57 primary colon cancers detected the following gene with MSI-H cancer-specific hypermethylation: RAB32, a ras family member and A-kinase-anchoring protein, was methylated in 14 of 25 (56%) MSI-H cancers but in none of 32 non-MSI-H cancers or 23 normal colonic specimens. RAB32 hypermethylation correlated with RAB32 mRNA down-regulation and with hMLH1 hypermethylation. In addition, the protein-tyrosine phosphatase receptor type Ogene, PTPRO, was frequently methylated in right-sided tumors. This methylation screening strategy should identify additional genes inactivated by epigenetic silencing in colorectal and other cancers.
... To this end, a common pattern observed in cancers suggests that somatic epigenetic alterations precede pro-oncogenic mutations, and that the abnormal epigenome affects the frequency of occurrence of subsequent genetic alterations that drive tumorigenesis. [14][15][16][17] Recent genome-wide data also imply that epigenetic anomalies can be a key factor in cancer onset and progression. [18][19][20][21][22] DNA methylation, an essential element in transcriptional regulation, 23 is one of a few major epigenetic mechanisms. ...
Aberrant DNA methylation is frequently observed in disease, including many cancer types, yet the underlying mechanisms remain unclear. Because germline and somatic mutations in the genes that are responsible for DNA methylation are infrequent in malignancies, additional mechanisms must be considered. Mycoplasmas spp., including Mycoplasma hyorhinis, efficiently colonize human cells and may serve as a vehicle for delivery of enzymatically active microbial proteins into the intracellular milieu. Here, we performed, for the first time, genome-wide and individual gene mapping of methylation marks generated by the M. hyorhinis CG- and GATC-specific DNA cytosine methyltransferases (MTases) in human cells. Our results demonstrated that, upon expression in human cells, MTases readily translocated to the cell nucleus. In the nucleus, MTases selectively and efficiently methylated the host genome at the DNA sequence sites free from pre-existing endogenous methylation, including those in a variety of cancer-associated genes. We also established that mycoplasma is widespread in colorectal cancers, suggesting that either the infection contributed to malignancy onset or, alternatively, that tumors provide a favorable environment for mycoplasma growth. In the human genome, 11% of GATC sites overlap with CGs (e.g., CGATmCG); therefore, the methylated status of these sites can be perpetuated by human DNMT1. Based on these results, we now suggest that the GATC-specific methylation represents a novel type of infection-specific epigenetic mark that originates in human cells with a previous exposure to infection. Overall, our findings unveil an entirely new panorama of interactions between the human microbiome and epigenome with a potential impact in disease etiology.
... In an independent study, we also observed a significant association of hypermethylation of ADAMTS14 in the normal colon mucosa mainly in elder African-Americans with CRC ( Figure 5). The tendency of ADAMTS14 hypermethylation in normal mucosa to occur in the distal colon distinguishes this phenomenon from the generalized hypermethylation that is more prominent in tumors of the proximal colon [49][50][51]. Clustering of methylation of MGMT and ADAMTS14 (Figure 6a) in normal mucosa supports the concept of a field for cancerization in some individuals at high risk for CRC that involves the aberrant methylation of several loci, including, but not restricted to MGMT and ADAMTS14 [24,36]. We do not suggest, however, that these genes play an active role in this field defect. ...
Somatic hypermethylation of the O6-methylguanine-DNA methyltransferase gene (MGMT) was previously associated with G > A transition mutations in KRAS and TP53 in colorectal cancer (CRC). We tested the association of MGMT methylation with G > A mutations in KRAS and TP53 in 261 CRCs. Sixteen cases, with and without MGMT hypermethylation, were further analyzed by exome sequencing. No significant association of MGMT methylation with G > A mutations in KRAS, TP53 or in the whole exome was found (p > 0.5 in all comparisons). The result was validated by in silico comparison with 302 CRCs from The Cancer Genome Atlas (TCGA) consortium dataset. Transcriptional silencing associated with hypermethylation and stratified into monoallelic and biallelic. We also found a significant clustering (p = 0.001) of aberrant hypermethylation of MGMT and the matrix metalloproteinase gene ADAMTS14 in normal colonic mucosa of CRC patients. This suggested the existence of an epigenetic field defect for cancerization disrupting the methylation patterns of several loci, including MGMT or ADAMTS14, that may lead to predictive biomarkers for CRC. Methylation of these loci in normal mucosa was more frequent in elder (p = 0.001) patients, and particularly in African Americans (p = 1 × 10-5), thus providing a possible mechanistic link between somatic epigenetic alterations and CRC racial disparities in North America.
... Thus, the understanding of the molecular pathology of CRC is crucial in the identifications of treatments. Accumulation of multiple genetic alterations transforms normal colonic epithelial cells to adenocarcinoma cells (4)(5)(6). Genetic alterations are associated with the activation of proto-oncogenes (KRAS and BRAF) (7)(8)(9)(10)(11) and the inactivation of tumor suppression genes (APC, DCC/SMAD4, TP53 and PTEN) (12)(13)(14)(15). The APC/β-catenin pathway plays a key role in CRC. ...
Dysregulation of microRNAs has been reported to be involved in the progression of human colorectal cancers (CRCs). Loss of the adenomatous polyposis coli (APC) gene is a common initiating event in CRCs. PTEN inactivation by mutation or allelic loss also occurs in CRCs. miR‑135b was reported to be upregulated in CRCs and its overexpression was due to APC/β‑catenin and PTEN/PI3K pathway deregulation. APC was proven to be a target of miR‑135b and forms a feedback loop with miR‑135b. In the present study, we found that ubiquitin‑specific peptidase 13 (USP13) was a target of miR‑135b. miR‑135b downregulated the expression of USP13, and reduced the stability of PTEN. miR‑135b promoted cell proliferation and glycolysis that could be reversed by the overexpression of USP13 or PTEN. Moreover, knockdown of USP13 upregulated the levels of endogenous miR‑135b, but not those in CRC cells with PTEN mutation. The results showed positive feedback loops between miR‑135b and PTEN inactivation in CRCs.
... hMLH1 is commonly inactivated in the methylation pathway [44]. MMR system alterations, and most frequently hMLH1, are implicated in the MSI pathway [45]. ...
The aim of this study was to determine the frequency of p16 and hMLH1 genes simultaneous methylation in colorectal cancer patients with Microsatellite Instability (MSI) tumors. We also wanted to analyze the relationship with other clinical features, with BRAF gene V600E mutation and with prognosis. Samples from fifty one patients with MSI positive sporadic colorectal cancer were included. DNA was extracted from tumor samples. Promoter methylation was analyzed using bisulfite modification and was detected by quantitative methylation-specific PCR. BRAF gene was amplified using specific primers and mutations were detected by real time PCR. Simultaneous methylation was transformed in a new variable called CMETH2. Frequency of CMETH2 was analyzed and compared with other clinicopathological variables. 33.3 % of patients were positive for CMETH2 and 25 % had BRAF V600E mutation. CMETH2 was related with proximal location, with poorly differentiated tumors and with BRAF V600E mutation. CMETH2 only showed influence in the overall survival (OS) in patients with distal tumors. However, with regard to the disease free survival (DFS) measure, CMETH2 was independent prognostic factor. We were able to discriminate tumors with high methylation features using a transformation analysis of variables into a new computed one (CMETH2). CMETH2 has demonstrated to be a useful prognostic factor in MSI tumors. The prognostic value of CMETH2 in DFS was independent of other clinicopathological variables. The use of CMETH2 could help in the election of the best therapeutic alternative for CCR patients with MSI tumors.
... 8 It is recommended that patients at high risk undergo radical resection due to the possibility of regional LNM. Given that the development of colorectal cancer is known to be the result of accumulating genetic alterations, [9][10][11] it seems prudent to take into account histologic features of the primary tumor in addition to molecular biological characteristics for the prediction of regional LNM in T1 colorectal cancer. However, to the best of our knowledge, there are limited reports on predicting regional LNM in T1 colorectal cancer using molecular biological characteristics. ...
The estimation of regional lymph node metastasis (LNM) risk in T1 colorectal cancer is based on histologic examination and imaging of the primary tumor. High-frequency microsatellite instability (MSI-H) is likely to decrease the possibility of metastasis to either regional lymph nodes or distant organs in colorectal cancers. This study evaluated the clinical implications of MSI in T1 colorectal cancer with emphasis on the usefulness of MSI as a predictive factor for regional LNM.
A total of 133 patients who underwent radical resection for T1 colorectal cancer were included. Genomic DNA was extracted from normal and tumor tissues and amplified by polymerase chain reaction (PCR). Five microsatellite markers, BAT-25, BAT-26, D2S123, D5S346, and D17S250, were used. MSI and clinicopathological parameters were evaluated as potential predictors of LNM using univariate and multivariate analyses.
Among 133 T1 colorectal cancer patients, MSI-H, low-frequency microsatellite instability (MSI-L), and microsatellite stable (MSS) colorectal cancers accounted for 7.5%, 6%, and 86.5%, respectively. MSI-H tumors showed a female predominance, a proximal location and more retrieved lymph nodes. Twenty-two patients (16.5%) had regional LNM. Lymphovascular invasion and depth of invasion were significantly associated with LNM. There was no LNM in 10 MSI-H patients; however, MSI status was not significantly correlated with LNM. Disease-free survival did not differ between patients with MSI-H and those with MSI-L/MSS.
MSI status could serve as a negative predictive factor in estimating LNM in T1 colorectal cancer, given that LNM was not detected in MSI-H patients. However, validation of our result in a different cohort is necessary.
... In addition to genomic DNA instability being a common phenomenon in CRC, epigenetic instability is also a common occurrence in colorectal neoplasms. A new concept was introduced in 1999 by Toyota It is important to note that the CIMP concept has not been widely accepted by all researchers in this field and much debate as to whether the CIMP tumours represent a biologically distinct group of CRCs or are an artificially selected group from a continuum of tumours displaying different degrees of methylation at specific loci, has taken place over the past few years (95,102). The recognition of several CIMP groups has strengthened the notion that CIMPs may be a unique molecular subgroup of CRCs defined by a high proportion of aberrantly methylated gene promoters that arise by distinct and unique mechanisms (7). ...
... Almost all CRCs progress from benign neoplasms into adenocarcinoma through a stepwise sequence characterized by histological changes that start with aberrant crypt focus (ACF) and benign tubular adenomas, which can progress to advanced adenomas with a high risk of malignant progression, and can further proceed to invasive adenocarcinoma [49]. Epigenetic alterations have now been linked to specific steps in the adenoma-carcinoma sequence, and are believed to play a central role in the initiation and progression of CRC [50,51]. ...
... Although previous studies failed to find any relation between MSI and age [22,24], it has been shown that women displaying MSI and methylated MLH1 are significantly older [30,26]. This agrees with our observations and with the fact that MLH1 methylation is known to be an age related phenomena [31][32][33]. The inverse relationship between MSI and BMI is in accordance to other reports [30]. ...
Microsatellite instability (MSI) and aneuploidy are inversely related phenomena. We tested whether ploidy status influences the clinical impact of MSI in endometrioid endometrial cancer (EEC). We analyzed 167 EECs for MSI and ploidy. Tumors were classified in three categories according to MSI and ploidy status. Associations with clinicopathological and molecular variables, survival, and treatment response were assessed.
All MSI tumors (23%) were scored as diploid, and 14% of microsatellite stable (MSS) tumors presented aneuploidy. MSI tumors associated with older age at diagnosis, non-obesity, high histological grade, and advanced surgical stage. MSS-aneuploid tumors also associated with higher grade and advanced stage. In multivariate survival analysis MSI did not influence disease-free survival (DFS) or cancer-specific survival (CSS). However, when just diploid tumors were considered for the analysis, MSI significantly contributed to worse DFS and CSS, and the same was observed for aneuploidy when MSS tumors were analyzed alone. In diploid tumors, a differential response to postoperative radiotherapy (RT) was observed according to MSI, since it predicted poor DFS and CSS in the multivariate analysis.
We conclude that ploidy status influences the clinical impact of MSI in EEC. Among diploid tumors those with MSI have poor clinical outcome and respond worse to RT.
... However, once this transformation happens, the genetic alterations supersede the epigenetic alterations driving the cancer phenotype. 27 On the other hand, he analyzed DNA hypomethylation events and proposed a "wear and tear" stochastic model for neoplastic transformation wherein accumulation of errors in methylation replication occurs in the colon crypt stem cells during aging. 28 He presented two examples of DNA demethylation in CRC, which didn't fit in the "wear and tear" model. ...
The Barcelona Conference on Epigenetics and Cancer (BCEC) entitled "Challenges, opportunities and perspectives" took place November 21-22, 2013 in Barcelona. The 2013 BCEC is the first edition of a series of annual conferences jointly organized by five leading research centers in Barcelona. These centers are the Institute of Predictive and Personalized Medicine of Cancer (IMPPC), the Biomedical Campus Bellvitge with its Program of Epigenetics and Cancer Biology (PEBC), the Centre for Genomic Regulation (CRG), the Institute for Biomedical Research (IRB), and the Molecular Biology Institute of Barcelona (IBMB). Manuel Perucho and Marcus Buschbeck from the Institute of Predictive and Personalized Medicine of Cancer put together the scientific program of the first conference broadly covering all aspects of epigenetic research ranging from fundamental molecular research to drug and biomarker development and clinical application. In one and a half days, 23 talks and 50 posters were presented to a completely booked out audience counting 270 participants.
DNA methylation (DNAm) overwrites information about multiple extrinsic factors on the genome. Age is one of these factors. Age causes characteristic DNAm changes that are thought to be not only major drivers of normal ageing but also precursors to diseases, cancer being one of these. Although there is still much to learn about the relationship between ageing, age-related diseases and DNAm, we now know how to interpret some of the effects caused by age in the form of changes in methylation marks at specific loci. In fact, these changes form the basis of the so called "epigenetic clocks", which translate the genomic methylation profile into an "epigenetic age". Epigenetic age does not only estimate chronological age but can also predict the risk of chronic diseases and mortality. Epigenetic age is believed to be one of the most accurate metrics of biological age. Initial evidence has recently been gathered pointing to the possibility that the rate of epigenetic ageing can be slowed down or even reversed. In this review, we discuss some of the most relevant advances in this field. Expected outcome is that this approach can provide insights into how to preserve health and reduce the impact of ageing diseases in humans.
Background:
CpG Island Methylator Phenotype (CIMP) is an epigenetic phenotype in CRC characterized by hypermethylation of CpG islands in promoter regions of tumor suppressor genes, leading to their transcriptional silencing and loss of function. While the prevalence of CRC differs across geographical regions, no studies have compared prevalence of CIMP-High phenotype across regions. The purpose of this project was to compare the prevalence of CIMP across geographical regions after adjusting for variations in methodologies to measure CIMP in a meta-analysis.
Methods:
We searched PubMed, Medline, and Embase for articles focusing on CIMP published from 2000 to 2018. Two reviewers independently identified 111 articles to be included in final meta-analysis. We classified methods used to quantify CIMP into 4 categories: a) Classical (MINT marker) Panel group b) Weisenberg-Ogino (W-O) group c) Human Methylation Arrays group and d) Miscellaneous group. We compared the prevalence of CIMP across geographical regions after correcting for methodological variations using meta-regression techniques.
Results:
The pooled prevalence of CIMP-High across all studies was 22% (95% confidence interval:21-24%; I2 = 94.75%). Pooled prevalence of CIMP-H across Asia, Australia, Europe, North America and South America was 22, 21, 21, 27 and 25%, respectively. Meta-regression analysis identified no significant differences in the prevalence of CIMP-H across geographical regions after correction for methodological variations. In exploratory analysis, we observed variations in CIMP-H prevalence across countries.
Conclusion:
Although no differences were found for CIMP-H prevalence across countries, further studies are needed to compare the influence of demographic, lifestyle and environmental factors in relation to the prevalence of CIMP across geographical regions.
The genome of cancer cells accumulates numerous genetic and epigenetic somatic alterations ultimately conferring capabilities for unrestrained growth, invasion of local tissues, migration, and colonization of distant organs. Many of these new capabilities require the disruption of the cell-to-cell interactions between the cancer cell and its microenvironment. These interactions are mediated, among other factors, by the activity of extracellular enzymes that reshape not only the extracellular compartment of the cancer cells but also that of the neighboring non-cancerous stroma cells. Cell surface metallopeptidases play a crucial role in this process, by cleaving and modifying fundamental components of the extracellular compartment. The transcriptional profile of cell surface metallopeptidases becomes deregulated in several human cancers by genetic and epigenetic alterations, contributing to the tumor phenotype. In this article, we describe two common strategies to analyze somatic epigenetic alterations of cell surface metallopeptidases, i.e., high-resolution single locus analysis and high-throughput multi-loci analysis, presenting several illustrative analyses performed on our CRC collection. These analyses demonstrate that cell surface metallopeptidases, particularly those belonging to the ADAMTS gene family, frequently undergo somatic DNA hypermethylation in CRC suggesting the existence of an underlying mechanism or a strong selection process favoring the transcriptional silencing of these genes.
Colorectal cancers (CRCs) are thought to arise through accumulation of genetic and epigenetic alterations. CRC genomes exhibit dual-faceted DNA methylation abnormality, global hypomethylation with CpG island hypermethylation, and CRCs are classified into two groups based on whether their genomes exhibit microsatellite instability (MSI) or chromosomal instability (CIN). In addition, a subset of CRCs is characterized by concurrent hypermethylation of multiple CpG islands, known as the CpG island methylator phenotype (CIMP). Genomic instability and epigenetic alterations are tightly linked, and CRCs with MSI largely overlap CIMP-positive tumors, while CIN is associated with global DNA hypomethylation. Dysregulation of histone methylation and altered expression of histone modifying enzymes are also commonly observed in CRC, indicating their critical roles in CRC development. Evidence now suggests that DNA and histone methylation could potentially serve as biomarkers useful for CRC diagnosis, risk assessment and prediction of therapeutic effects and prognosis. Although many studies examining clinical applications are still at an early phase, it is anticipated that further investigation will lead to improved prevention and management of CRC.
The quantitative assessment of methylation at specific sequences can be requested whenever a pathological condition can be identified or stratified if it exceeds a given methylation threshold level. Real-time qPCR technology can be consistently exploited for detecting the presence and the amount of specific methylation patterns in sequences of interest, after bisulfite conversion of DNA (Methylight). This chapter provides a protocol for assessing the methylation status of five surrogate markers (CACNA1G, IGF2, NEUROG1, RUNX3, and SOCS1) for the presence of the CpG Island Methylator Phenotype (CIMP) in human colorectal cancer samples. Methylation level at each locus is expressed as a percentage relative to a fully-methylated, M.SssI-treated reference DNA sample (Percentage of Methylated Reference, PMR). Each methylation datum is normalized against the amount of fully converted DNA, assessed with a control reaction targeting the repetitive element ALU-C4. A sample is defined as CIMP+ if showing a PMR>;10 in at least three of the five markers. This chapter also provides the methods for M.SssI and Bisulfite modifications most suitable for use with Methylight technology in FFPE samples.
Research reveals that epigenetic processes are emerging as a central regulatory layer in cell homeostasis and is recognized as a common hallmark in cancer and other diseases. Disrupted DNA methylation profiles, noncoding RNA expression, and histone modification patterns occur at all steps of tumor evolution triggering the malignant phenotype. Evolving cutting-edge technologies are providing new insights into cell physiology and allowing researchers to perform more comprehensive epigenomic studies. In cancer, reliable panels of biomarkers are arising, informative of cancer cell behavior and functional alterations – especially involving changes in DNA methylation – and are being identified as targets for potential therapeutic intervention. It is the aim of this chapter to summarize recent literature on the latest epigenetic advances in the understanding of cancer development and progression, with a special focus on DNA methylation alterations and their value in clinical oncology for cancer management.
Rationale:
Only a small portion of the known heritability of cardiovascular diseases such as heart failure can be explained based on single gene mutations. Chromatin structure and regulation provide a substrate through which genetic differences in non-coding regions may impact cellular function and response to disease, but the mechanisms are unknown.
Objective:
We conducted genome-wide measurements of DNA methylation in different strains of mice that are susceptible and resistant to isoproterenol-induced dysfunction to test the hypothesis that this epigenetic mark may play a causal role in the development of heart failure.
Methods and results:
BALB/cJ and BUB/BnJ mice, determined to be susceptible and resistant to isoproterenol-induced heart failure respectively, were administered the drug for 3 weeks via osmotic minipump. Reduced representational bisulfite sequencing was then used to compare the differences between the cardiac DNA methylome in the basal state between strains and then following isoproterenol treatment. Single base resolution DNA methylation measurements were obtained and revealed a bimodal distribution of methylation in the heart, enriched in lone intergenic CpGs and depleted from CpG islands around genes. Isoproterenol induced global decreases in methylation in both strains; however, the basal methylation pattern between strains shows striking differences that may be predictive of disease progression prior to environmental stress. The global correlation between promoter methylation and gene expression (as measured by microarray) was modest and revealed itself only with focused analyses of transcription start site and gene body regions (in contrast to when gene methylation was examined in toto). Modules of co-methylated genes displayed correlation with other protein-based epigenetic marks supporting the hypothesis that chromatin modifications act in a combinatorial manner to specify transcriptional phenotypes in the heart.
Conclusions:
This study provides the first single base-resolution map of the mammalian cardiac DNA methylome and the first case-control analysis of the changes in DNA methylation with heart failure. The findings demonstrate marked genetic differences in DNA methylation that are associated with disease progression.
Methylation of cytosines is the most frequent epigenetic modification. Normal DNA methylation patterns are tightly regulated and occur in developmentally regulated and tissue-specific patterns. Aberrant DNA methylation has severe consequences for cells, tissues, and organisms and is a feature of many diseases including cancer. Promoter hypermethylation of tumor suppressor genes frequently occurs in cancer and leads to gene silencing. Loss of DNA methylation contributes to decreased genome stability. Aberrant DNA methylation can be caused by mutations in genes involved in the regulation of DNA methylation patterns or by microRNAs mediating their downregulation.
Gastrointestinal malignancies, including colorectal cancer (CRC), pancreatic cancer, and esophageal cancer, have been classically seen as genetic diseases, involving mutations and/or deletions in oncogenes and tumor suppressor genes. Recent evidence demonstrates that epigenetic changes coexist with these genetic changes and contribute to the malignant phenotype. This review will focus on epigenetic dysregulation in gastrointestinal malignancies involving multiple mechanisms of epigenetic control. Interactions between studied epigenetic alterations and genetic alterations are common.
We are in an era where the potential exists for deriving comprehensive profiles of DNA alterations characterizing each form of human cancer. Such profiles would provide invaluable insight into mechanisms underly- ing the evolution of each tumor type and will provide molecular markers, which could radically improve cancer detection. To date, no one type of DNA change has been defined which accomplishes this purpose. Herein, by using a candidate gene approach, we show that one category of DNA alteration, aberrant methylation of gene promoter regions, can enor- mously contribute to the above goals. We have now analyzed a series of promoter hypermethylation changes in 12 genes (p16INK4a, p15INK4b, p14ARF, p73, APC,5 BRCA1, hMLH1, GSTP1, MGMT, CDH1, TIMP3, and DAPK), each rigorously characterized for association with abnormal gene silencing in cancer, in DNA from over 600 primary tumor samples rep- resenting 15 major tumor types. The genes play known important roles in processes encompassing tumor suppression, cell cycle regulation, apopto- sis, DNA repair, and metastastic potential. A unique profile of promoter hypermethylation exists for each human cancer in which some gene changes are shared and others are cancer-type specific. The hypermethy- lation of the genes occurs independently to the extent that a panel of three to four markers defines an abnormality in 70 -90% of each cancer type. Our results provide an unusual view of the pervasiveness of DNA alter- ations, in this case an epigenetic change, in human cancer and a powerful set of markers to outline the disruption of critical pathways in tumori- genesis and for derivation of sensitive molecular detection strategies for virtually every human tumor type.
BackgroundAdjuvant chemotherapy can improve 5-year survival in Dukes' C colorectal carcinoma. Improved selection of patients who will respond to adjuvant treatments is required. We investigated whether site of tumour origin, sex, and presence of microsatellite instability (MSI) phenotype were associated with a survival benefit from adjuvant chemotherapy.MethodsWe analysed data for 656 consecutive patients with Dukes' C colorectal carcinoma, with median follow-up of 54 months (range 7–104) and mean age 66·7 years (SD 12·9). We screened tumour samples by PCR for deletions in the BAT-26 mononucleotide repeat to establish MSI status. Details of chemotherapy and survival were obtained by review of hospital and health-department records. Adjuvant chemotherapy (fluorouracil and levamisole) was given with curative intent to 272 (42%) patients.FindingsStriking survival benefits were seen for patients who had right-sided tumours and who received adjuvant chemotherapy compared with those who did not (48 vs 27% alive at end of study [95% Cl 0·25–0·56], p<·0001), for women (53 vs 33% [0·25–0·56], p<0·0001), and for patients with MSI tumours (90 vs 35% [0·01–0·53], p=0·0007). MSI-positive tumours were slightly more frequent in women than in men (10 vs 7%). Right-sided tumours were more frequently MSI positive than left-sided tumours (20 vs 1%). Men with right-sided tumours benefited from chemotherapy (37 vs 12% [0·24–0·69], p=0·0007) but men with left-sided tumours did not.InterpretationThe survival benefits seen in patients treated with adjuvant chemotherapy suggest that data from previous trials of adjuvant chemotherapy should be reassessed and the predictive value of MSI status confirmed. Validation of our results will allow better selection of patients for chemotherapy.
In vivo bromodeoxyuridine (BrdUrd) labelling of the human large bowel was performed and a detailed histochemical localisation of label in sections of crypts was undertaken using a monoclonal antibody to BrdUrd containing DNA. Flow cytometric studies on extracted nuclei were also performed (data presented elsewhere). The average crypt in the human large bowel (excluding the rectum) was 82 cells in height and 41 cells in circumference, with a total of about 2000 cells (assuming a topographical correction factor of 0.6). Ten per cent of the cells were replicating their DNA--that is, were in the S phase of the cell cycle--and 0.4% were in mitosis. The median position for the labelling index versus cell position frequency plot is at the 20th cell position--at a quarter of the crypt height. The lower and upper limits of the cell proliferation are given by the 5th and 95th percentiles at cell positions 4 and 43 respectively. The peak labelling index is about 30% and it occurs at cell position 15. The labelling index at the crypt base, the probable stem cell zone, is about 14%, suggesting that these cells have a longer cell cycle. Taking a value of 8.6 hours for the duration of the S phase (deduced from the flow cytometric data) and assuming a growth fraction of 1.0 for the mid-crypt, these data provide an estimate of about 30 hours for the cell cycle time. The rectal crypts are about the same size but contain about 30% fewer S phase cells. The data also yielded a per cent BrdUrd labelled mitosis curve.
Transforming growth factor-beta (TGF-beta) is a potent inhibitor of epithelial cell growth. Human colon cancer cell lines
with high rates of microsatellite instability were found to harbor mutations in the type II TGF-beta receptor (RII) gene.
Eight such examples, due to three different mutations, were identified. The mutations were clustered within small repeated
sequences in the RII gene, were accompanied by the absence of cell surface RII receptors, and were usually associated with
small amounts of RII transcript. RII mutation, by inducing the escape of cells from TGF-beta-mediated growth control, links
DNA repair defects with a specific pathway of tumor progression.
We report that CpG island methylation, an epigenetic modification of DNA known to correlate closely with silencing of gene transcription, appears in the oestrogen receptor (ER) gene in a subpopulation of cells which increases as a direct function of age in human colonic mucosa. This same methylation change characterizes virtually all cells in all 45 colorectal tumours examined, including the earliest stages of tumour formation. ER gene expression is diminished or absent in colorectal tumours, and introduction of an exogenous ER gene in cultured colon carcinoma cells resulted in marked growth suppression. Our data suggest that methylation associated inactivation of the ER gene in ageing colorectal mucosa could be one of the earliest events that predispose to sporadic colorectal tumorigenesis.
Genomic instability at simple repeated sequences (SRS) is a landmark for some sporadic and hereditary cancers of the colon. We have identified several human tumour cell lines with up to 1,000-fold increases in mutation rates for endogenous microsatellite sequences, relative to normal cells or tumour cells without the mutator phenotype and show that they are very early events in tumorigenesis. Our in vivo and in vitro results show that the genomic instability persists after transformation and that microsatellite mutations accumulate as consecutive somatic slippage events of a single or a few repeated units. This mechanism may account for the repeat expansions in triplet hereditary diseases and the same defect in replication fidelity in non-polyposis colon cancer could also contribute to the non-mendelian anticipation in these diseases.
Spontaneous errors in DNA replication have been suggested to play a significant role in neoplastic transformation and to explain the chromosomal alterations seen in cancer cells. A defective replication factor could increase the mutation rate in clonal variants arising during tumour progression, but despite intensive efforts, increases in tumour cell mutation rates have not been unambiguously shown. Here we use an unbiased genomic fingerprinting technique to show that 12 per cent of colorectal carcinomas carry somatic deletions in poly(dA.dT) sequences and other simple repeats. We estimate that cells from these tumours can carry more than 100,000 such mutations. Only tumours with affected poly(dA.dT) sequences carry mutations in the other simple repeats examined, and such mutations can be found in all neoplastic regions of multiple tumours from the same patient, including adenomas. Tumours with these mutations show distinctive genotypic and phenotypic features. We conclude that these mutations reflect a previously undescribed form of carcinogenesis in the colon (predisposition to which may be inherited) mediated by a mutation in a DNA replication factor resulting in reduced fidelity for replication or repair (a 'mutator mutation').
Precise mapping of DNA methylation patterns in CpG islands has become essential for understanding diverse biological processes such as the regulation of imprinted genes, X chromosome inactivation, and tumor suppressor gene silencing in human cancer. We describe a new method, MSP (methylation-specific PCR), which can rapidly assess the methylation status of virtually any group of CpG sites within a CpG island, independent of the use of methylation-sensitive restriction enzymes. This assay entails initial modification of DNA by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequent amplification with primers specific for methylated versus unmethylated DNA. MSP requires only small quantities of DNA, is sensitive to 0.1% methylated alleles of a given CpG island locus, and can be performed on DNA extracted from paraffin-embedded samples. MSP eliminates the false positive results inherent to previous PCR-based approaches which relied on differential restriction enzyme cleavage to distinguish methylated from unmethylated DNA. In this study, we demonstrate the use of MSP to identify promoter region hypermethylation changes associated with transcriptional inactivation in four important tumor suppressor genes (p16, p15, E-cadherin, and von Hippel-Lindau) in human cancer.
The authors are grateful to the members of their laboratories for their contributions to the reviewed studies and for their critical reading of the manuscript and to F. Giardiello and S. Hamilton for photographs of colorectal lesions. The authors are supported by Public Health Service grants CA 43460, CA 57345, and CA 62924. B. V. is an Investigator of the Howard Hughes Medical Institute.
Somatic mutations in DNA mismatch repair genes have been observed in sporadic tumors as well as cell lines and xenografts derived from such tumors implicating genetic defects of mismatch repair genes in the development of such tumors. However, the proportion of sporadic tumors in which mismatch repair genes have been inactivated has not been determined accurately. We have analyzed 66 sporadic colorectal tumors for the expression of hMLH1 by immunohistochemistry and identified 4 tumors that do not express hMLH1. These four colorectal tumors, a colon tumor cell line (SW48) and an endometrial tumor cell line (AN3CA), did not express hMLH1, despite the absence of mutations in its coding sequence. Cytosine methylation of the hMLH1 promoter region was found in these four colorectal tumors, whereas cytosine methylation of the hMLH1 promoter region was absent in adjacent normal tissue or in nine tumors that expressed hMLH1. In addition, cytosine methylation of the hMLH1 promoter region was observed in the SW48 and AN3CA cell lines that do not express hMLH1 but not in four tumor cell lines known to express hMLH1 mRNA. Our data indicate that DNA methylation is likely to be a common mode of mismatch repair gene inactivation in sporadic tumors.
Promoter region CpG island methylation is associated with tumor suppressor gene silencing in neoplasia. GenBank sequence analyses
revealed that a number of CpG islands are juxtaposed to multiple Alu repeats, which have been proposed as “de novo methylation centers.” These islands also contain multiple Sp1 elements located upstream and downstream of transcription start,
which have been shown to protect CpG islands from methylation. We mapped the methylation patterns of the E-cadherin(E-cad) and von Hippel-Lindau (VHL) tumor suppressor gene CpG island regions in normal and neoplastic cells. Although unmethylated in normal tissue, these islands
were embedded between densely methylated flanking regions containing multiple Alu repeats. These methylated flanks were segregated
from the unmethylated, island CpG sites by Sp1-rich boundary regions. Finally, in human fibroblasts overexpressing DNA methyltransferase,
de novomethylation of the E-cad CpG island initially involved sequences at both ends of the island and the adjacent, flanking regions and progressed with
time to encompass the entire CpG island region. Together, these data suggest that boundaries exist at both ends of a CpG island
to maintain the unmethylated state in normal tissue and that these boundaries may be progressively overridden, eliciting thede novo methylation associated with tumor suppressor gene silencing in neoplasia.
De novo methylation of promoter region CpG islands has been increasingly associated with transcriptional inactivation of important genes in neoplasia. To study the potential mechanisms underlying aberrant methylation in cancer, we have determined the methylation patterns of selected genes in colorectal cancers with and without microsatellite instability (MI), which results from defects in one of several base mismatch repair genes. A total of 47 colorectal cancers were analyzed, of which 15 were MI+ (32%). We now report that both the frequency and the extent of de novo methylation are strikingly increased in MI+ cancers. Hypermethylation of the p16 gene was found in 60% of MI+ cancers, compared to only 22% in MI- cancers (P = 0.02). Similarly, hypermethylation of the thrombospondin-1 (TSP-1) gene, an angiogenesis inhibitor, was increased in MI+ cancers (27% versus 0%; P = 0.008). Extensive methylation of insulin-like growth factor II (IGF2) and hypermethylated in cancer-1 (HIC-1) genes was observed in 60 and 80% of MI+ cancers, respectively, as contrasted with 6 and 38% of MI- cancers (P = 0.0002 and 0.01, respectively). Furthermore, 60% of the MI+ cancers displayed the hypermethylation events at two or more loci in a concordant manner compared to only 9% of the MI- cancers (P < 0.001). These results demonstrate a strong link between promoter hypermethylation and genetic instability due to deficient DNA repair.
An exacerbated genomic instability characterizes hereditary and sporadic gastrointestinal cancer of the microsatellite mutator phenotype (MMP), generating somatic frameshift mutations in genes containing mononucleotide repeats. We have recently shown that approximately 50, 40, and 30% of MMP+ colon tumors harbor frameshift mutations in (G)8, (A)8, and (C)8 tracks within the proapoptotic gene BAX and the hMSH3 and hMSH6 DNA mismatch repair genes, respectively. Here we report a higher incidence of frameshift mutations in these 3 genes in a panel of 25 MMP+ gastric adenocarcinomas: 64% in BAX and hMSH3, and 52% in hMSH6. These results support a multiple mutator gene model for the stepwise unfolding of the MMP and further illustrate the importance of the escape from apoptosis in gastrointestinal cancer. The tumor suppressor role played by BAX is also supported by the finding of other somatic BAX mutations, including recurrent missense mutations, not only in gastrointestinal cancer of the MMP but also in gastrointestinal cancer without the MMP.
The comparative typing of matched tumor and blood DNAs at dinucleotide repeat (microsatellite) loci has revealed in tumor DNA the presence of alleles that are not observed in normal DNA. The occurrence of these additional alleles is possibly due to replication errors (RERs). Although this observation has led to the recognition of a subtype of colorectal cancer with a high incidence of RERs (caused by a deficiency in DNA mismatch repair), a thorough analysis of the RER frequency in a consecutive series of colorectal cancers had not been reported. It is shown here that the extensive typing of 88 colorectal tumors reveals a bimodal distribution for the frequency of RER at microsatellite loci. Within the major mode (75 tumors, RER- subtype), the probability that a locus exhibited instability did not differ significantly among loci and tumors, being 0.02. The subsequent development of a statistical test for an operational discrimination between the RER- and RER+ subtypes indicated that the probability of misclassification did not exceed 0.001 in this series. The frequency of K-ras mutation was found to be equivalent in the two subtypes. However, in the RER+ tumors, the p53 gene mutation was less frequently detected, the adenomatous polyposis coli (APC) mutation was rare, and the biallelic inactivation of either of these genes was not observed. Furthermore, the concomitant occurrence of APC and tumor growth factor beta receptor type II gene alterations was found only once. These data suggest that the repertoires of genes that are frequently altered in RER+ and RER- tumors may be more different than previously thought.
In December 1997, the National Cancer Institute sponsored "The International Workshop on Microsatellite Instability and RER Phenotypes in Cancer Detection and Familial Predisposition," to review and unify the field. The following recommendations were endorsed at the workshop. (a) The form of genomic instability associated with defective DNA mismatch repair in tumors is to be called microsatellite instability (MSI). (b) A panel of five microsatellites has been validated and is recommended as a reference panel for future research in the field. Tumors may be characterized on the basis of: high-frequency MSI (MSI-H), if two or more of the five markers show instability (i.e., have insertion/deletion mutations), and low-frequency MSI (MSI-L), if only one of the five markers shows instability. The distinction between microsatellite stable (MSS) and low frequency MSI (MSI-L) can only be accomplished if a greater number of markers is utilized. (c) A unique clinical and pathological phenotype is identified for the MSI-H tumors, which comprise approximately 15% of colorectal cancers, whereas MSI-L and MSS tumors appear to be phenotypically similar. MSI-H colorectal tumors are found predominantly in the proximal colon, have unique histopathological features, and are associated with a less aggressive clinical course than are stage-matched MSI-L or MSS tumors. Preclinical models suggest the possibility that these tumors may be resistant to the cytotoxicity induced by certain chemotherapeutic agents. The implications for MSI-L are not yet clear. (d) MSI can be measured in fresh or fixed tumor specimens equally well; microdissection of pathological specimens is recommended to enrich for neoplastic tissue; and normal tissue is required to document the presence of MSI. (e) The "Bethesda guidelines," which were developed in 1996 to assist in the selection of tumors for microsatellite analysis, are endorsed. (f) The spectrum of microsatellite alterations in noncolonic tumors was reviewed, and it was concluded that the above recommendations apply only to colorectal neoplasms. (g) A research agenda was recommended.
The discovery of numerous hypermethylated promoters of tumour-suppressor genes, along with a better understanding of gene-silencing mechanisms, has moved DNA methylation from obscurity to recognition as an alternative mechanism of tumour-suppressor inactivation in cancer. Epigenetic events can also facilitate genetic damage, as illustrated by the increased mutagenicity of 5-methylcytosine and the silencing of the MLH1 mismatch repair gene by DNA methylation in colorectal tumours. We review here current mechanistic understanding of the role of DNA methylation in malignant transformation, and suggest Knudson's two-hit hypothesis should now be expanded to include epigenetic mechanisms of gene inactivation.
Aberrant methylation of promoter region CpG islands is associated with transcriptional inactivation of tumor-suppressor genes in neoplasia. To understand global patterns of CpG island methylation in colorectal cancer, we have used a recently developed technique called methylated CpG island amplification to examine 30 newly cloned differentially methylated DNA sequences. Of these 30 clones, 19 (63%) were progressively methylated in an age-dependent manner in normal colon, 7 (23%) were methylated in a cancer-specific manner, and 4 (13%) were methylated only in cell lines. Thus, a majority of CpG islands methylated in colon cancer are also methylated in a subset of normal colonic cells during the process of aging. In contrast, methylation of the cancer-specific clones was found exclusively in a subset of colorectal cancers, which appear to display a CpG island methylator phenotype (CIMP). CIMP+ tumors also have a high incidence of p16 and THBS1 methylation, and they include the majority of sporadic colorectal cancers with microsatellite instability related to hMLH1 methylation. We thus define a pathway in colorectal cancer that appears to be responsible for the majority of sporadic tumors with mismatch repair deficiency.
Aberrant DNA methylation is a common phenomenon in human cancer, but its patterns, causes, and consequences are poorly defined. Promoter methylation of the DNA mismatch repair gene MutL homologue (MLH1) has been implicated in the subset of colorectal cancers that shows microsatellite instability (MSI). The present analysis of four MspI/HpaII sites at the MLH1 promoter region in a series of 89 sporadic colorectal cancers revealed two main methylation patterns that closely correlated with the MSI status of the tumors. These sites were hypermethylated in tumor tissue relative to normal mucosa in most MSI(+) cases (31/51, 61%). By contrast, in the majority of MSI(-) cases (20/38, 53%) the same sites showed methylation in normal mucosa and hypomethylation in tumor tissue. Hypermethylation displayed a direct correlation with increasing age and proximal location in the bowel and was accompanied by immunohistochemically documented loss of MLH1 protein both in tumors and in normal tissue. Similar patterns of methylation were observed in the promoter region of the calcitonin gene that does not have a known functional role in tumorigenesis. We propose a model of carcinogenesis where different epigenetic phenotypes distinguish the colonic mucosa in individuals who develop MSI(+) and MSI(-) tumors. These phenotypes may underlie the different developmental pathways that are known to occur in these tumors.
Aberrant methylation of 5' CpG islands is thought to play an important role in the inactivation of tumor suppressor genes in cancer. In colorectal cancer, a group of tumors is characterized by a hypermethylator phenotype termed CpG island methylator phenotype (CIMP), which includes methylation of such genes as p16 and hMLH1. To study whether CIMP is present in gastric cancer, the methylation status of five newly cloned CpG islands was examined in 56 gastric cancers using bisulfite-PCR. Simultaneous methylation of three loci or more was observed in 23 (41%) of 56 cancers, which suggests that these tumors have the hypermethylator phenotype CIMP. There was a significant concordance between CIMP and the methylation of known genes including p16, and hMLH1; methylation of p16 was detected in 16 (70%) of 23 CIMP+ tumors, 1 (8%) of 12 CIMP intermediate tumors, and 1 (5%) of 21 CIMP- tumors (P<0.0001). Methylation of the hMLH1 gene was detected in three of five tumors that showed microsatellite instability, and all three of the cases were CIMP+. The CIMP phenotype is an early event in gastric cancer, being present in the normal tissue adjacent to cancer in 5 of 56 cases. These results suggest that CIMP may be one of the major pathways that contribute to tumorigenesis in gastric cancers.
Colorectal cancers (CRCs) are characterized by multiple genetic (mutations) and epigenetic (CpG island methylation) alterations, but it is not known whether these evolve independently through stochastic processes. We have recently described a novel pathway termed CpG island methylator phenotype (CIMP) in CRC, which is characterized by the simultaneous methylation of multiple CpG islands, including several known genes, such as p16, hMLH1, and THBS1. We have now studied mutations in K-RAS, p53, DPC4, and TGFbetaRII in a panel of colorectal tumors with or without CIMP. We find that CIMP defines two groups of tumors with significantly different genetic lesions: frequent K-RAS mutations were found in CIMP(+) CRCs (28/41, 68%) compared with CIMP(-) cases (14/47, 30%, P = 0.0005). By contrast, p53 mutations were found in 24% (10/41) of CIMP(+) CRCs vs. 60% (30/46) of CIMP(-) cases (P = 0.002). Both of these differences were independent of microsatellite instability. These interactions between CIMP, K-RAS mutations, and p53 mutations were preserved in colorectal adenomas, suggesting that they occur early in carcinogenesis. The distinct combinations of epigenetic and genetic alterations in each group suggest that activation of oncogenes and inactivation of tumor suppressor genes is related to the underlying mechanism of generating molecular diversity in cancer, rather than simply accumulate stochastically during cancer development.
We have applied a methylation‐sensitive restriction endonuclease, NotI, to the existing amplified fragment length polymorphism (AFLP) method and developed NotI‐MseI methylation‐sensitive‐AFLP (MS‐AFLP). NotI‐MseI MS‐AFLP allows the analysis of DNA methylation alterations at the NotI sites scattered over the genome. Hypermethylation and hypomethylation are visualized by the decrease and increase in the band intensity of DNA fingerprints. Identification of consistent changes can be facilitated through parallel electrophoresis of multiple samples. DNA fragments exhibiting alterations can be cloned from fingerprint bands by amplification of gel‐eluted DNA with the same pair of primers used for radioactive fingerprint presentation. Fluorescent NotI‐MseI MS‐AFLP offers a safer method of studying the alterations in DNA methylation, and may be applied to the hybridization of DNA microarrays in the future. Using NotI‐MseI MS‐AFLP, we observed frequent hypomethylation of a satellite DNA repeat sequence in a majority of breast tumors.
Background: Hypermethylation of a CpG-rich promoter (CpG island) blocks expression of the corresponding gene. The CpG island methylator phenotype (CIMP), defined as a variable pattern of hypermethylation of CpG islands in tumor suppressor genes, may be associated with carcinogenesis. To determine whether CIMP is associated with the development of hepatocellular carcinoma (HCC) and with exposure to environmental agents, we examined the methylation status of CpG islands in HCCs from countries with various HCC risks. Methods: We examined the methylation status of 12 CpG islands (eight for known genes) in 85 HCC tumors from various geographic locations by use of bisulfite–polymerase chain reaction methylation assays and analyzed results with univariate and multivariable methods. All statistical tests were two-sided. Results: Eight CpG islands were hypermethylated. The frequency of hypermethylation in the 85 tumors was 62% for the estrogen receptor (ER), 42% for p16, 18% for cyclooxygenase-2, 21% for the T-type calcium channel gene, 38% for MINT31, 28% for MINT1, 15% for MINT27, and 11% for MINT2 (the latter four CpG islands are not yet associated with genes). Methylation levels of the eight frequently methylated CpG islands were positively correlated (from R =. 2 [P = .05] to R =. 6 [P<.001]), supporting the presence of CIMP. p16 methylation had statistically significant geographic variation (34.4% in tumors from China and Egypt versus 12.2% in tumors from the United States and Europe, difference = 22.2%; 95% confidence interval [CI] = 11.2% to 33.2%; P<.001). Similar geographic variations were observed for ER methylation and CIMP. This observation was partly related to higher methylation in tumors from patients with cirrhosis (33.6% for patients with cirrhosis versus 11.7% for those without it; difference = 21.9%; 95% CI = 10.9% to 32.8%; P<.001) or hepatitis (34.2% for patients with hepatitis versus 6.2% for those without it; difference = 28%; 95% CI = 18.3% to 37.6%; P<.001). Conclusion: Geographic variations in the methylation status of various CpG islands indicate that environmental factors may influence the frequent and concordant degree of hypermethylation in multiple genes in HCC tumors. [J Natl Cancer Inst 2002;94:755–61]
The DNA repair protein O6-methylguanine DNA methyltransferase (MGMT) removes alkyl adducts from the O6 position of guanine. MGMT expression is decreased in some tumor tissues, and lack of activity has been observed in some cell lines. Loss of expression is rarely due to deletion, mutation, or rearrangement of the MGMT gene, but methylation of discrete regions of the CpG island of MGMT has been associated with the silencing of the gene in cell lines. We used methylation-specific PCR to study the promoter methylation of the MGMT gene. All normal tissues and expressing cancer cell lines were unmethylated, whereas nonexpressing cancer cell lines were methylated. Among the more than 500 primary human tumors examined, MGMT hypermethylation was present in a subset of specific types of cancer. In gliomas and colorectal carcinomas, aberrant methylation was detected in 40% of the tumors, whereas in non-small cell lung carcinomas, lymphomas, and head and neck carcino- mas, this alteration was found in 25% of the tumors. MGMT methylation was found rarely or not at all in other tumor types. We also analyzed MGMT expression by immunohistochemistry in relation to the methyla- tion status in 31 primary tumors. The presence of aberrant hypermethy- lation was associated with loss of MGMT protein, in contrast to retention of protein in the majority of tumors without aberrant hypermethylation. Our results suggest that epigenetic inactivation of MGMT plays an im- portant role in primary human neoplasia.
We have applied a methylation-sensitive restriction endonuclease, NotI, to the existing amplified fragment length polymorphism (AFLP) method and developed NotI-MseI methylation-sensitive-AFLP (MS-AFLP). NotI-MseI MS-AFLP allows the analysis of DNA methylation alterations at the NotI sites scattered over the genome. Hypermethylation and hypomethylation are visualized by the decrease and increase in the band intensity of DNA fingerprints. Identification of consistent changes can be facilitated through parallel electrophoresis of multiple samples. DNA fragments exhibiting alterations can be cloned from fingerprint bands by amplification of gel-eluted DNA with the same pair of primers used for radioactive fingerprint presentation. Fluorescent NotI-MseI MS-AFLP offers a safer method of studying the alterations in DNA methylation, and may be applied to the hybridization of DNA microarrays in the future. Using NotI-MseI MS-AFLP, we observed frequent hypomethylation of a satellite DNA repeat sequence in a majority of breast tumors.
Mutations in the k-ras and TP53 genes, as well as microsatellite instability (MIN), are frequent genetic alterations in colorectal carcinomas and represent 3 different mechanisms in the carcinogenic process. Both the incidence of colorectal cancer and the frequency of genetic alterations in such tumours have been related to different clinico-pathological variables, including age and gender of the patient and location of the tumour. A number of studies have also reported associations between different types of genetic alterations. We therefore wanted to explore the relationship between these genetic and clinico-pathological variables using multivariate analysis on material from 282 colorectal carcinomas. Three logistic regression models were constructed: 1) the presence of K-ras mutations was dependent on MIN and age and gender of patient, with an especially low frequency among younger males and in tumours with MIN (overall p = 0.0003); 2) the presence of TP53 mutations was only dependent on tumour location, with a positive association to cancers occurring distally (p = 0.002); and 3) the presence of MIN was dependent on age, gender and K-ras and TP53 mutations, as well as on tumour location. MIN was most frequent among younger male and older female patients, was rare in tumours with K-ras or TP53 mutations and was found almost exclusively in the proximal colon (overall p < 0.0001). Our data confirm that different genetic pathways to colorectal cancer dominate in the proximal and distal segments of the bowel and suggest that the K-ras- and MIN-dependent pathways are influenced by different sex-related factors. Int. J. Cancer 74:664–669, 1997.© 1997 Wiley-Liss, Inc.
Genetic instability has long been hypothesized to be a cardinal feature of cancer. Recent work has strengthened the proposal that mutational alterations conferring instability occur early during tumour formation. The ensuing genetic instability drives tumour progression by generating mutations in oncogenes and tumour-suppressor genes. These mutant genes provide cancer cells with a selective growth advantage, thereby leading to the clonal outgrowth of a tumour. Here, we discuss the role of genetic instability in tumour formation and outline future work necessary to substantiate the genetic instability hypothesis.
Methylation of cytosines in CpG islands silences gene expression. CpG island methylator phenotype (CIMP) in colorectal cancers is characterized by abnormal methylation of multiple CpG islands including those in several tumor suppressor genes such as p16, hMLH1, and THBS1. CpG island methylation has not been well characterized in adenomas. We evaluated methylation status at p16, MINT2, and MINT31 loci, which are frequently methylated in colorectal carcinomas, in 108 colorectal adenomas from a prospective study of 50 patients without cancer. Methylation at one or more loci was present in 48% (52 of 108) of adenomas with 25% (19 of 76) CIMP-high (two or more methylated loci) and 32% (24 of 76) CIMP-low (one methylated locus). The p16 gene was methylated in 27% (19 of 71) of adenomas. Methylation status of different adenomas from the same patient was not correlated (odds ratio, 0.93; P = 0.77). Adenomas with tubulovillous or villous histology were frequently methylated: 73% (17 of 26) versus 41% (35 of 85) of tubular adenomas (odds ratio, 3.46; P = 0.02). High levels of microsatellite instability were more frequent in adenomas without methylation (13% versus 2%; odds ratio, 8.48; P = 0.05). Our results indicate that methylation plays an important role early in colorectal tumorigenesis. CpG island methylation is more common in adenomas with tubulovillous/villous histology, a characteristic associated with more frequent predisposition to invasive carcinoma. Methylation is distinct from microsatellite instability and develops in individual adenomas rather than resulting from a field defect in an individual patient.
Although vertebrate DNA is generally depleted in the dinucleotide CpG, it has recently been shown that some vertebrate genes contain CpG islands, regions of DNA with a high G + C content and a high frequency of CpG dinucleotides relative to the bulk genome. In this study, a large number of sequences of vertebrate genes were screened for the presence of CpG islands. Each CpG island was then analysed in terms of length, nucleotide composition, frequency of CpG dinucleotides, and location relative to the transcription unit of the associated gene. CpG islands were associated with the 5′ ends of all housekeeping genes and many tissue-specific genes, and with the 3′ ends of some tissue-specific genes. A few genes contained both 5′ and 3′ CpG islands, separated by several thousand base-pairs of CpG-depleted DNA. The 5′ CpG islands extended through 5′-flanking DNA, exons and introns, whereas most of the 3′ CpG islands appeared to be associated with exons. CpG islands were generally found in the same position relative to the transcription unit of equivalent genes in different species, with some notable exceptions.
It has been suggested that cancer represents an alteration in DNA, heritable by progeny cells, that leads to abnormally regulated expression of normal cellular genes; DNA alterations such as mutations, rearrangements and changes in methylation have been proposed to have such a role. Because of increasing evidence that DNA methylation is important in gene expression (for review see refs 7, 9-11), several investigators have studied DNA methylation in animal tumours, transformed cells and leukaemia cells in culture. The results of these studies have varied; depending on the techniques and systems used, an increase, decrease, or no change in the degree of methylation has been reported. To our knowledge, however, primary human tumour tissues have not been used in such studies. We have now examined DNA methylation in human cancer with three considerations in mind: (1) the methylation pattern of specific genes, rather than total levels of methylation, was determined; (2) human cancers and adjacent analogous normal tissues, unconditioned by culture media, were analysed; and (3) the cancers were taken from patients who had received neither radiation nor chemotherapy. In four of five patients studied, representing two histological types of cancer, substantial hypomethylation was found in genes of cancer cells compared with their normal counterparts. This hypomethylation was progressive in a metastasis from one of the patients.
We have used a combination of genetics and pharmacology to assess the effects of reduced DNA methyltransferase activity on ApcMin-induced intestinal neoplasia in mice. A reduction in the DNA methyltransferase activity in Min mice due to heterozygosity of the DNA methyltransferase gene, in conjunction with a weekly dose of the DNA methyltransferase inhibitor 5-aza-deoxycytidine, reduced the average number of intestinal adenomas from 113 in the control mice to only 2 polyps in the treated heterozygotes. Hence, DNA methyltransferase activity contributes substantially to tumor development in this mouse model of intestinal neoplasia. Our results argue against an oncogenic effect of DNA hypomethylation. Moreover, they are consistent with a role for DNA methyltransferase in the generation of the C to T transitions seen at high frequency in human colorectal tumors.
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The mutational theory of cancer (Knudson 1971, 1985) has gained overwhelming support as germ-line and somatic mutations have been shown to activate the malignant potential of oncogenes and to inactivate the repressor function of tumor suppressor genes (Bishop 1991). The analysis of these tumor-specific mutations has yielded fundamental information on the mechanisms of carcinogenesis, but their etiology has remained poorly understood. There is no agreement in the estimation of the relative contribution of insults by genotoxic agents and of endogenous DNA replication errors to the genesis of these mutations in cancer (Ames and Gold 1990; Weinstein 1991).
The concept that spontaneous errors in DNA replication may be fundamental in transformation was put forward (Loeb et al. 1974; Cairns 1975) in an attempt to explain the genomic instability of cancer cells (Schimke et al. 1986; Cheng and Loeb 1993). A defective DNA replication factor could enhance the error rate in the...
DNA replication errors (RERs) in repeated nucleotide sequences due to defective mismatch repair genes have been reported in a subset of sporadic colorectal carcinomas and in the majority of tumors from patients with hereditary nonpolyposis colorectal cancer syndrome (HNPCC). We detected RER in 18 cases (13%) in a prospective series of 137 sporadic stage II and III (Dukes' B and C) colorectal carcinomas. The clinical and pathological features of the RER-positive cases differed from those without RER. The patients with RER-positive cancers tended to be somewhat younger (60 +/- 5 years, range 22-83, versus 66 +/- 1, range 27-90, P = 0.2 with unequal variances) and had a marked preponderance of tumors proximal to the splenic flexure (17/18, 94%, versus 41/119, 34%, P < 0.0001). Only two RER-positive patients (11%) had a family history of colorectal cancer. In comparison to the 41 RER-negative proximal colonic cancers, RER-positive cancers had more frequent exophytic growth (P = 0.04), large size (P = 0.03), poor differentiation (P = 0.0004), extracellular mucin production (P = 0.003) and Crohn's-like lymphoid reaction (P = 0.003), and a trend toward less frequent p53 gene product overexpression by immunohistochemistry (3/17, 18%, versus 18/41, 44%, P = 0.06). We conclude that a subset of sporadic colorectal carcinomas has unique biological features that may indicate inherited germline mutation, de novo germline mutation, or somatic mutations of the mismatch repair genes involved in HNPCC.
Colorectal tumor DNA was examined for somatic instability at (CA)n repeats on human chromosomes 5q, 15q, 17p, and 18q. Differences between tumor and normal DNA were detected in 25 of the 90 (28 percent) tumors examined. This instability appeared as either a substantial change in repeat length (often heterogeneous in nature) or a minor change (typically two base pairs). Microsatellite instability was significantly correlated with the tumor's location in the proximal colon (P = 0.003), with increased patient survival (P = 0.02), and, inversely, with loss of heterozygosity for chromosomes 5q, 17p, and 18q. These data suggest that some colorectal cancers may arise through a mechanism that does not necessarily involve loss of heterozygosity.
This review focuses on the genomic instability underlying the microsatellite mutator phenotype (MMP) pathway for cancer. MMP was discovered by the application of DNA fingerprinting by Arbitrarily Primed PCR (AP-PCR) to the analysis of somatic genetic alterations in colon tumors. The unbiased nature of AP-PCR permitted to infer, from the mobility shifts observed in some fingerprint bands, the accumulation by a subset of colon tumors of hundreds of thousands of somatic mutations in simple repeated sequences or microsatellites. We deduced that this enormous agglomeration of clonal mutations was due to the previous occurrence of 'mutator mutations' in DNA replication or repair factors leading to a decreased fidelity of replication. These mutator mutations appeared to be the remote cause for the development of these MMP tumors, whose existence unmistakably validated the hypothesis of 'cancer as a mutator phenotype'. Since these original observations, rapid progress has occurred in the field. The mutator mutations were identified as those occurring in members of the DNA mismatch repair gene family, which are also associated with hereditary non-polyposis colorectal cancer (HN-PCC). In this review I discuss the experimental approach that allowed the discovery of MMP and the features of the genomic instability of these tumors. I also review recent developments that affect the understanding of the role of the mismatch repair mutator mutations in the unfolding of MMP during carcinogenesis.
Cancers of the microsatellite mutator phenotype (MMP) show exaggerated genomic instability at simple repeat sequences. More
than 50 percent (21 out of 41) of human MMP+ colon adenocarcinomas examined were found to have frameshift mutations in a tract of eight deoxyguanosines [(G)8] within BAX, a gene that promotes apoptosis. These mutations were absent in MMP− tumors and were significantly less frequent in (G)8 repeats from other genes. Frameshift mutations were present in both BAX alleles in some MMP+ colon tumor cell lines and in primary tumors. These results suggest that inactivating BAX mutations are selected for during the progression of colorectal MMP+ tumors and that the wild-type BAX gene plays a suppressor role in a p53-independent pathway for colorectal carcinogenesis.
Mutations in the k-ras and TP53 genes, as well as microsatellite instability (MIN), are frequent genetic alterations in colorectal carcinomas and represent 3 different mechanisms in the carcinogenic process. Both the incidence of colorectal cancer and the frequency of genetic alterations in such tumours have been related to different clinico-pathological variables, including age and gender of the patient and location of the tumour. A number of studies have also reported associations between different types of genetic alterations. We therefore wanted to explore the relationship between these genetic and clinico-pathological variables using multivariate analysis on material from 282 colorectal carcinomas. Three logistic regression models were constructed: 1) the presence of K-ras mutations was dependent on MIN and age and gender of patient, with an especially low frequency among younger males and in tumours with MIN (overall p = 0.0003); 2) the presence of TP53 mutations was only dependent on tumour location, with a positive association to cancers occurring distally (p = 0.002); and 3) the presence of MIN was dependent on age, gender and K-ras and TP53 mutations, as well as on tumour location. MIN was most frequent among younger male and older female patients, was rare in tumours with K-ras or TP53 mutations and was found almost exclusively in the proximal colon (overall p < 0.0001). Our data confirm that different genetic pathways to colorectal cancer dominate in the proximal and distal segments of the bowel and suggest that the K-ras- and MIN-dependent pathways are influenced by different sex-related factors.
Eukaryotic mismatch repair (MMR) has been shown to require two different heterodimeric complexes of MutS-related proteins: MSH2-MSH3 and MSH2-MSH6. These two complexes have different mispair recognition properties and different abilities to support MMR. Alternative models have been proposed for how these MSH complexes function in MMR. Two different heterodimeric complexes of MutL-related proteins, MLH1-PMS1 (human PMS2) and MLH1-MLH3 (human PMS1) also function in MMR and appear to interact with other MMR proteins including the MSH complexes and replication factors. A number of other proteins have been implicated in MMR, including DNA polymerase delta, RPA (replication protein A), PCNA (proliferating cell nuclear antigen), RFC (replication factor C), Exonuclease 1, FEN1 (RAD27) and the DNA polymerase delta and epsilon associated exonucleases. MMR proteins have also been shown to function in other types of repair and recombination that appear distinct from MMR. MMR proteins function in these processes in conjunction with components of nucleotide excision repair (NER) and, possibly, recombination.
Colon cancer of the microsatellite mutator phenotype (MMP) exhibits significant genotype differences from cancer without the MMP. Twenty-nine MMP-positive gastric cancers were analyzed to clarify if these genotype differences were also associated with distinctive clinicopathologic features.
Alterations of p53, beta2-microglobulin (beta2M ), hMLH1, and hMSH2 genes were analyzed by using polymerase chain reaction, single-strand conformational polymorphism, sequencing, microallelotyping, hypermethylation assays, and immunostaining. The results were contrasted with mutations in BAX, hMSH3, and hMSH6, genes target for the MMP.
Tumors with the MMP had a significantly lower incidence of p53 gene mutations than the other tumors and often contained beta2M gene somatic mutations. Many tumors contained concomitant genetic and epigenetic alterations in DNA mismatch repair genes, hMLH1, hMSH2, hMSH3, and hMSH6. Gastric cancer of the MMP was associated with well/moderate differentiation, distal location, and better survival.
Analysis of somatic alterations in microsatellite sequences and in cancer genes target for the MMP is useful for the classification of groups of gastric cancers with different prognosis. The results further support the concept that (gastric) cancer of the MMP represents a distinctive oncogenic pathway because the mutated cancer genes are usually different from those found in tumors without the MMP.
Colorectal cancer (CRC) occurring in the proximal colon and among women may represent a distinct subtype of the disease. In the present study of 120 sporadic CRCs, we used methylation-specific PCR to test whether methylation of the CpG island in the 5' region of the p16INK4a tumor suppressor gene was associated with anatomical location, gender, or other clinicopathological characteristics. Overall, 18.3% of the tumors had detectable p16INK4a methylation. A marked preponderance of methylated tumors occurred within the proximal colon; cancers occurring proximal to the sigmoid colon were 13.1 times more likely to contain methylated p16INK4a compared with distal tumors. In addition, female patients were 8.8 times more likely than males to have methylation-positive cancers, and p16INK4a methylation was also associated with poorly differentiated tumors. The localization of tumors with p16INK4a methylation within the proximal colon and among female patients specifically adds to a growing database of molecular alterations that define important subtypes of sporadic CRC. The potentially reversible nature of CpG methylation may provide novel therapeutic opportunities for this increasing subtype of the disease, which, due to anatomical location, presents a great challenge for early detection.
It is difficult to observe human tumor progression as precursor lesions are systematically removed. Alternatives to direct observations, commonly used to reveal the hidden past of species and populations, are sequence comparisons or molecular clocks. Noncoding microsatellite (MS) loci were employed as molecular tumor clocks in 13 human mutator phenotype (MSI(+)) colorectal tumors. Quantitative analysis revealed that specific patterns of somatic MS mutations accumulate with division after loss of mismatch repair (MMR). Tumors had unique patterns of MS mutation, and, therefore, based on this model, each tumor had its own unique history. Loss of MMR occurred very early relative to terminal clonal expansion, with an estimated average of 2,300 divisions since loss of MMR and 280 divisions since expansion. Contrary to the classical adenoma-cancer sequence, MSI(+) adenomas were nearly as old as cancers (2,000 versus 2,400 divisions since loss of MMR). Negative clinical examinations preceded six tumors, independently documenting an absence of visible precursors during early MSI(+) adenoma or cancer progression. These findings further extend a window beyond visible progression since loss of MMR appears to start a genetic phase involving clone sizes or phenotypes below a threshold of clinical detection. This previously occult prologue before visible neoplasia is longer and therefore likely more important than generally appreciated.
Cancer development and progression is dictated by a series of alterations in genes such as oncogenes, tumor suppressor genes, DNA repair genes, and others. DNA methylation is an epigenetic modification that is profoundly altered in most cancers. Recently, hypermethylation of CpG-rich areas located in the promoter of genes (CpG islands) has been shown to be commonly implicated in silencing tumor suppressor genes in cancer. By cloning and characterizing a large number of such CpG islands hypermethylated in colon cancer, we found that two processes explain most of these events. Age-related CpG island methylation in a subset of cells in normal tissues, followed by intensification of methylation in cancer cells explains the majority of hypermethylation events in colon cancer and may provide a mechanistic link between aging and cancer formation. Most of the other CpG islands methylated in colon cancer can be explained by a newly described phenotype, the CpG island methylator phenotype (CIMP) which results in multiple methylation events in a subset of cancers. CIMP accounts for the majority of sporadic colon cancers characterized by microsatellite instability, as well as most tumors with k-ras mutations. Understanding further the factors that lead to, and modulate, aberrant methylation in cancer may provide novel avenues for prevention and treatment of this disease.