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The CpG Island Methylator Phenotype and Chromosomal Instability Are Inversely Correlated in Sporadic Colorectal Cancer
Abstract
The CpG island methylator phenotype (CIMP) is one of the mechanisms involved in colorectal carcinogenesis (CRC). Although CIMP is probably the cause of high-frequency microsatellite instability (MSI-H) sporadic CRCs, its role in microsatellite stable (MSS) tumors is debated. The majority of MSS CRCs demonstrate chromosomal instability (CIN) with frequent loss of heterozygosity (LOH) at key tumor suppressor genes. We hypothesized that the majority of sporadic CRCs without CIN would be associated with CIMP.
We tested 126 sporadic CRCs for MSI and LOH and categorized tumors into MSI, LOH, or MSI-/LOH- subgroups. Methylation status was evaluated using 6 CIMP-related markers (MINT1, MINT2, MINT31, p16(INK4alpha), p14(ARF), and hMLH1) and 6 tumor suppressor genes (PTEN, TIMP3, RUNX3, HIC1, APC, and RARbeta2). BRAF V600E mutation analysis was performed using allele-specific polymerase chain reaction and DNA sequencing.
We observed frequent methylation at all 12 loci in all CRCs. BRAF V600E mutations correlated with the MSI (P < .0001) and MSI-/LOH- (P = .03) subgroups. MSI and MSI-/LOH- tumors exhibited more promoter methylation than CRCs with LOH (P < .0001). We also found an inverse correlation between the frequencies of methylation and LOH (rho = -0.36; P < .0001).
The associations between methylation frequencies at CIMP-related markers and MSI or MSI-/LOH- sporadic CRCs suggest that the majority of these tumors evolve through CIMP. These findings suggest that CIN and CIMP represent 2 independent and inversely related mechanisms of genetic and epigenetic instability in sporadic CRCs and confirm that MSI cancers arise as a consequence of CIMP.
... the expression and behaviour of genes that regulate cell growth and differentiation [1][2][3]. Several crucial gene defects in sporadic CRC have been identified, and specific molecular phenotypes have been described, including chromosomal instability (CIN), microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP) [1,[3][4][5]. Although somatic mutations in the POLE gene are found in 3-7% of CRCs, mutations within the proofreading (exonuclease) domain of POLE are present in only 1-2% of CRCs [6][7][8][9]. ...
... the expression and behaviour of genes that regulate cell growth and differentiation [1][2][3]. Several crucial gene defects in sporadic CRC have been identified, and specific molecular phenotypes have been described, including chromosomal instability (CIN), microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP) [1,[3][4][5]. Although somatic mutations in the POLE gene are found in 3-7% of CRCs, mutations within the proofreading (exonuclease) domain of POLE are present in only 1-2% of CRCs [6][7][8][9]. ...
... As previously reported, pathogenic somatic POLE mutations are usually found in the early stages of CRC in the right side of the colon and relatively younger patients with CRC. CIN, MSI, and CIMP constitute the three major mechanisms of genomic or epigenetic instability in CRC [1,2,5]. Experimental evidence has consistently supported the presence of CIMP in a subset of CRCs and correlates with the presence of BRAF V600E mutations [1,22,23]. ...
Background
Mutations in the POLE gene result in an ultra-hypermutated phenotype in colorectal cancer (CRC); however, the molecular characterisation of epigenetic alterations remains unclear. We examined the genetic and epigenetic profiles of POLE -mutant CRC to elucidate the clinicopathological features of the associated genetic and epigenetic alterations.
Results
Tumour tissues (1,013) obtained from a cohort of patients with CRC were analysed to determine associations between the proofreading domain mutations of POLE with various clinicopathological variables, microsatellite instability (MSI) status, BRAF and KRAS mutations, and the methylation status of key regions of MLH1 , MGMT , and SFRP2 promoters by calculating the methylation scores (range 0–6). Only four cases (0.4%) exhibited pathogenic POLE hotspot mutations (two p.P286R [c.857C > G], one p.V411L [c.1231G > C], and p.S459F [c.1376C > T] each), which were mutually exclusive to BRAF and KRAS mutations and MSI. CRC patients were divided into four subgroups: patients with POLE mutations (POLE, 0.4%, n = 4), patients with both MSI and extensive methylation in MLH1 (MSI-M, 2.9%, n = 29), patients with MSI but no extensive methylation in MLH1 (MSI-U, 3.6%, n = 36), and patients without MSI (non-MSI, 93.2%, n = 944). The POLE group was younger at diagnosis (median 52 years, P < 0.0001), with frequent right-sided tumour localisation (frequency of tumours located in the right colon was 100%, 93.1%, 36.1%, and 29.9% in POLE, MSI-M, MSI-U, and non-MSI, respectively; P < 0.0001), and was diagnosed at an earlier stage (frequency of stages I–II was 100%, 72.4%, 77.8%, and 46.6% in POLE, MSI-M, MSI-U, and non-MSI, respectively, P < 0.0001). The mean methylation score in POLE was not different from that in MSI-U and non-MSI, but the methylation signature was distinct from that of the other subgroups. Additionally, although the examined number of POLE -mutant tumours was small, the number of CD8-positive cells increased in tumours with partial methylation in the MLH1 gene.
Conclusions
CRC patients with POLE proofreading mutations are rare. Such mutations are observed in younger individuals, and tumours are primarily located in the right colon. Diagnosis occurs at an earlier stage, and distinct epigenetic alterations may be associated with CD8 cell infiltration.
... Materials and Methods section) showed the presence of 100% red colonies generated from three of the cell lines (L428, L1236, and HDLM2), indicating the nonfunctional status of TP53 and the clonal homogeneity of these cell lines ( Figure S2A). Sequencing of p53 cDNA confirmed the presence of the mutations in L428 (exon4), L1236 (exon [10][11], and HDLM2 (exon [8][9][10][11], in agreement with a previously published study [21]. FISH analysis for the TP53 gene also revealed a deletion of one allele of TP53 in HDLM2 and a high copy numbers in the L428 cell line were associated with TP53 breakpoint rearrangement ( Figure S2B). ...
... Materials and Methods section) showed the presence of 100% red colonies generated from three of the cell lines (L428, L1236, and HDLM2), indicating the nonfunctional status of TP53 and the clonal homogeneity of these cell lines ( Figure S2A). Sequencing of p53 cDNA confirmed the presence of the mutations in L428 (exon4), L1236 (exon [10][11], and HDLM2 (exon [8][9][10][11], in agreement with a previously published study [21]. FISH analysis for the TP53 gene also revealed a deletion of one allele of TP53 in HDLM2 and a high copy numbers in the L428 cell line were associated with TP53 breakpoint rearrangement ( Figure S2B). ...
... Cancers 2018,10, 233 ...
Background: Microsatellite and chromosomal instability have been investigated in Hodgkin lymphoma (HL). Materials and Methods: We studied seven HL cell lines (five Nodular Sclerosis (NS) and two Mixed Cellularity (MC)) and patient peripheral blood lymphocytes (100 NS-HL and 23 MC-HL). Microsatellite instability (MSI) was assessed by PCR. Chromosomal instability and telomere dysfunction were investigated by FISH. DNA repair mechanisms were studied by transcriptomic and molecular approaches. Results: In the cell lines, we observed high MSI in L428 (4/5), KMH2, and HDLM2 (3/5), low MSI in L540, L591, and SUP-HD1, and none in L1236. NS-HL cell lines showed telomere shortening, associated with alterations of nuclear shape. Small cells were characterized by telomere loss and deletion, leading to chromosomal fusion, large nucleoplasmic bridges, and breakage/fusion/bridge (B/F/B) cycles, leading to chromosomal instability. The MC-HL cell lines showed substantial heterogeneity of telomere length. Intrachromosmal double strand breaks induced dicentric chromosome formation, high levels of micronucleus formation, and small nucleoplasmic bridges. B/F/B cycles induced complex chromosomal rearrangements. We observed a similar pattern in circulating lymphocytes of NS-HL and MC-HL patients. Transcriptome analysis confirmed the differences in the DNA repair pathways between the NS and MC cell lines. In addition, the NS-HL cell lines were radiosensitive and the MC-cell lines resistant to apoptosis after radiation exposure. Conclusions: In mononuclear NS-HL cells, loss of telomere integrity may present the first step in the ongoing process of chromosomal instability. Here, we identified, MSI as an additional mechanism for genomic instability in HL.
... Enrolment of FLEMEN-GHO participants started in 1985. From August 1985 until November 1990, a random sample of the households living in a geographically defined area of Northern Belgium was investigated with the goal to recruit an equal number of participants in each of six subgroups by sex and age (20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37)(38)(39)(40)(41)(42)(43)(44)(45)(46)(47)(48)(49)(50)(51)(52)(53)(54)(55)(56)(57)(58)(59), and �60 years). All household members with a minimum age of 20 years were invited to take part, given that the quota of their sex-age group had not yet been satisfied. ...
... The control of the Rb/E2F pathway is disrupted in all human cancers [39], including colorectal cancer. Finally, a growing body of evidences supports that the methylation phenotype of CpG sites is one of underlying mechanisms in colorectal carcinogenesis [40], especially during the early stages of oncogenic transformation [41][42][43]. ...
Platelet Endothelial Aggregation Receptor 1 (PEAR1) modulates angiogenesis and platelet contact-induced activation, which play a role in the pathogenesis of colorectal cancer. We therefore tested the association of incident colorectal cancer and genetic and epigenetic variability in PEAR1 among 2532 randomly recruited participants enrolled in the family-based Flemish Study on Environment, Genes and Health Outcomes (51.2% women; mean age 44.8 years). All underwent genotyping of rs12566888 located in intron 1 of the PEAR1 gene; in 926 participants, methylation at 16 CpG sites in the PEAR1 promoter was also assessed. Over 18.1 years (median), 49 colorectal cancers occurred, all in different pedigrees. While accounting for clustering of risk factors within families and adjusting for sex, age, body mass index, the total-to-HDL cholesterol ratio, serum creatinine, plasma glucose, smoking and drinking, use of antiplatelet and nonsteroidal anti-inflammatory drug, the hazard ratio of colorectal cancer contrasting minor-allele ( T ) carriers vs . major-allele ( GG ) homozygotes was 2.17 (95% confidence interval, 1.18–3.99; P = 0.013). Bootstrapped analyses, from which we randomly excluded from two to nine cancer cases, provided confirmatory results. In participants with methylation data, we applied partial least square discriminant analysis (PLS-DA) and identified two methylation sites associated with higher colorectal cancer risk and two with lower risk. In-silico analysis suggested that methylation of the PEAR1 promoter at these four sites might affect binding of transcription factors p53, PAX5, and E2F-1, thereby modulating gene expression. In conclusion, our findings suggest that genetic and epigenetic variation in PEAR1 modulates the risk of colorectal cancer in white Flemish. To what extent, environmental factors as exemplified by our methylation data, interact with genetic predisposition and modulate penetrance of colorectal cancer risk is unknown.
... There are known different oncogenic drivers of colon cancer, including microsatellite instability (MSI), CpG island methylator phenotype (CIMP), and loss of heterozygosity (LOH, also known as chromosomal instability). 20 MSI tumors account for 15% of colon cancers and are divided into tumors with germ-line mutation of mismatch repair proteins caused by Lynch syndrome and sporadic hypermethylation (thus silencing) of the mismatch repair proteins caused by CIMP. Patients with Lynch syndrome are diagnosed at a much younger age, and CIMP tumors are more common in elderly patients and have a higher rate of KRAS or BRAF mutations. ...
... The presence of LOH is inversely related to the degree of methylation in CIMP tumors. 20 As we continue to dissect and characterize the molecular heterogeneity of colon cancers, we are able to identify patients with differential benefıt from adjuvant chemotherapy. Sargent and colleagues correlated MSI status with survival and response to adjuvant infusional 5-FU in 456 patients with colon cancer and reported that patients with MSI tumors had better outcomes as compared with patients with microsatellite stable (MSS) tumors, but the improved prognosis was abrogated in the face of adjuvant 5-FU treatment. ...
Colon cancer is among the most common cancers in the United States, and the median age of patients at diagnosis is 70. Medical oncologists are commonly asked to comprehensively evaluate elderly patients to estimate individual risk/benefit ratios for adjuvant treatment. Although 40% of patients with colon cancer are elderly, clinical trials enroll mainly younger patients. Consequently, we are forced to depend on subgroup analyses, observational studies, and personal experience to guide recommendations. Decision-making in adjuvant therapy for colon cancer is increasingly complex, as we subdivide patients with stage II to III colon cancer by molecular as well as anatomic staging to predict which are likely to benefit from chemotherapy and then whether the addition of oxaliplatin to 5-fluorouracil (5-FU) is worth the toxicity. It is likely that the tumor biology of younger and older patients differs, and more research is needed to dissect out the biologic heterogeneity of both the tumors and their elderly hosts to help guide treatment. We recognize that our evaluations should not solely be based on temporal age and factor physiology, pharmacology, psychology, functional status, and social support into these considerations. Older patients who are treated must be monitored closely for toxicities when undergoing treatment. Although there is a clear need for clinical trials in this population, treatment decisions confront us today in the absence of definitive evidence. How can we help our patients navigate through these important choices?
... of colorectal cancer: the chromosomal instability (CIN) pathway with activation of oncogenes and deactivation of tumor suppressor genes, [15] the genetic instability pathway due to alteration of mismatch repair (MMR) genes, [16] and finally, the pathway with hypermethylation of oncogene promoters. [17] However, it still remains under ongoing research whether these differences translate into actual significant difference in tumor prognosis and mortality. ...
... [31,35] Finally, the third tumorigenic pathway involves the hypermethylation of oncogene promoters which leads to silencing of protein expression (CpG island methylator phenotype). [17] Left-sided cancers and especially rectal cancers express TP53, APC, and COX-2 pathways more than right-sided cancers. [12] RCC are usually more poorly differentiated as demonstrated in various studies in the current literature contributing to their worse prognosis compared to the LCC. ...
... Concerning molecular pathways in the CRC onset, the most well-established are: (I) the DNA mismatch repair pathway, which is related to the Lynch syndrome as well as to sporadic CRC cases with loss of DNA mismatch repair (MMR) protein activity; (II) the chromosomal instability (CIN) pathway, that is exemplified by the familial adenomatous polyposis syndrome and presents gross chromosomal abnormalities such as deletions, insertions and loss of heterozygosity; and (III) the hypermethylation phenotype, which presents a high frequency of CpG island methylation (7,8). ...
Colorectal cancer represents the third most common cancer and about 20% are diagnosed with synchronous metastatic disease. From a historical point of view, surgery remains the mainstream treatment for resectable colorectal liver metastases (CRLM). Furthermore, disease outcomes are improving due significant advances in systemic treatments and diagnostic methods. However, the optimal timing for neoadjuvant chemotherapy or upfront surgery for CRLM has not yet been established and remains an open question. Thus, patient selection combining image workouts, time of recurrence, positive lymph nodes, and molecular biomarkers can improve the decision-making process. Nevertheless, molecular profiling is rising as a promising field to be incorporated in the multimodal approach and guide patient selection and sequencing of treatment. Tumor biomakers, genetic profiling, and circulating tumor DNA have been used to offer as much personalized treatment as possible, based on the precision oncology concept of tailored care rather than a guideline-based therapy. This review article discusses the role of molecular pathology and biomarkers as prognostic and predictor factors in the diagnosis and treatment of resectable CRLM.
... LS carriers have up to a 55% chance of developing CRC during their lives, but exact risk estimates depend on the specific MMR gene involved [8][9][10]. A hallmark of LS-associated tumors is microsatellite instability (MSI-H), although this is also detected in a minority of sporadic CRCs [11,12]. To prevent CRC development, LS carriers are advised to undergo biennial colonoscopy [13]. ...
Colorectal cancer (CRC) colonoscopic surveillance is effective but burdensome. Circulating tumor DNA (ctDNA) analysis has emerged as a promising, minimally invasive tool for disease detection and management. Here, we assessed which ctDNA assay might be most suitable for a ctDNA-based CRC screening/surveillance blood test. In this prospective, proof-of-concept study, patients with colonoscopies for Lynch surveillance or the National Colorectal Cancer screening program were included between 7 July 2019 and 3 June 2022. Blood was drawn, and if advanced neoplasia (adenoma with villous component, high-grade dysplasia, ≥10 mm, or CRC) was detected, it was analyzed for chromosomal copy number variations, single nucleotide variants, and genome-wide methylation (MeD-seq). Outcomes were compared with corresponding patients’ tissues and the MeD-seq results of healthy blood donors. Two Lynch carriers and eight screening program patients were included: five with CRC and five with advanced adenomas. cfDNA showed copy number variations and single nucleotide variants in one patient with CRC and liver metastases. Eight patients analyzed with MeD-seq showed clustering of Lynch-associated and sporadic microsatellite instable lesions separate from microsatellite stable lesions, as did healthy blood donors. In conclusion, whereas copy number changes and single nucleotide variants were only detected in one patient, cfDNA methylation profiles could discriminate all microsatellite instable advanced neoplasia, rendering this tool particularly promising for LS surveillance. Larger studies are warranted to validate these findings.
... According to recent research, cancerous colonic cells accumulate genetic and epigenetic changes via at least three different routes, including chromosomal instability (CIN), microsatellite instability (MSI), and the CpG island methylator phenotype (CIMP) [17,18]. The most prevalent kind of genomic instability, known as CIN, results in a disparity in the number of chromosomes that is "manifested as aneuploidy" and affects 60-80% of CRCs [19,20]. ...
Colorectal cancer (CRC) is comprised of transformed cells and non-malignant cells including cancer-associated fibroblasts (CAF), endothelial vasculature cells, and tumor-infiltrating cells. These nonmalignant cells, as well as soluble factors (e.g., cytokines), and the extracellular matrix (ECM), form the tumor microenvironment (TME). In general, the cancer cells and their surrounding TME can crosstalk by direct cell-to-cell contact and via soluble factors, such as cytokines (e.g., chemokines). TME not only promotes cancer progression through growth-promoting cytokines but also provides resistance to chemotherapy. Understanding the mechanisms of tumor growth and progression and the roles of chemokines in CRC will likely suggest new therapeutic targets. In this line, a plethora of reports has evidenced the critical role of chemokine receptor type 4 (CXCR4)/C-X-C motif chemokine ligand 12 (CXCL12 or SDF-1) axis in CRC pathogenesis. In the current review, we take a glimpse into the role of the CXCR4/CXCL12 axis in CRC growth, metastasis, angiogenesis, drug resistance, and immune escape. Also, a summary of recent reports concerning targeting CXCR4/CXCL12 axis for CRC management and therapy has been delivered.
... Approximately 60% of the somatic inactivation of MMR genes is copresented with a BRAF mutation (BRAFm). The tumorigenesis of BRAFm tumors is related to extensive DNA methylation of the CpG islands and MLH1 promoter methylation that causes an MSI phenotype [118,119]. Only 5-10% of MSS tumors co-occur with a BRAF mutation and the addition of ICIs to the targeted therapy is based on the increase of T cell infiltration caused by inhibiting BRAF with BRAF, MEK, and EGFR inhibitors. ...
Simple Summary
The implementation of immunotherapy in the therapeutic landscape of colorectal carcinoma has been difficult due to the inefficacy reported in early clinical trials. Nevertheless, a small subset of tumors deficient in DNA mismatch repair proteins show excellent responses to immune checkpoint inhibitors, with long-lasting results. Most of our patients do not have these alterations and, therefore, immunotherapy appears not to be effective. In the current review, we attempt to describe the main mechanisms of resistance to immunotherapy presented by these tumors, how to cope with them, and the potential use of other biomarkers of response to immunotherapy.
Abstract
Colorectal cancer (CRC) is the third most frequent cancer and the second most common cause of cancer-related death in Europe. High microsatellite instability (MSI-H) due to a deficient DNA mismatch repair (dMMR) system can be found in 5% of metastatic CRC (mCRC) and has been established as a biomarker of response to immunotherapy in these tumors. Therefore, immune checkpoint inhibitors (ICIs) in mCRC with these characteristics were evaluated with results showing remarkable response rates and durations of response. The majority of mCRC cases have high levels of DNA mismatch repair proteins (pMMR) with consequent microsatellite stability or low instability (MSS or MSI-low), associated with an inherent resistance to ICIs. This review aims to provide a comprehensive analysis of the possible approaches to overcome the mechanisms of resistance and evaluates potential biomarkers to establish the role of ICIs in pMMR/MSS/MSI-L (MSS) mCRC.
... Particularly, the TCGA classified CRC in different molecular subsets, including the chromosome instability phenotypes (CIN), accounting for 70% of cases, the MSI phenotype, accounting for 20%, and the CpG island methylation phenotype (CIMP), accounting for 10% [61] (Figure 1). Although some studies showed that some MSI CRC cases harbouring also CIMP and CIN overlap with different molecular phenotypes, TCGA classified MSI CRC as a distinct molecular phenotype [62,63]. Approximately 3% to 5% of all CRCs have dMMR associated with LS. ...
Microsatellite instability (MSI) has been identified in several tumors arising from either germline or somatic aberration. The presence of MSI in cancer predicts the sensitivity to immune checkpoint inhibitors (ICIs), particularly PD1/PD-L1 inhibitors. To date, the predictive role of MSI is currently used in the selection of colorectal cancer patients for immunotherapy; moreover, the expansion of clinical trials into other cancer types may elucidate the predictive value of MSI for non-colorectal tumors. In clinical practice, several assays are used for MSI testing, including immunohistochemistry (IHC), polymerase chain reaction (PCR) and next-generation sequencing (NGS). In this review, we provide an overview of MSI in various cancer types, highlighting its potential predictive/prognostic role and the clinical trials performed. Finally, we focus on the comparison data between the different assays used to detect MSI in clinical practice.
... In the colon, 18% (50/272) of cancers had strong MCC CpG island hypermethylation, and these were diploid or showed copy number gain ( Figure 1F). This is similar to CIMP-H, which has an inverse correlation with loss of heterozygosity in key tumor suppressor genes [26]. In the rectum, there was no difference in the methylation patterns between diploid and CNV cancers ( Figure 1G). ...
Simple Summary
DNA hypermethylation of specific regulatory regions causes gene silencing that is an important cancer-promoting mechanism. A subset of colorectal cancers display concordant hypermethylation and silencing of multiple genes, and this appears to change the way in which tumors respond to some cancer therapies. The aim of this study was to evaluate how the presence of the MCC gene silencing relates to the highly methylated subset of colorectal cancers and how it may affect therapy responsiveness. We found that strong MCC silencing is found throughout the hypermethylated subset, but MCC expression is also lost or reduced in some other tumors which show hypomethylated regions of the gene. In cell culture experiments, the deletion of MCC increased the responsiveness of cancer cells to the chemotherapy drug irinotecan (SN38), and this was further augmented by a targeted cancer drug, the PARP-inhibitor Olaparib.
Abstract
Chemotherapy is a mainstay of colorectal cancer treatment, and often involves a combination drug regime. CpG island methylator phenotype (CIMP)-positive tumors are potentially more responsive to the topoisomerase-inhibitor irinotecan. The mechanistic basis of the increased sensitivity of CIMP cancers to irinotecan is poorly understood. Mutated in Colorectal Cancer (MCC) is emerging as a multifunctional tumor suppressor gene in colorectal and liver cancers, and has been implicated in drug responsiveness. Here, we found that CIMP tumors undergo MCC loss almost exclusively via promoter hypermethylation rather than copy number variation or mutations. A subset of cancers display hypomethylation which is also associated with low MCC expression, particularly in rectal cancer, where CIMP is rare. MCC knockdown or deletion was found to sensitize cells to SN38 (the active metabolite of irinotecan) or the PARP-inhibitor Olaparib. A synergistic effect on cell death was evident when these drugs were used concurrently. The improved SN38/irinotecan efficacy was accompanied by the down-regulation of DNA repair genes. Thus, differential methylation of MCC is potentially a valuable biomarker to identify colorectal cancers suitable for irinotecan therapy, possibly in combination with PARP inhibitors.
... [60] Cancer CIMP status has been assessed as a predictive marker for 5-FU responsiveness. [61] Colorectal cancer with CIMP is distinct from those with chromosomal instability, and there are two forms of nuclear derangement represented alternative pathways for colorectal cancer development, [62,63] which overlap somewhat as hypermethylation can occur in APC and is part of the chromosomal instability pathway, [64] or in the MLH1 gene, triggering MSI. [65] MLH1 accounts for approximately 40% of the cases of the hereditary colorectal cancer and Lynch syndrome. ...
Epigenetic alterations, including DNA methylation, histone modification, loss of genome imprinting, chromatin remodeling and noncoding RNAs, are associated with human carcinogenesis. Among them, DNA methylation is a fundamental epigenetic process to modulate gene expression. In cancer cells, altered DNA methylation includes hypermethylation of site-specific CpG island promoter and global DNA hypomethylation. Detection of aberrant gene promoter methylation has been applied to clinic to stratify risk in cancer development, detect early cancer and predict clinical outcomes. Environmental factors associated with carcinogenesis are also significantly related to aberrant DNA methylation. Importantly, epigenetic changes, including altered DNA methylation, are reversible and thus, used as targets for cancer therapy or chemoprevention. An increasing number of recent studies reported DNA methylation level to be a useful biomarker for diagnosis, risk assessment and prognosis prediction for gastrointestinal cancers. This review summarized the accumulated evidence for clinical application to use aberrant DNA methylation levels in gastrointestinal cancers, including colorectal, gastric and esophageal cancer.
... CIMP-H with MLH1 methylation was especially common in MSI-H SBA and microsatellite and chromosomally stable (MACS) SBA [75], suggesting similarities with CRC [80][81][82][83]. Meanwhile, an inverse correlation was seen between aberrant methylation and SBA with CIN [75], as described in CRC [84,85]. Approximately 50% of the SBA tumors analyzed were CIN, characterized by frequent KRAS mutation and low-level methylation [75], while the remaining SBA tumors were MSI-H and MACS, characterized by the lack of KRAS mutations and greater incidence of high-level methylation and BRAF mutations [75], implicating two molecularly distinct SBA subtypes with unique tumorigenesis pathways. ...
Simple Summary
Small bowel adenocarcinoma (SBA) is a rare malignancy with worse prognosis compared to other cancers of the gastrointestinal tract. Over 90% of SBA tumors harbor targetable genetic alterations. Molecular analysis to identify these alterations, using tissue- or blood-based next generation sequencing, is critical and may impact treatment decisions. The aim of our review is to highlight molecular drivers of SBA tumorigenesis. We highlight key mutational and transcriptomic differences between SBA and colorectal cancer, from which much of the clinical management of SBA is currently extrapolated. We provide evidence that SBA is a molecularly unique intestinal malignancy, with distinct genomic alterations predictive of response to targeted therapy and immunotherapy.
Abstract
Small bowel adenocarcinoma (SBA) is a rare malignancy, with lower incidence, later stage at diagnosis, and poor overall prognosis compared to other cancers of the gastrointestinal tract. Owing to the rarity of the disease along with the paucity of high-quality tissue samples and preclinical models, little is known about the molecular alterations characteristic of SBA. This is reflected by the fact that the clinical management of SBA is primarily extrapolated from colorectal cancer (CRC). Recent advances in genomic profiling have highlighted key differences between these tumors, establishing SBA as a molecularly unique intestinal cancer. Moreover, comprehensive molecular analysis has identified a relatively high incidence of potentially targetable genomic alterations in SBA, predictive of response to targeted and immunotherapies. Further advances in our knowledge of the mutational and transcriptomic landscape of SBA, guided by an increased understanding of the molecular drivers of SBA, will provide opportunities to develop novel diagnostic tools and personalized therapeutic strategies.
... No exact etiology for CRC has been identified. Some theories suggest the possible role of diet, lifestyle, environmental factors, inherited mutations, and racial disparity (10)(11)(12)(13). Inherited CRCs can be attributed to hereditary non-polyposis CRC (HNPCC), familial adenomatous polyposis (FAP), and closely related variant syndromes. ...
In the United States, CRC is the third most common type of cancer and the second leading cause of cancer-related death. Although the incidence of CRC among the Hispanic population has been declining, recently, a dramatic increase in CRC incidents among HL younger than 50 years of age has been reported. The incidence of early-onset CRC is more significant in HL population (45%) than in non-Hispanic Whites (27%) and African-Americans (15%). The reason for these racial disparities and the biology of CRC in the HL are not well understood. We performed this study to understand the biology of the disease in HL patients. We analyzed formalin-fixed paraffin-embedded tumor tissue samples from 52 HL patients with mCRC. We compared the results with individual patient clinical histories and outcomes. We identified commonly altered genes in HL patients (APC, TP53, KRAS, GNAS, and NOTCH). Importantly, mutation frequencies in the APC gene were significantly higher among HL patients. The combination of mutations in the APC, NOTCH, and KRAS genes in the same tumors was associated with a higher risk of progression after first-line of chemotherapy and overall survival. Our data support the notion that the molecular drivers of CRC might be different in HL patients.
... MSI-H is rare in colorectal cancers with MSH3 copy number alterations but common in diploid cancers (Figure 3b). MSH3 copy number alterations reflect chromosomal instability (CIN), which is known to show inverse correlation with CIMP-H [40]. Here, we found that CIMP-H was rare in cancers with only one positive EMAST marker. ...
MSH3 gene or protein deficiency or loss-of-function in colorectal cancer can cause a DNA mismatch repair defect known as “elevated microsatellite alterations at selected tetranucleotide repeats” (EMAST). A high percentage of MSI-H tumors exhibit EMAST, while MSI-L is also linked with EMAST. However, the distribution of CpG island methylator phenotype (CIMP) within the EMAST spectrum is not known. Five tetranucleotide repeat and five MSI markers were used to classify 100 sporadic colorectal tumours for EMAST, MSI-H and MSI-L according to the number of unstable markers detected. Promoter methylation was determined using methylation-specific PCR for MSH3, MCC, CDKN2A (p16) and five CIMP marker genes. EMAST was found in 55% of sporadic colorectal carcinomas. Carcinomas with only one positive marker (EMAST-1/5, 26%) were associated with advanced tumour stage, increased lymph node metastasis, MSI-L and lack of CIMP-H. EMAST-2/5 (16%) carcinomas displayed some methylation but MSI was rare. Carcinomas with ≥3 positive EMAST markers (13%) were more likely to have a proximal colon location and be MSI-H and CIMP-H. Our study suggests that EMAST/MSI-L is a valuable prognostic and predictive marker for colorectal carcinomas that do not display the high methylation phenotype CIMP-H.
... A small percentage of CRCs that arise via the MSI pathway are inherited as the result of a germline mutation in one of the mismatch repair (MMR) genes (Lynch syndrome/hereditary nonpolyposis colon cancer [HNPCC]; about 2% to 5% of all cases of CRCs). The most common mechanism of MMR inactivation is through an acquired methylation of the MLH1, MSH2, MSH6 and PMS2 genes promoter 42 , and in particular hMLH1 was not expressed in most of sporadic CRCs. On this basis, of how many genes promoter are mutated by the degree of MSI can be cate gorized as high MSI (MSI-H) when two or more genes are involved, low MSI(MSI-L) if only one marker is involved, and MSS if none. ...
not available Bangladesh J Med Microbiol 2017; 11 (2): 28-33
... Съществува тясна корелация между CIMP позитивните тумори и мутацията V600E на BRAF, като някои резултати са в подкрепа на хипотезата, че при CIMP има активиран BRAF (42). Метилация на CpG острови се открива при аденоми на дебелото черво и приблизително в 35-40% от всички КРК (16). ...
... The latter type of cancer was found to display a "CpG island methylator phenotype" (CIMP) [89]. CIMP was reported to be negatively linked with genetic abnormalities in colorectal cancer [90,91] which imply that it can offer an alternative biological pathway for carcinogenesis [92]. Other cancers types which illustrate frequent and attendant deactivation of a number of genes via hypermethylation have also been designated as CIMP. ...
Abnormal epigenetic modifications are a trademark of cancer, and endocrine system related organs cancers are without exception. Lately, studies have acknowledged an ever-growing number of epigenetic modifications in both DNA methylation and histone modifications in the endocrine system organs cancers. Novel ultra-deep sequencing and microarray technologies have permitted to study the genome-wide epigenetic patterns in some endocrine system organs cancer types such as parathyroid gland, adrenocortical, and breast carcinomas. However, up till now, in other types of cancer, such as the multiple endocrine neoplasia syndromes, thyroid cancer, the tumor information is scare to candidate genes alone. Future research are required to focus in this direction to cover the deepen understanding of the functional role of these epigenetic modifications in endocrine system cancers, as well as defining their possible clinical utilizations.
... The CpG island Methylator phenotype involves widespread hypermethylation of numerous promotor CpG island loci, which are usually protected from methylation in normal cells (Rhee et al., 2017). CIMP has been demonstrated to be an important molecular pathway in colorectal cancer by silencing tumour suppressor genes such as p16, p14, MGMT and hMLH1 (Goel et al., 2007;Worthley and Leggett, 2010). This process increases with age and in patients with chronic inflammation and has been identified to be the second most frequent cause of sporadic CRC with 35-40% of CRC positive for CIMP (Boland and Goel, 2010). ...
The IGF-1 axis was an area of significant interest in cancer therapy following promising preclinical studies but led to disappointing clinical trials. Further scrutinization of this pathway is, therefore, warranted. The IGF-1 axis has been demonstrated to inhibit autophagy via the Akt/PI3K pathway and induce autophagy via the ERK pathway. Autophagy has been associated with chemotherapy resistance in tumour cells. My work in this thesis involved investigating the expression of an iso-form of IGF-1 referred to as IGF1-Ec or Mechanogrowth Factor (MGF) in colorectal cancer tissues and polyps with immunohistochemistry. Further work was done with fluorescent nanoparticles which have exciting potential to improve the diagnostic yield of investigations including colonosco-py, improve immunohistochemistry assessment of tissue biopsies and help in surgery with in-traoperative delineation of tumours. In addition, I investigated the relationship between autopha-gy and apoptosis with a view towards developing a model for further work in investigating the ef-fect of MGF in autophagy. Semi-quantitative immunohistochemistry for MGF on colonic tissues including normal, polyp and cancer tissues demonstrated a significantly higher expression of MGF in colonic polyps (with higher expression with worsening dysplasia, p=0.001) and cancer compared to normal colon tissues (p<0.001). Semiconductor CdTe quantum dots and gold nanoparticles were synthesised and conju-gated to the MGF peptide and antibody. Gold nanoparticles were successfully characterised with immunodots and applied to the HT29 and SW620 colorectal cancer cell lines and to tissues includ-ing normal, colon cancer and polyp tissues reflecting the results from conventional immunohisto-chemistry. Autophagy inducers were administered to the cell lines HT29 and SW620 and inhibited with the use of Bafilomycin and 3-MA. Immunohistochemistry for LC3B was used to confirm the induction of autophagy, and cell viability studies were used to demonstrate significantly increased cell viability with autophagy induction and significant reduction of cell viability with inhibition of autophagy (p<0.01 at 24 hours). This model can be subjected to the application of MGF and assess its effects on cell viability. MGF is overexpressed in colonic polyps and cancer with low levels of expression in normal colon tissues offering an opportunity for the use of fluorescent gold nanoparticles to augment polyp and cancer detection in colonoscopy and intraoperative tumour delineation.
... The presence of CIMP has been correlated with BRAF mutations (BRAF V600E) in both microsatellite stable and MSI colon cancers [105,109,111,113]. CRCs with chromosomal instability (CIN) and CIMP have been shown to correlate inversely [114,115] and develop in two separate pathways [116]. ...
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.
... The CIMP pathway is based on epigenetic instability, and it is characterized by a vast hypermethylation of the promoter region of MMR enzymes, such as MLH1, which is abundant in CpG islands. This fact will probably result in chromosomal instability, with frequent loss of heterozygosity at key tumor suppressor genes [19]. These alterations have been identified in approximately 20-35% of CRC, and are characteristic of the serrated polyps that progress to CRC [20]. ...
Colon cancer is one of the most frequently diagnosed malignancies in adults, considering both its incidence and prevalence. Anatomically, the right colon is considered as being from the cecum to the splenic flexure, and the left colon is from the splenic flexure to the rectum. Sidedness is a surrogate of a wide spectrum of colorectal cancer (CRC) biology features (embryology, microbiome, methylation, microsatellite instability (MSI), BRAF, aging, KRAS, consensus molecular subtypes (CMS), etc.), which result in prognostic factors. Different molecular subtypes have been identified, according to genomic and transcriptomic criteria. A subgroup harboring a BRAF mutation has been described, and represents approximately 10% of the patients diagnosed with colon cancer. This subgroup has morphological, clinical, and therapeutic characteristics that differ substantially from patients who do not carry this genetic alteration. Unfortunately, there is no established standard of care for this particular cohort of patients. This manuscript aims to study the biology of this subgroup of colon cancer, to understand the current approach in clinical research.
... ERK activation can trigger further excitation of downstream Ras protein, and the activated Ras-ERK signaling pathway is a key event in regulating cell proliferation and apoptosis. 7,8 Studies have shown that up-regulation of DNMT1 can inhibit the expression of RASSF1A, [9][10][11] while over-expression of RASSF1A can inhibit cell proliferation, enhance cell migration and apoptosis [12][13][14] Given the potentially reversible nature of DNA methylation changes, which often precede genetic events in multistage colon cancer, this presents an anticipated and hopeful opportunity for cancer prevention and treatment. At present, there are many studies exploring the treatment of cancer by inhibiting the abnormal methylation of DNA in cancer cells. ...
Objective
To evaluate 5-Aza-CdR’s inhibited effects on migration, proliferation, and apoptosis in colon cancer cells and its potential mechanisms.
Methods
HCT-116, SW480, and SW620 were divided into HCT116 group, HCT116+5-Aza-CdR group, SW480 group, SW480+5-Aza-CdR group, SW620 group and SW620+5-Aza according to experimental needs. MTT test was chosen to investigate cell proliferation; Transwell test was used to evaluate cell migration; scratch assay was used to investigate cell invasion; flow cytometry was used to investigate apoptosis; immunofluorescence assay was used to investigate the protein level of DNMT1 and RASSF1A in cells; qRT-PCR was used to examine DNMT1, RASSF1A, RAS, Raf1, MEK, Grb2 and ERK transcription levels.
Results
Compared with HCT116 group, 5-Aza-CdR+HCT116 group inhibited cell proliferation, increased apoptosis rate, decreased invasive ability, decreased DNMT1 expression, increased expression of RASSF1A, decreased expression of RAS, Raf1, MEK, Grb2 and ERK. SW480 was compared with 5-Aza-CdR+SW480 group and SW620 group with 5-Aza-CdR+SW620 group. Their change trend of detection index was similar to that in HCT-116 group and HCT116+5-Aza-CdR group.
Conclusion
5-Aza-CdR can obviously inhibit the proliferation, migration and invasion of three colon cancer cell lines. Its mechanism maybe relies on the inhibition of DNMT1 mRNA level and protein level and the enhancement of RASSF1A mRNA level and protein level.
... Most of the tumors are histologically moderately differentiated, class of BRAF mutated, TP53 wildtype, CIN negative and histologically poor differentiated signet ring cells. Frequently present in older female and rightsided colon.37,38 iv) Group 4 (MSI-L & CIMP low) Characteristic features are mutated KRAS and MGMT methylation. ...
Molecular subtypes-based therapies offer new potential
framework for desired and precise outcome in clinical settings. Current
treatment strategies in colorectal cancer is largely 'one drug fit all'
model for patients that display same pathological conditions. However,
CRC is a very heterogenous set of malignancy that does not support for
above criteria. Each subtype displays different pathological and genetic
signatures. Based on these features, therapeutic stratification for
individual patients may be designed, which may ultimately lead to
improved therapeutic outcome. In this comprehensive review, we have
attempted to briefly outline major CRC pathways. A detailed overview of
molecular subtypes and their clinical significance has been discussed.
Present and future methods, governing CRC subtyping in the era of
personalized therapy with a special emphasis on CMS subtypes of CRC has
been reviewed. Together, discovery and validation of new CRC patients
stratification methods, screening for novel therapeutic targets, and
enhanced diagnosis of CRC may improve the treatment outcome.
... DNA methylation status, therefore, appears to be a fundamental factor in carcinogenesis of CRC process. Specifically, it has previously been shown that hypermethylation of MMR genes results in MSI-sporadic CRC; through CpG Island Methylator Phenotype (CIMP), this was linked with chromosomal instability (CIN) in colon malignancy (where promoter methylation of GATA4, GATA5, p16 was previously shown to result in chromosomal loss or gain); changes in methylation status have been reported in a variety of genes relevant to these particular pathways [15][16][17][18][19][20]. Moreover, to date many studies have highlighted the potential benefits of implementing DNA-based aberrant methylation status assays in different biologic fluids as strategies for colorectal carcinoma early detection [21]. ...
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 "CpG island methylator phenotype" (CIMP) was found to be exhibited in the latter type of cancer [50] . CIMP is negatively linked with genetic aberrations in colorectal cancer [51,52] , which imply that it can offer an alternative pathway for carcinogenesis [53] . Other cancers that demonstrate frequent and accompanied deactivation of certain genes via hypermethylation likewise have been designated as CIMP. ...
... Loss of genomic stability and increasing multiple mutations facilitates the development of CRCs. Chromosomal instability, aberrant DNA methylation, instability of microsatellite and defect in DNA repair are mechanisms that all involved in CRC (Boland & Goel, 2010;Goel et al., 2007;Pino & Chung, 2010;Sideris & Papagrigoriadis, 2014). About 70% of sporadic colorectal cancers are due to somatic mutations. ...
Purpose: Colorectal cancer is known as the most common gastrointestinal cancers. As the age increases, the risk for this cancer also increases, so the only way to improve and hope for life in these patients is early diagnosis of the disease. So far, numerous molecular studies have been carried out on microRNAs in colorectal cancer. In addition, since some of them can be identified as cancer biomarkers. Therefore, in this study we have investigated the expression level of Mir-30d and Mir-181a as cancer biomarkers. Method: The changes of Mir-30d and Mir-181a expression levels in 60 colorectal tumor tissues and 60 adjacent tumor tissues, after RNA extraction and cDNA synthesis were surveyed using the Real Time-PCR method. Results: The results have reported a considerable reduction in the expression level of Mir-30d in tumor tissues, as well as a significant increase in the expression level of Mir-181a tumor expression in tumor tissues (P<0.05). In addition, the correlation between Mir-30d and Mir181a showed that there was a significant difference between the level of expression of mir-30d with age and TNM stage of CRC (P<0.05), whilst these correlations were not observed for Mir-181a (P>0.05).
... MSI-H tumours are considered to have better prognosis compared to MS-S cancers. MSI-H cancers harbouring the BRAF V600E mutation usually have deficient MMR (dMMR) through the hypermethylation of the MLH1 gene and the CpG island methylator phenotype (CIMP+ pathway) and are exclusively sporadic [14]. Patients with simultaneous detection of BRAF V600E mutation and dMMR in their tumours have better prognosis in comparison with those with BRAF V600E mutation and proficient MMR (pMMR) [15,16]. ...
This is a case of a patient who presented to the emergency department with acute abdominal pain due to bowel obstruction. An extended right hemicolectomy with ileosigmoid anastomosis due to an obstructing mass on the splenic flexure was urgently performed. During operation, liver and peritoneal lesions were detected and samples were also sent for histological analysis. Pathology report was consistent with poorly differentiated mucinous adenocarcinoma with signet ring cells; peritoneal lesions were confirmed histologically as metastatic. Genetic testing revealed the BRAF V600E mutation and mismatch repair deficiency (dMMR). After progressing on 1st line chemotherapy, the patient has a continuing and long-lasting partial response to 2nd line treatment with pembrolizumab.
... The second major pathway of CRC carcinogenesis, occurring in 20% of CRCs, is the transcriptional inactivation of tumor suppressor genes by methylation of cytosine nucleotides at promoter CpG islands, termed CpG island methylator phenotype (CIMP-high) [3]. As expected, CIMP-high and CIN have been shown to be inversely correlated with near mutual exclusivity [4,5]. ...
... In addition, we performed molecular characterization of tissue samples from 35 patients (both tumor and normal) using microsatellite instability, CpG island methylator phenotype (CIMP) and 5-hydroxymethylation assay. CIMP is one of the mechanisms involved in colorectal carcinogenesis [38]. Our studies showed that both non-tumorous tissue samples (nearby and healthy) had a stable microsatellite profile and no CIMP phenotype. ...
The aim of the work was to evaluate whether or not there is glycolytic reprogramming in the neighboring cells of colorectal cancer (CRC). Using postoperative material we have compared the functional capacity of oxidative phosphorylation (OXPHOS) in CRC cells, their glycolytic activity and their inclination to aerobic glycolysis, with those of the surrounding and healthy colon tissue cells. Experiments showed that human CRC cannot be considered a hypoxic tumor, since the malignancy itself and cells surrounding it exhibited even higher rates of OXPHOS than healthy large intestine. The absence of acute hypoxia in colorectal carcinomas was also confirmed by their practically equal glucose-phosphorylating capacity as compared with surrounding non-tumorous tissue and by upregulation of VEGF family and their ligands. Studies indicated that human CRC cells in vivo exert a strong distant effect on the energy metabolism of neighboring cells, so that they acquire the bioenergetic parameters specific to the tumor itself. The growth of colorectal carcinomas was associated with potent downregulation of the creatine kinase system. As compared with healthy colon tissue, the tumor surrounding cells display upregulation of OXPHOS and have high values of basal and ADP activated respiration rates. Strong differences between the normal and CRC cells in the affinity of their mitochondria for ADP were revealed; the corresponding K m values were measured as 93.6 7 7.7 mM for CRC cells and 84.9 7 9.9 mM for nearby tissue; both these apparent K m (ADP) values were considerably (by almost 3 times) lower in comparison with healthy colon tissue cells (256 7 34 mM).
... The end consequence of such events is cellular overproduction of reactive oxygen species (ROS) and reactive nitrogen species (RNS). Damaged cells undergo apoptosis or acquire mutations that accumulate in and cause cell proliferation leading to ROS-induced carcinogenesis [3]. ...
Zinc is a trace element widely known for its marked antioxidant properties. To gain more insight into the site- and time- specific mechanisms by which it induces chemoprevention, this study was elaborated over a pre-cancerous model of colon carcinogenesis.
Colon cancer was induced by 1,2-dimethylhydrazine (DMH) in mice (20 mg/kg for 2 weeks) and groups of animals were supplemented with or without zinc sulfate (ZnSO4, 200 mg/L) in drinking water for 4, 10 or 14 weeks. Colon tissues were collected for pathological observation, analyzing aberrant crypt (AC) and aberrant crypt foci (ACF) formations, multiplicity and distribution. Similarly, histological assessment and mucin production, as well as oxidative stress markers estimation was performed for the different groups.
Results showed a significant increase in ACF and AC numbers, ACF multiplicity and demonstrated stronger distal occurrence than in the proximal after DHM administration. Histopathological analysis presented marked structural alterations and mucin loss in the distal than the proximal colons. A significant increase in myeloperoxidase (MPO), nitric oxide (NO), L-ornithine and malondialdehyde (MDA) levels was observed followed by a significant decrease in antioxidant markers (superoxide dismutase (SOD), catalase (CAT) and reduced glutathione (GSH)). Oral ZnSO4 supplementation (continuous or partial) induced significant decrease in ACF, AC numbers and multiplicity, restored histological architecture and mucin production, and a significant decrease in proinflammatory markers while it reduced antioxidants to normal levels.
From this study, insight was obtained on the use of ZnSO4 as a chemopreventive agent and shed light on its potential, as a supplement in nutraceutical approaches.
... Colorectal cancers segregate into two mutually exclusive categories based on exhibiting genomic instability at either the microsatellite level (due to defects in mismatch repair) or the chromosomal level [1,74]. APC mutations are particularly well-represented within the subset of colorectal cancers that feature widespread chromosomal damage [3] and also play an important role in this phenotype [75]. ...
The acquisition of biallelic mutations in the APC gene is a rate-limiting step in the development of most colorectal cancers and occurs in the earliest lesions. APC encodes a 312-kDa protein that localizes to multiple subcellular compartments and performs diverse functions. APC participates in a cytoplasmic complex that promotes the destruction of the transcriptional licensing factor β-catenin; APC mutations that abolish this function trigger constitutive activation of the canonical WNT signaling pathway, a characteristic found in almost all colorectal cancers. By negatively regulating canonical WNT signaling, APC counteracts proliferation, promotes differentiation, facilitates apoptosis, and suppresses invasion and tumor progression. APC further antagonizes canonical WNT signaling by interacting with and counteracting β-catenin in the nucleus. APC also suppresses tumor initiation and progression in the colorectal epithelium through functions that are independent of canonical WNT signaling. APC regulates the mitotic spindle to facilitate proper chromosome segregation, localizes to the cell periphery and cell protrusions to establish cell polarity and appropriate directional migration, and inhibits DNA replication by interacting directly with DNA. Mutations in APC are often frameshifts, insertions, or deletions that introduce premature stop codons and lead to the production of truncated APC proteins that lack its normal functions and possess tumorigenic properties. Therapeutic approaches in development for the treatment of APC-deficient tumors are focused on the inhibition of canonical WNT signaling, especially through targets downstream of APC in the pathway, or on the restoration of wild-type APC expression.
Today, treatment options for cancer patients typically include surgery, radiation therapy, immunotherapy, and chemotherapy. While these therapies have saved lives and reduced pain and suffering, cancer still takes millions of lives every year around the world. Researchers are now developing advanced therapeutic strategies such as immunotherapy, targeted therapy, and combination nanotechnology for drug delivery. In addition, the identification of new biomarkers will potentiate early-stage diagnosis. Molecular Targets and Cancer presents information about cancer diagnosis and therapy in a simple way. It covers several aspects of the topic with updated information on par with medical board levels. The book features contributions from experts and includes an overview of cancer from basic biology and pathology, classifications, surveillance, prevention, diagnosis, types of cancer, treatment and prognosis. The first part of this book introduces the reader to cancer epidemiology, genetic alterations in cancer, exogenous and endogenous factors in carcinogenesis, roles for growth factors in cancer progression, cell signaling in cancer, transcription factors in cancer, and cancer genetics and epigenetics. This comprehensive guide is a valuable resource for oncologists, researchers, and all medical professionals who work in cancer care and research.
Colorectal carcinoma (CRC), a foremost basis of malignancy-related death worldwide, evolves due to the stepwise amassing of a succession of genetic and epigenetic modifications. Epigenetic indicators are significant molecular hallmarks of malignancy. They ensure very initially in disease pathogenesis, including virtually all vital malignancy-related pathways and, in particular, can be exploited as clinically significant cancer biomarkers for diagnosis, prognostication, and the prophecy of treatment response. Similarly, as gene changes in the malignant growth genome, a subset of driver genes are attempted to assume a useful part in CRC. The headways in our understanding of abnormal methylation in CRC have prompted epigenetic changes being created as clinical biomarkers for diagnostic and prognostic applications and the function of non-coding RNAs as epigenetic controllers. Beforehand, mass transcriptomics analysis is used to group CRC grounded on its distinctive molecular and clinicopathological features for prediction and the patients' analysis. The introduction of single-cell transcriptomics turned the table by empowering the assessment of expression levels of specific neoplastic cells inside a solitary tumor. Transcriptome investigation of CRC and ingenuity pathway study uncovered better improvement and identified with cell movement, growth, development, proliferation, DNA replication, recombination and their relation with transcriptomics, etc. Progress in the appraisal of epigenetic alterations in CRC and their clinical applications has indicated that these changes will be ordinarily utilized soon as molecular markers to coordinate the anticipation and treatment of CRC. The most recent upgrading of our understanding of CRC and progress in genomic knowledge has prompted the recognizable proof of an assortment of epigenetic alterations firmly associated with cancer inception as well as progression.
Malgré les diagnostics précoces et les avancées thérapeutiques, le taux de mortalité chez les patients diagnostiqués d’un CCR au stade métastatique reste très élevé. L’objectif de ce travail a été d’étudier le rôle de la chimiokine CXCL12 et ses deux récepteurs CXCR4 et CXCR7 dans processus métastatique. J’ai comparé l’expression de la chimiokine CXCL12 dans des tumeurs coliques humaines avec les tissus sains associés puis je me suis intéressée aux mécanismes de régulation de cette expression et plus particulièrement la régulation épigénétique. J’ai montré que le promoteur de CXCL12 est méthylé dans 35% des CCR et qu’un défaut d’acétylation des histones du promoteur entraîne la perte d’expression de CXCL12. Des enzymes impliquées dans la régulation des mécanismes épigénétiques, potentiellement liées à ce défaut d’acétylation ont été identifiées par l’analyse des tumeurs par PCR Array et parmi ces facteurs, j’ai identifié l’histone acétyl-transférase PCAF dont l’expression est diminuée dans les tumeurs. Enfin, pour comprendre le rôle respectif de CXCR4 et de CXCR7 dans la dissémination métastatique, j’ai invalidé l’expression du gène des récepteurs dans la lignée colique humaine SW480 par Crispr-Cas9, puis j’ai comparé la capacité migratoire des cellules in vitro et leur potentiel métastatique in vivo. L’induction d’une perte d’expression du récepteur CXCR7 n’a pas eu d’impact sur le développement des métastases pulmonaire et hépatique in vivo, mais a entraîné une baisse de la migration in vitro.
Histomorphology has been a mainstay of cancer diagnosis in anatomic pathology for many years. DNA methylation profiling is an additional emerging tool that will serve as an adjunct to increase accuracy of pathological diagnosis. Genome-wide interrogation of DNA methylation signatures, in conjunction with machine learning methods, has allowed for the creation of clinical-grade classifiers, most prominently in central nervous system and soft tissue tumors. Tumor DNA methylation profiling has led to the identification of new entities and the consolidation of morphologically disparate cancers into biologically coherent entities, and it will progressively become mainstream in the future. In addition, DNA methylation patterns in circulating tumor DNA hold great promise for minimally invasive cancer detection and classification. Despite practical challenges that accompany any new technology, methylation profiling is here to stay and will become increasingly utilized as a cancer diagnostic tool across a range of tumor types.
Expected final online publication date for the Annual Review of Pathology: Mechanisms of Disease, Volume 17 is January 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Numerous clinical studies in an adjuvant setting have been conducted and the combination therapy of 5-fluorouracil and oxaliplatin has been established as the standard treatment for Stage III and as an option for high-risk Stage II patients. Biologics such as bevacizumab and antiepidermal growth factor receptor antibodies have failed to show additional survival benefits. The indication of adjuvant chemotherapy has been determined according to the pathological stage. Nevertheless, a pathological diagnosis does not necessarily result in selection of the optimal treatment. To improve treatment decisions, many trials have aimed to stratify patients into treatment groups using genomic testing. Recently, gene signature, Immunoscore, and circulating tumor DNA (ctDNA) assays have been reported and among them, ctDNA was shown to be a promising accurate predictive marker for recurrence. Treatment of ctDNA-positive patients with aggressive chemotherapy may reduce recurrence rates. The ultimate goal is to accurately predict the risk of recurrence and to prevent recurrence in colon cancer patients. In this review we focus on the clinical development of adjuvant chemotherapy and stratification of patients according to risk of recurrence and the future direction of adjuvant chemotherapy.
Diet and nutrition play key roles in the maintenance of genomic stability. Obesity is the result of an excess of caloric intake in comparison with energy expenditure. In itself, this leads to oxidative stress and DNA damage. DNA-reactive mutagens including those formed during high temperature–cooking processes of red meats or from other processing methods are still common, albeit unintentional, components of the diet of many individuals. Improved food storage technologies may be leading to a reduction in fungal contaminants such as aflatoxin B1, but endogenously or exogenously formed reactive species, inhibitors of DNA repair, or of the mitotic spindle occur in the human diet, and may also lead to genomic instability. Some of these may become incorporated into the diet through the uptake of environmental contaminants by food plants and animals. Conversely, various nutrients and phytochemicals may be protective. Carotenoids, vitamin D, and selenium are among the best studied nutrients here. Various phytochemicals, including isothiocyanates such as sulforaphane or polyphenols such as genistein or curcumin, have differing mechanisms of promoting genomic stability. Polymorphisms in genes for nutrient uptake, metabolism, and excretion will determine the optimal dietary intake for an individual. Human studies are essential to quantifying and overcoming diet-related genomic instability.
Colorectal cancer (CRC) is one of the major solid tissue malignancies affecting the worldwide population. CRC is the third most common cancer and fourth among the major contributors of cancer-related mortality worldwide. CRC incidence rate exhibits a considerable variation with geographical location and with race and ethnicity. The variation in CRC incidence with geographical location is so conspicuous that CRC is regarded as the marker of the socioeconomic development of nations. The role played by the genetic variants especially SNPs in modulating the risk of CRC is of very diverse nature. In this chapter, we would be discussing the effects of SNPs in the low penetrance genes depending upon the type of pathways these genes are involved in. Numerous pathways, which are known to get affected by genetic variations, can be categorized as: cell cycle regulatory, transcription regulatory, DNA repair, folate metabolism, fat metabolism, xenobiotic and inflammatory pathways.
Grape pomace (GP), a by-product of the wine and juice industry, is rich in several bioflavonoids and dietary fibers. We hypothesized that grape pomace has protective effects against colitis-associated colorectal cancer (CRC). Nine-week-old female mice were fed a control diet (CON) or CON with 5% grape pomace (GP) for 2 weeks, when mice were subjected to azoxymethane (AOM)/dextran sulfate sodium (DSS) induced-CRC induction. GP supplementation ameliorated the disease activity index (DAI) score, reduced tumor number, tumor size and pathological scores in AOM/DSS treated mice. Furthermore, dietary GP suppressed colonic expression of inflammatory cytokines, IL-1β and TNF-α, and inhibited NF-κB inflammatory signaling, while increased anti-inflammatory cytokine TGF-β mRNA expression. Colorectal inflammation is known to enhance Wnt signaling and cell proliferation. In agreement, the content of β-catenin, a key downstream mediator of Wnt signaling, was reduced as was the expression of Cyclin D1, phosphorylation and content of p53 and PCNA level in GP-fed mice. In addition, GP reduced the expression of ALDH1, a marker of cell stemness, and increased the expression of Cdx2, a key transcription factor initiating epithelial cell differentiation. Consistently, DNA methylation of the promoter region of Cdx2 gene and hypermethylation of CpG island methylator phenotype (CIMP), which commonly occurs during CRC carcinogenesis, was alleviated in the GP group. In conclusion, GP supplementation suppressed colitis-associated CRC carcinogenesis, which was associated with the suppression of inflammation and cell proliferation and the enhancement of DNA demethylation in Cdx2 and CIMP genes in the colon. These data suggest that dietary GP supplementation has preventive effects against colorectal carcinogenesis.
Cancer is a sickness, initiated and driven via accumulation and interaction of genetic and epigenetic modification of genes involved in regulation of cell communication, signaling and growth division. Epigenetics is known as heritable changes in the expression of genes which are different from mutations that are not attributable to modification of DNA sequence. There are two leading epigenetic mechanisms; histone modification and DNA methylation. The acts of epigenetics in controlling of gene expression have been considered as elementary process in the pathogenesis of a variety of malignancies, for instance reproductive organs cancers. Recently, numerous exciting discoveries in epigenetics field have been focused in the study of reproductive cancers organs in females. Epigenetic modifications in the DNA of cancer patients and precancerous lesions provide the promise of novel biomarkers for early cancer prediction, diagnosis, prognosis, and treatment response. In addition, various epigenetic modifications represent potential targets of novel therapeutic strategies and treatments of cancer. In the future, pioneering diagnostic methodologies, technologies and treatment regimens will be based on epigenetic mechanisms and may be integrated into the gynecologist's practice. Keywords: Cancer, DNA methylation, Epigenetics, Histones modifications, Female, Urogenital organs
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.
Colorectal cancer (CRC) is a prevalent disease and a major cause of mortality in the world. Several factors including population aging, poor dietary habits, obesity, insufficient physical activity, and smoking can explain its increased prevalence. CRC is a heterogeneous disease both histopathologically and in term of its molecular and genetic aspects. Melatonin a derivative of tryptophan, is synthesized and released from pineal gland but it is also found in numerous extrapineal tissues including retina, testes, lymphocytes, Harderian gland, gastrointestinal tract, etc. This molecule has several tasks which enhance physiological functions such as antioxidant, antiaging, immunomodulatory, and tumor inhibition. Multiple immunocytochemical studies reported melatonin in the intestinal mucosa where its concentration is greater than in the blood. These findings suggest that melatonin may have a potential inhibitory role in CRC progression. The purpose of this review is to examine the effects of melatonin in molecular pathogenesis and signaling pathways of CRC. Melatonin, a derivative of tryptophan, is synthesized and released from pineal gland but it is also found in numerous extrapineal tissues including retina, testes, lymphocytes, Harderian gland, gastrointestinal tract, etc. This molecule has several tasks which enhance physiological functions such as antioxidant, antiaging, immunomodulatory, and tumor inhibition. Multiple immunocytochemical studies reported melatonin in the intestinal mucosa where its concentration is greater than in the blood.
Straipsnyje pateikiami literatūros duomenys apie mikrosatelitų nestabilumą ir heterozigotiškumo praradimą sergant įvairių lokalizacijų vėžiu. Šie genetiniai pokyčiai yra svarbūs kancerogenezei. Mikrosatelitų nestabilumo ir heterozigotiškumo praradimas gali būti prognoziniu, o kai kuriais atvejais predikciniu žymeniu (rodyti atsaką į gydymą). Daugiausia duomenų yra apie mikrosatelitų nestabilumą sergant storosios žarnos vėžiu. Duomenys apie mikrosatelitų nestabilumą kitų lokalizacijų vėžio atvejais dar kaupiami, taigi, šia tema publikuojamų straipsnių skaičius auga.
Colorectal cancer is a heterogeneous disease entity in terms of both molecular carcinogenesis and morphologic multistep pathways. Three molecular carcinogenesis pathways have been identified: (1) chromosomal instability (CIN), (2) microsatellite instability (MSI), and (3) CpG island methylator phenotype (CIMP). The two morphologic multistep pathways are the classical pathway (the so-called adenoma–carcinoma sequence) and the serrated neoplasia pathway. CRC continues to be a significant public health problem, with a less than 10% of 5-year prognosis for metastatic CRC. Our increased understanding of the molecular events underlying CRC carcinogenesis will enable the development of new targeted therapies and the identification of clinical biomarkers that will inform their effective usage.
Introduction Epigenetic modifications cause heritable changes in the expression of the genome without changes in the primary DNA sequence. Epigenetics play an important role in normal development, and epigenetic aberrations have been implicated in a number of human diseases, including cancer. In mammalian cells, two primary mechanisms mold the epigenetic landscape – DNA methylation and histone modifications. The focus of this chapter is to summarize the role of DNA methylation in cancer development and progression. The importance of DNA methylation In eukaryotes, DNA methylation is most often found on the 5ʹ position of cytosine bases that are part of CpG dinucleotides (m⁵C). All types of DNA sequences, including genes, intergenic DNA, and repetitive sequences, are targets of methylation. In normal cells, there is generally a paucity of methylation in regions called CpG islands (CGIs), which are stretches of sequence enriched in CpG dinucleotides. These are often preferentially located in the 5ʹ regions of genes. CpG dinucleotides have been progressively depleted from the eukaryotic genome over the course of evolution, and constitute about 1–2% of mammalian sequences (1). About 70% of the remaining CpG dinucleotides in the mammalian genome are methylated (2). This methylation is thought to play an important role in the co-ordination of chromosomal structure and integrity, and facilitating the functional segregation of active and silent chromatin. Repetitive sequences such as Alu repeats and transposons are frequently heavily methylated, and this state may serve to maintain a transcriptionally repressed state in these regions (3,4).
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.
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.
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 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.
A subgroup of colorectal cancers (CRC) referred to as the CpG island methylator phenotype (CIMP+) shows simultaneous methylation of multiple CpG islands. The clinicopathological and molecular characteristics of this phenotype remain uncertain however.
We analysed methylation of CpG islands in the p16 and MDR1 genes and MINT-2 clone in 275 stage II/III CRCs.
Concurrent methylation of two or more CpG islands was observed in 32% of cases and was considered to represent CIMP+. These were often poorly differentiated, had less TP53 mutations, and originated frequently in the proximal or higher stage CRC compared with CIMP- tumours (p<0.05 for each). CIMP+ had no prognostic significance in stage II or stage III CRC treated by surgery alone. hMLH1 methylated tumours comprised the majority (81%) of cases with microsatellite instability, were frequently observed in older female patients, were often poorly differentiated or CIMP+, and contained wild-type K-ras (p<0.05 for each). Females who were heterozygous or homozygous for the C677T MTHFR polymorphism were at increased risk of developing CIMP+ CRC (odds ratio 2.17, 95% confidence interval 1.03-4.57; p=0.037).
These observations made in a relatively large unselected series of CRC support the notion that CIMP+ characterises a subgroup of tumours with distinctive phenotypic features.
Colorectal cancer (CRC) can progress through two pathways of genomic instability: chromosomal (CIN) and microsatellite instability (MSI). We hypothesized that these two pathways are not always independent and that some tumors therefore show a significant degree of overlap between these two mechanisms. We classified 209 high-risk stage II and stage III sporadic CRCs based on their MSI status, using a National Cancer Institute-recommended panel of microsatellite markers, and also identified MSI-associated mutations of CRC target genes such as TGFbetaRII. Evidence for CIN was gathered by identifying loss of heterozygosity (LOH) events on chromosomal arms 1p, 2p, 3p, 5q, 17p, and 18q, which are regions harboring mismatch-repair and tumor-suppressor genes that are significant in CRC development. Results of all molecular markers tested were correlated with clinicopathological variables of the cohort, including treatment outcome. Of the 209 cases, 65% cancers were microsatellite stable, 21% were MSI-low, and 14% were MSI-high (MSI-H). Overall, 51% of the tumors had at least one LOH event, with most frequent chromosomal losses observed on 18q (72.5%), followed by 5q (22%), 17p (21%), and 3p (14%). Interestingly, we observed a significant degree of overlap between MSI and CIN pathways. Of 107 cancers with LOH events, 7 (6.5%) were also MSI-H, and of 30 cancers that were MSI-H, 7 (23.3%) also had one or more LOH events. We also found that 37.8% of microsatellite-stable cancers had no LOH events identified, thus comprising a subgroup of tumors that were not representative of either of these two pathways of genomic instability. Our data suggest that molecular mechanisms of genomic instability are not necessarily independent and may not be fully defined by either the MSI or CIN pathways.
The RAS-RAF-MEK-ERK-MAP kinase pathway mediates the cellular response to extracellular signals that regulate cell proliferation, differentiation, and apoptosis. Mutation of the RAS proto-oncogene occurs in various thyroid neoplasms such as papillary thyroid carcinomas (PTCs), follicular thyroid adenomas and carcinomas. A second genetic alteration frequently involved in PTC is RET/PTC rearrangements. Recent studies have shown that BRAF, which is a downstream signaling molecule of RET and RAS, is frequently mutated in melanomas. This study tests whether BRAF is also mutated in thyroid tumors and cell lines. We analyzed BRAF gene mutation at codon 599 in thyroid tumors using mutant-allele-specific PCR and in 10 thyroid tumor cell lines by DNA sequencing of the PCR-amplified exon 15. We found that BRAF was mutated in 8 of 10 thyroid tumor cell lines, including 2 of 2 papillary carcinoma cell lines, 4 of 5 anaplastic carcinoma cell lines, 1 of 2 follicular carcinoma cell lines, and 1 follicular adenoma cell line. BRAF mutation at codon 599 was detected in 21 of 56 PTC (38%) but not in 18 follicular adenomas and 6 goiters. BRAF mutation occurred in PTC at a significantly higher frequency in male patients than in female patients. To test whether BRAF mutation may cooperate with RET/PTC rearrangements in the oncogenesis of PTC, we tested whether BRAF-mutated PTCs were also positive for RET/PTC rearrangements. Immunohistochemical staining was conducted to evaluate RET/PTC rearrangements by using two different anti-RET antibodies. Surprisingly, we found that a large number of BRAF-mutated PTCs (8 of 21) also expressed RET, indicating that the RET proto-oncogene is rearranged in these BRAF-mutated PTCs. These observations suggest that mutated BRAF gene may cooperate with RET/PTC to induce the oncogenesis of PTC.
Loss of PTEN tumor suppressor function is observed in tumors of breast, prostate, thyroid, and endometrial origin. Allelic losses in the proximity of the PTEN locus (10q23) also occur in sporadic colorectal cancers (CRCs), but biallelic inactivation of this site has not been frequently demonstrated. We hypothesized that alternative mechanisms of PTEN allelic inactivation, such as promoter hypermethylation, might be operative in CRC and that PTEN inactivation may be related to recognized forms of genomic instability. We characterized a cohort of 273 sporadic CRCs by determining their microsatellite instability (MSI) status. Of these, 146 cancers were examined for PTEN promoter methylation by methylation-specific PCR. Mutations at the poly(A)6 repeat sequences in PTEN exons 7 and 8 and deletions at the 10q23 locus were also identified using microsatellite analysis. The presence of PTEN protein was determined by immunostaining, and the results were correlated with the promoter methylation status. We observed that PTEN promoter hypermethylation was a frequent occurrence in MSI-high (MSI-H) tumors (19.1% of MSI-H versus 2.2% of MSI-low/microsatellite stable tumors; P = 0.002). A PTEN mutation or a deletion event was present in 60% of the tumors with promoter region hypermethylation. Hypermethylation of the PTEN promoter correlated significantly with either decreased or complete loss of PTEN protein expression (P = 0.004). This is the first demonstration of PTEN inactivation as a result of promoter hypermethylation in MSI-H sporadic CRCs. These data suggest that this silencing mechanism plays a major role in PTEN inactivation and, in colon cancer, may be more important than either allelic losses or inactivating mutations. The significant correlation of PTEN hypermethylation with MSI-H tumors further suggests that PTEN is an additional important "target" of methylation along with the hMLH1 gene in the evolution of MSI-H CRCs and also confers the "second hit" in the biallelic inactivation mechanism for some proportion of tumors.
Germ-line mutations of the APC gene are associated with familial adenomatous polyposis, and somatic mutations occur frequently in sporadic colorectal cancer. However, to abrogate APC function, both alleles must be inactivated. Recently, it has been demonstrated that epigenetic modification of the APC promoter influences APC silencing. Here we examined the influence of APC methylation on APC expression in tumors with and without LOH at the APC locus.
137 sporadic colorectal cancer specimens were investigated for LOH at the 5q locus. The methylation status of the APC promoter was determined by methylation-specific PCR. APC expression was performed by immunohistochemistry.
Expression was reduced or lost in 110 of 137 (80%) tumors and LOH at 5q was found in 13 of 132 (10%) tumors. There was no difference in 5q LOH between tumors with or without intact APC expression. Vice versa, there was no difference in the APC expression in tumors with 5q LOH. Aberrant APC promoter methylation was detected in 33 of 118 (28%) tumors investigated. Of the tumors with 5q LOH for which methylation data were available, 4 of 11 (36%) were methylated versus 28 of 105 (27%) of those without LOH. No difference in methylation was observed in tumors without 5q LOH and normal APC expression and those without 5q LOH and reduced or missing APC expression. Importantly, none of the tumors with 5q LOH and normal APC staining were aberrantly methylated, whereas 50% of the cancers with LOH at 5q and reduced or absent staining were hypermethylated.
This report suggests that tumors with 5q LOH and reduced APC expression are more frequently hypermethylated at the APC promoter compared to those tumors with 5q LOH and normal APC expression. The association among APC promoter methylation status, 5q LOH, and reduced or lost APC expression suggests that de novo methylation plays an important role as a "second hit" in silencing APC expression in colorectal neoplasia.
BRAF mutations are common in sporadic colorectal cancers (CRCs) with a DNA mismatch repair (MMR) deficiency that results from promoter methylation of hMLH1, whereas KRAS mutations are common in MMR proficient CRCs associated with promoter methylation of MGMT. The aim of this study was to further investigate the link between genetic alterations in the RAS/RAF/ERK pathway and an underlying epigenetic disorder.
Activating mutations of BRAF and KRAS were identified and correlated with promoter methylation of 11 loci, including MINT1, MINT2, MINT31, CACNA1G, p16(INK4a), p14(ARF), COX2, DAPK, MGMT, and the two regions in hMLH1 in 468 CRCs and matched normal mucosa.
BRAF V599E mutations were identified in 21 (9%) of 234 CRCs, and KRAS mutations were identified in 72 (31%) of 234 CRCs. Mutations in BRAF and KRAS were never found in the same tumor. CRCs with BRAF mutations showed high-level promoter methylation in multiple loci, with a mean number of methylated loci of 7.2 (95% CI, 6.6 to 7.9) among 11 loci examined (P < .0001). Tumors with KRAS mutations showed low-level promoter methylation, and CRCs with neither mutation showed a weak association with promoter methylation, with an average number of methylated loci of 1.8 (95% CI, 1.5 to 2.1) and 1.0 (95% CI, 0.79 to 1.3), respectively.
In CRC, the methylation status of multiple promoters can be predicted through knowledge of BRAF and, to a lesser extent, KRAS activating mutations, indicating that these mutations are closely associated with different patterns of DNA hypermethylation. These changes may be important events in colorectal tumorigenesis.
DNA hypermethylation in CpG-rich promoters is now recognized as a common feature of human neoplasia. However, the pathophysiology of hyper-methylation (why, when, where) remains obscure. Cancers can be classified according to their degree of methylation, and those cancers with high degrees of methylation (the CpG island methylator phenotype, or CIMP) represent a clinically and aetiologically distinct group that is characterized by 'epigenetic instability'. Furthermore, CIMP-associated cancers seem to have a distinct epidemiology, a distinct histology, distinct precursor lesions and distinct molecular features.
It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP)," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI). We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF) in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.
The relationship between global hypomethylation, chromosomal instability (CIN), and microsatellite instability (MSI) remains unclear in colorectal cancer. The aim of this study was to investigate the relationship between global methylation status, loss of heterozygosity (LOH), and MSI in sporadic colorectal cancer.
We determined global methylation levels in 80 sporadic colorectal cancers, 51 adjacent normal tissues, and 20 normal tissues using the long interspersed nucleotide elements-combined bisulfite restriction analysis method. We also analyzed 80 colorectal cancers for MSI status and LOH at chromosomes 5q21, 8p12-22, 17p13, and 18q21.
We identified 14 cases of MSI (17.5%) and 58 cases of LOH (72.5%). LOH was observed more frequently in microsatellite stable (MSS) cancers than in MSI cancers at all loci. Colorectal cancers showed significantly lower global methylation levels than did normal tissues (41.0+/-9.7% versus 54.3+/-6.5%; P<0.001). MSS cancers showed significantly lower global methylation levels when compared with MSI cancers (39.5+/-9.4% versus 48.2+/-8.2%; P=0.003). Tumors with global hypomethylation (with <or=40% of methylation levels) had a significantly increased number of chromosomal loci with LOH than did tumors without global hypomethylation (1.9 versus 0.9; P<0.001); 11 tumors (13.9%) lacked both MSI and LOH. This subgroup had significantly higher global methylation levels (46.8+/-8.7%) than did MSS cancers with LOH (38.0+/-9.0%; P=0.006).
These data showed a significant association between global hypomethylation and chromosomal instability in sporadic colorectal cancer. This suggests that global hypomethylation plays an important role in inducing genomic instability in colorectal carcinogenesis.
The concept of CpG island methylator phenotype (CIMP) is not universally accepted. Even if specific clinicopathological features have been associated with CIMP, investigators often failed to demonstrate a bimodal distribution of the number of methylated markers, which would suggest CIMP as a distinct subtype of colorectal cancer. Previous studies primarily used methylation specific polymerase chain reaction which might detect biologically insignificant low levels of methylation.
To demonstrate a distinct genetic profile of CIMP colorectal cancer using quantitative DNA methylation analysis that can distinguish high from low levels of DNA methylation.
We developed quantitative real time polymerase chain reaction (MethyLight) assays and measured DNA methylation (percentage of methylated reference) of five carefully selected loci (promoters of CACNA1G, CDKN2A (p16), CRABP1, MLH1, and NEUROG1) in 460 colorectal cancers from large prospective cohorts.
There was a clear bimodal distribution of 80 microsatellite instability-high (MSI-H) tumours according to the number of methylated promoters, with no tumours showing 3/5 methylated loci. Thus we defined CIMP as having >or=4/5 methylated loci, and 17% (78) of the 460 tumours were classified as CIMP. CIMP was significantly associated with female sex, MSI, BRAF mutations, and wild-type KRAS. Both CIMP MSI-H tumours and CIMP microsatellite stable (MSS) tumours showed much higher frequencies of BRAF mutations (63% and 54%) than non-CIMP counterparts (non-CIMP MSI-H (0%, p<10(-5)) and non-CIMP MSS tumours (6.6%, p<10(-4)), respectively).
CIMP is best characterised by quantitative DNA methylation analysis. CIMP is a distinct epigenotype of colorectal cancer and may be less frequent than previously reported.
It has long been considered that genetic instability is an integral component of human neoplasia. In a small fraction of tumours, mismatch repair deficiency leads to a microsatellite instability at the nucleotide sequence level. In other tumours, an abnormal chromosome number (aneuploidy) has suggested an instability, but the nature and magnitude of the postulated instability is a matter of conjecture. We show here that colorectal tumours without microsatellite instability exhibit a striking defect in chromosome segregation, resulting in gains or losses in excess of 10(-2) per chromosome per generation. This form of chromosomal instability reflected a continuing cellular defect that persisted throughout the lifetime of the tumour cell and was not simply related to chromosome number. While microsatellite instability is a recessive trait, chromosomal instability appeared to be dominant. These data indicate that persistent genetic instability may be critical for the development of all colorectal cancers, and that such instability can arise through two distinct pathways.
Neoplastic cells simultaneously harbor widespread genomic hypomethylation, more regional areas of hypermethylation, and increased DNA-methyltransferase (DNA-MTase) activity. Each component of this "methylation imbalance" may fundamentally contribute to tumor progression. The precise role of the hypomethylation is unclear, but this change may well be involved in the widespread chromosomal alterations in tumor cells. A main target of the regional hypermethylation are normally unmethylated CpG islands located in gene promoter regions. This hypermethylation correlates with transcriptional repression that can serve as an alternative to coding region mutations for inactivation of tumor suppressor genes, including p16, p15, VHL, and E-cad. Each gene can be partially reactivated by demethylation, and the selective advantage for loss of gene function is identical to that seen for loss by classic mutations. How abnormal methylation, in general, and hypermethylation, in particular, evolve during tumorigenesis are just beginning to be defined. Normally, unmethylated CpG islands appear protected from dense methylation affecting immediate flanking regions. In neoplastic cells, this protection is lost, possibly by chronic exposure to increased DNA-MTase activity and/or disruption of local protective mechanisms. Hypermethylation of some genes appears to occur only after onset of neoplastic evolution, whereas others, including the estrogen receptor, become hypermethylated in normal cells during aging. This latter change may predispose to neoplasia because tumors frequently are hypermethylated for these same genes. A model is proposed wherein tumor progression results from episodic clonal expansion of heterogeneous cell populations driven by continuous interaction between these methylation abnormalities and classic genetic changes.
CpG islands are short stretches of CpG rich regions that are frequently associated with the promoter region of genes. Aberrant methylation of CpG islands is one mechanism of inactivating tumor suppressor genes (TSGs) in neoplasia, and there is growing evidence that altered cytosine methylation play important roles in cancer development. However, the differences in global CpG island methylation patterns between normal and cancer cells remain poorly understood. By examining a large number of loci in a series of cancers, global methylation profiles can be constructed. Such studies revealed that in colorectal cancer, there appears to be two types of methylation that are associated with cancer progression: type A (for age-related) methylation, and type C (for cancer-specific) methylation. Initially, type A methylation arises as a function of age in normal colorectal epithelial cells. By affecting genes that regulate the growth and/or differentiation of these cells, such methylation may result in a predisposition state that precedes tumor formation in the colon. Type C methylation, by contrast, was found exclusively in a subset of cancers, which display a CpG island methylator phenotype (CIMP). CIMP is a novel molecular instability pathway that appears to be responsible for most cases of aberrant TSG methylation in colorectal cancer, and which has important interactions with genetic pathways as well. In fact, CIMP+ tumors account for the majority of sporadic colorectal cancers with microsatellite instability, through methylation of the mismatch repair gene hMLH1. This model whereby age-related methylation increases cell-susceptibility to transformation and cancer-specific methylation results in neoplastic progression in a subset of cases may be applicable to many human neoplasms.
Some studies have shown an inverse relationship between microsatellite instability in colon cancer and mutations in p53 and K-ras, whereas others have not. We therefore evaluated these features in a population-based sample of 496 individuals with colon cancer. Microsatellite instability was determined by a panel of 10 tetranucleotide repeats, the Bethesda consensus panel of mono- and dinucleotide repeats, and coding mononucleotide repeats in transforming growth factor-beta receptor type II, hMSH3, BAX, hMSH6, and insulin-like growth factor receptor type II. Mutations in codons 12 and 13 in K-ras were evaluated by sequencing. p53 overexpression (as detected by immunohistochemistry) was used as an indicator of p53 mutation; this was evaluated in 275 of the tumors. K-ras mutations were present in 33.2% of tumors, p53 overexpression in 51.5%, and microsatellite instability (as determined by the Bethesda consensus panel) in 12.5%. K-ras mutations were significantly less common in unstable tumors than stable tumors (11.8% versus 36.9%, P: < 0.001). p53 overexpression was significantly less common in unstable tumors than stable tumors (20.0% versus 55.7%, P: < 0.001). These inverse relationships between microsatellite instability and ras gene mutations and p53 overexpression were shown to be independent of tumor site in logistic regression analyses. All other measures of instability also showed statistically significant inverse relationships independent of tumor site with alterations in ras and p53, and instability results determined by the panel of 10 tetranucleotide repeats were highly significantly related to those determined by the Bethesda consensus panel. Coding mononucleotide repeat mutations were significantly more common in unstable tumors than stable tumors (85.7% versus 1.0%, P: < 0.001). We conclude that there is an inverse relationship between microsatellite instability and mutations in p53 and K-ras, and that the molecular profile of colon cancers with microsatellite instability is characterized by relatively infrequent mutations in K-ras and p53 and relatively frequent mutations in coding mononucleotide repeats.
High-level microsatellite instability (MSI-H) is demonstrated in 10 to 15% of sporadic colorectal cancers and in most cancers presenting in the inherited condition hereditary nonpolyposis colorectal cancer (HNPCC). Distinction between these categories of MSI-H cancer is of clinical importance and the aim of this study was to assess clinical, pathological, and molecular features that might be discriminatory. One hundred and twelve MSI-H colorectal cancers from families fulfilling the Bethesda criteria were compared with 57 sporadic MSI-H colorectal cancers. HNPCC cancers presented at a lower age (P < 0.001) with no sporadic MSI-H cancer being diagnosed before the age of 57 years. MSI was less extensive in HNPCC cancers with 72% microsatellite markers showing band shifts compared with 87% in sporadic tumors (P < 0.001). Absent immunostaining for hMSH2 was only found in HNPCC tumors. Methylation of hMLH1 was observed in 87% of sporadic cancers but also in 55% of HNPCC tumors that showed loss of expression of hMLH1 (P = 0.02). HNPCC cancers were more frequently characterized by aberrant beta-catenin immunostaining as evidenced by nuclear positivity (P < 0.001). Aberrant p53 immunostaining was infrequent in both groups. There were no differences with respect to 5q loss of heterozygosity or codon 12 K-ras mutation, which were infrequent in both groups. Sporadic MSI-H cancers were more frequently heterogeneous (P < 0.001), poorly differentiated (P = 0.02), mucinous (P = 0.02), and proximally located (P = 0.04) than HNPCC tumors. In sporadic MSI-H cancers, contiguous adenomas were likely to be serrated whereas traditional adenomas were dominant in HNPCC. Lymphocytic infiltration was more pronounced in HNPCC but the results did not reach statistical significance. Overall, HNPCC cancers were more like common colorectal cancer in terms of morphology and expression of beta-catenin whereas sporadic MSI-H cancers displayed features consistent with a different morphogenesis. No individual feature was discriminatory for all HNPCC cancers. However, a model based on four features was able to classify 94.5% of tumors as sporadic or HNPCC. The finding of multiple differences between sporadic and familial MSI-H colorectal cancer with respect to both genotype and phenotype is consistent with tumorigenesis through parallel evolutionary pathways and emphasizes the importance of studying the two groups separately.
The CpG island methylator phenotype (CIMP) is a newly described mechanism for carcinogenesis in colorectal carcinomas and adenomas characterized by methylation of multiple CpG islands. The causes of CIMP are unknown. We studied CIMP in hyperplastic polyps (HPs), with emphasis on patients with multiple HPs (5 to 10 HPs), large HPs (one HP >1 cm) or hyperplastic polyposis (>20 HPs). Methylation of p16, MINT1, MINT2, MINT31, and hMLH1 was analyzed by methylation-specific polymerase chain reaction in 102 HPs, 8 serrated adenomas, 19 tubular adenomas, and 9 adenocarcinomas from 17 patients, with multiple/large HPs or hyperplastic polyposis and in 16 sporadic HPs from 14 additional patients. Sporadic HPs were CIMP-negative (not methylated at any locus), but 43% of HPs from multiple/large HPs, or hyperplastic polyposis were CIMP-high (two or more methylated loci, P = 0.00001). Methylation among the four loci was correlated within HPs (odds ratio, 3.41; P = 0.002), and the methylation status of HPs within the same patient was also correlated (odds ratio, 5.92; P = 0.0001). CIMP-high HPs were present primarily in patients with a predominance of HPs in the right colon and/or serrated adenomas (P = 0.0009) and were associated with the absence of K-ras proto-oncogene mutations (odds ratio, 5.08; P = 0.03). Our findings of concordant CpG island methylation of HPs in multiple/large HPs or hyperplastic polyposis supports the concept that some patients have a hypermethylator phenotype characterized by methylation of multiple HPs and other colorectal lesions. The hypermethylator phenotype is related to patient-specific factors, such as carcinogenic exposure or genetic predisposition.
Methylation of CpG islands is increasingly recognized as an important event in colorectal carcinogenesis. We evaluated the extent of CpG island methylation in 426 sporadic colorectal cancers to define its relationship to microsatellite instability and to describe its clinicopathologic and genetic features.
Fresh cancer tissue was obtained from 417 consecutive individuals undergoing curative surgery for sporadic colorectal cancer. Methylation of p16 and hMLH1 promoters was determined by methylation-specific polymerase chain reaction (PCR), whereas methylation at MINT 1, 2, 12, and 31 loci was assessed by bisulfite PCR. Microsatellite instability and K-ras and p53 status were determined using microsatellite PCR, restriction enzyme-mediated PCR, and immunohistochemistry, respectively.
Individual loci were commonly methylated, but locus-specific phenotypic changes were not seen. CpG island methylation was associated with right-sided location, female sex, and older age, as well as high tumor grade, mucinous type, wild-type P53, microsatellite instability, and K-ras mutations. More than half of tumors showing CpG island methylation were microsatellite stable. Compared with microsatellite unstable cancers, they were more commonly left-sided, had fewer intraepithelial lymphocytes, presented later, and had a worse outcome.
Colorectal cancers with CpG island methylation have distinct clinicopathologic features and in some cases lead to sporadic microsatellite unstable cancers.
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.
DNA methylation is an important biologic event in colorectal cancer and in some cases is associated with the development of microsatellite instability (MSI). In this study, we sought to determine the prognostic significance of DNA methylation, both in univariate analysis and in concert with other clinicopathologic factors known to influence outcome.
Fresh tissue (625 cancers) was obtained from 605 individuals (age range, 29 to 99 years) undergoing curative surgery for colorectal cancer at one institution during a period of 8 years. Clinicopathologic details were recorded for all tumors, including stage, grade, type, vascular space invasion, and clinical follow-up to 5 years. Microsatellite status was assessed using standard markers. Methylation of p16 and hMLH1 promoters was determined by methylation-specific polymerase chain reaction (PCR), whereas methylation at methylated-in-tumor loci (MINT)1, MINT2, MINT12, and MINT31 loci were assessed by bisulfite-PCR.
Patients with microsatellite unstable tumors (12%) had better disease-specific survival than those with microsatellite stable (MSS) tumors (univariate analysis: hazard ratio [HR], 0.53; 95% CI, 0.27 to 1.0). Overall survival of individuals with MSS tumors was influenced by three independently significant factors: tumor stage (HR, 7.3; 95% CI, 5.1 to 10.4), heavy tumor methylation (HR, 2.1; 95% CI, 1.1 to 4.0), and vascular space invasion (HR, 1.9; 95% CI, 1.3 to 2.9). In MSS tumors, methylation at any single site was not independently predictive of survival. Neither methylation nor microsatellite status predicted a favorable response to chemotherapy.
DNA methylation is associated with a worse outcome in colorectal cancer, but this adverse prognostic influence is lost in those methylated tumors showing MSI. The mechanisms of these events warrant additional investigation.
Runt domain transcription factors are important targets of TGF-beta superfamily proteins and play a crucial role in mammalian development. Three mammalian runt-related genes, RUNX1, RUNX2 and RUNX3, have been described. RUNX3 has been shown to be a putative tumor suppressor gene localized to chromosome 1p36, a region showing frequent loss of heterozygosity events in colon, gastric, breast and ovarian cancers. Because of the important role of TGF-beta signaling in the human colon, we hypothesized that RUNX3 may serve as a key tumor suppressor in human colon cancers and colon cancer-derived cell lines. We examined RUNX3 expression and the frequency of RUNX3 promoter hypermethylation in 17 colon cancer cell lines and 91 sporadic colorectal cancers. Semiquantitative analysis of RUNX3 transcripts was performed by RT-PCR and de novo methylation of the RUNX3 promoter was studied by a methylation-specific PCR (MSP) assay. Nineteen of 91 informative tumors (21%) and 11 of 17 (65%) colon cancer cell lines exhibited hypermethylation of the RUNX3 promoter. Interestingly, RUNX3 promoter hypermethylation was more common in tumors exhibiting high frequency of microsatellite instability (MSI-H) (33% of MSI-H vs. 12% of MSI-L/MSS tumors; p = 0.012). Hypermethylation of the RUNX3 promoter correlated with loss of mRNA transcripts in all cell lines. RUNX3 promoter methylation was reversed and its expression restored in SW48 and HCT15 colon cancer cells after treatment with the demethylating agent 5-aza-2'-deoxycytidine, indicating that loss of expression is caused by epigenetic inactivation in colon carcinogenesis. This is the first demonstration of frequent de novo hypermethylation of the RUNX3 promoter in sporadic colon cancers. The significant association of RUNX3 promoter hypermethylation with MSI-H colon cancers suggests that RUNX3 is a novel target of methylation, along with the hMLH1 gene, in the evolution of MSI-H colorectal cancers.
Fifteen years after the first demonstration of epigenetic tumor-suppressor gene inactivation associated with promoter methylation, the field has reached a level of understanding that threatens a re-writing of established biologic concepts. In gastrointestinal malignancies, epigenetic analysis has led to novel hypotheses regarding the etiology of age-associated cancer susceptibility and the interactions between environmental exposures and neoplasia. Methylation profiling has uncovered a distinct pathway to colorectal neoplasia that may arise from a hitherto underestimated precursor lesion, the proximal hyperplastic polyp-serrated adenoma pathway. Epigenetic information has shown promise in clarifying susceptibility to cancer and defining poor prognosis groups in gastrointestinal cancers. Finally, the field has engendered renewed interest in therapeutic targeting of epigenetic regulatory molecules, and several such drugs are currently in clinical trials. It is likely that epigenetic pathways will be integrated in the routine management of gastrointestinal malignancies over the next decade.
Serrated adenomas (SA) of the colorectum show features intermediate between hyperplastic polyps (HP) and adenomas. HP and SA are related lesions and there is now strong evidence for a 'serrated-polyp pathway' to colorectal cancer (CRC) that is largely independent of the classic adenoma-to-carcinoma sequence. A recently recognized lesion in this pathway is a HP variant characterized by relatively large size, atypical histology and proximal location in the colorectum. This HP variant has been given a variety of names in the literature including 'sessile SA' and 'type I SA'. Because this lesion lacks the traditional cytology of colorectal adenoma and in order to avoid confusion with SA, it is referred to in this review as sessile serrated polyp. SA are characterized by a heterogeneous group of changes at the molecular level, but a high proportion have BRAFmutations and DNA methylation. They may develop in HP or sessile serrated polyps, or may arise de novo. In the serratedpolyp pathway, the advent of genetic instability is likely to be an important rate-limiting step that drives rapid neoplastic evolution. Methylation and inactivation of the DNA repair genes MLH1 and MGMT (O-6-methylguanine-DNA methyltransferase) have been proposed as critical steps leading to genetic instability. Stretches of DNA rich in the bases guanine and cytosine (CpG islands; where p represents a phosphodiester bond linking adjacent cytosine and guanine bases) that are normally unmethylated may become methylated in malignant human colorectal tumors. Subsets of colorectal cancers with an unusually high number of methylated CpG islands have been described as having the 'CpG-island-methylator phenotype' It is possible that many, if not all, CRCs with the CpG-island-methylator phenotype evolve through the serrated-polyp pathway that would, therefore, explain approximately 20% of all CRCs. The current lack of guidelines for managing serrated polyps may explain the static incidence of proximal CRC, despite the falling incidence rates for left-sided CRC during the same time period.
The concept of a CpG island methylator phenotype (CIMP), especially in microsatellite stable colon cancer, is not accepted universally. We therefore evaluated a large population-based sample of individuals with colon cancer and used univariate and multivariate analyses of CIMP with clinicopathologic variables and tumor mutations to determine the biologic relevance of this phenotype.
A total of 864 tumors from individuals with colon cancer from Utah and Northern California were evaluated by methylation-specific polymerase chain reaction of CpG islands in hMLH1, methylated in tumors (MINT) 1, MINT 2, MINT 31, and CDKN2A (p16). CIMP high was defined as methylation at 2 or more of these loci. The BRAF V600E mutation was determined by sequencing. Microsatellite instability had been determined previously.
In a multivariate analysis of microsatellite stable tumors, CIMP high was related significantly to the V600E BRAF mutation (odds ratio, 39.52; 95% confidence interval, 11.44-136.56), KRAS2 mutations (odds ratio, 2.22; 95% confidence interval, 1.48-3.34), older age (P trend = .03), and increased stage (P trend = .03), and these tumors were less likely to be located in the distal colon (odds ratio, .42; 95% confidence interval, .27-.65). CIMP-high unstable tumors also were more likely to have the V600E BRAF mutation, be located proximally, and occur in older individuals (in univariate analyses). However, CIMP-high unstable tumors were significantly more likely than their stable counterparts to be KRAS2 wild type, TP53 wild type, poorly differentiated, proximally located, occur at lower stages, and have the BRAF V600E mutation (64.1% vs 17.6%).
The evaluation of a large, population-based sample strongly supports the biologic relevance of CIMP in colon cancer. However, the presence or absence of microsatellite instability has a major effect on the expression of this phenotype.
CpG island methylation is present in various tumors, including colorectal carcinomas, and is thought to be an important mechanism in carcinogenesis. We evaluated the methylation status of primary colorectal tumors to determine its role in the adenoma to carcinoma sequence.
The methylation status of APC, THBS1, MGMT, hMLH1 and GSTP1, as determined by methylation specific PCR (MSP), and microsatellite instability (MSI) using three mononucleotide markers were assessed in 40 colorectal adenomas and 36 adenocarcinomas. The correlations of methylation status and MSI with the clinicopathologic parameters of the tumors were determined.
Of the 40 adenomas, 24 (60%) were methylated at one or more loci, and 12 (30%) at two or more loci (CpG island methylation phenotype-high, CIMP-H). Of 36 carcinomas, 27 (75%) were methylated at one or more loci and 11 (30.5%) at two or more loci (CIMP-H). THBSI was the most frequently methylated locus in both adenomas (n = 19, 47.5%) and carcinomas (n = 16, 44.4%). Overall, methylation status of adenomas and carcinomas did not differ significantly (P = 0.53), nor did the methylation status of individual genes. For adenomas, size (P = 0.049) and histologic classification of the villous components (P = 0.018) were each associated with methylation status. For carcinomas, however, no clinicopathologic variable was related to methylation status. MSI was detected in three adenomas (7.5%) and five carcinomas (13.9%), and was closely correlated with hMLH1 methylation (P < 0.001).
In colorectal tumors, CpG island methylation of tumor suppressor genes appears to be common and may be involved in the progression of adenomas.
We studied the relationships between genetic and epigenetic alterations in gastrointestinal cancer by integrating DNA copy number changes determined by arbitrarily primed PCR (AP-PCR) with DNA methylation variations estimated by methylation-sensitive amplified fragment length polymorphism (MS-AFLP). We analyzed about 100 different chromosomal regions by AP-PCR and over 150 random CpG loci by MS-AFLP in human colon and gastric carcinomas. DNA hypomethylation and hypermethylation alterations distributed gradually and increased with cancer patient age, in contrast with the age-independent genomic alterations. Increased DNA hypomethylation and hypermethylation correlated with increased genomic damage, but only hypomethylation was highly significant in multivariate analyses. We conclude that age-dependent accumulation of DNA demethylation precedes diploidy loss in a significant subset of gastrointestinal cancers.
JC virus (JCV) is a polyomavirus that ubiquitously infects humans and has been implicated in various human cancers. JCV encodes a "transforming" gene, T-antigen (T-Ag), which is believed to mediate the oncogenic potential of the virus. We have previously shown that JCV DNA sequences are usually present in human colorectal cancers (CRCs), and we have provided in vitro evidence that JCV can induce chromosomal instability (CIN) in CRC cells. This study tests the hypothesis that JCV T-Ag expression correlates with one or more forms of genomic or epigenetic instability in sporadic CRCs.
We characterized 100 sporadic CRCs for microsatellite instability (MSI) and CIN. PCR amplifications were performed for T-Ag sequences, and immunohistochemical (IHC) staining was performed to detect T-Ag expression. De novo methylation of the promoter regions of nine putative tumor suppressor genes thought to play a role in colorectal carcinogenesis was studied by methylation-specific PCR.
JCV T-Ag DNA sequences were found in 77% of the CRCs and 56% of these cancers (or 43% of the total) expressed T-Ag by IHC. Significant associations were observed between T-Ag expression and CIN in CRCs (P = .017) and between T-Ag expression and promoter methylation of multiple genes (P = .01).
The association between T-Ag expression and promoter methylation in CRC suggests that this viral oncogene may induce methylator phenotype and that JCV may be involved in CRC through multiple mechanisms of genetic and epigenetic instability.
To determine the methylation profile of multiple tumor-related genes during multistep hepatocarcinogenesis, we investigated the methylation status of CpG islands of 9 genes, using methylation-specific polymerase chain reaction for 60 paired hepatocellular carcinoma (HCC) and non-HCC liver tissue samples, 22 dysplastic nodule (DN), 30 liver cirrhosis (LC), 34 chronic hepatitis (CH) and 20 normal liver samples. The methylation status of 9 genes was correlated to the clinicopathological findings of HCC patients. All HCC samples showed methylation of at least one gene, whereas it was shown in 72.7% of DN and 40% of LC, but was not shown in CH and normal liver samples (P < 0.001). The number of genes methylated showed a stepwise increase with the progression of stages (0 for normal liver and CH, 0.5 for LC, 1.5 for DN, and 3.7 for HCC (P < 0.001)). The genes frequently methylated in HCC were APC (81.7%), GSTP1 (76.7%), RASSF1A (66.7%), p16 (48.3%), COX-2 (35%), and E-cadherin (33.3%). COX-2, p16, RASSF1A, and TIMP-3 were not methylated in LC and CH from patients without concurrent HCC. Chronic liver diseases with concurrent HCC showed higher methylation frequencies of the tested genes, and a higher number of methylated genes than those without concurrent HCC. HCC patients with methylation of E-cadherin or GSTP1 showed poorer survival than those without (P = 0.034 and 0.043, respectively). In conclusion, our results indicated that CpG island methylation of tumor-related genes is an early and frequent event, and accumulates step-by-step during a multistep hepatocarcinogenesis. CpG island methylation of E-cadherin or GSTP1 might serve as a potential biomarker for prognostication of HCC patients.
Cancer epigenetics comes of age
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CpG island methylation as an early event during adenoma progression in carcinogenesis of sporadic colorectal cancer
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A.); and research for CALGB 9865 was supported
- Mildred-Scheel-Stiftung Germany
Mildred-Scheel-Stiftung, Germany (to C.N.A.); and research for CALGB 9865 was supported, in part, by grants from the National Cancer Institute (CA31946) to the Cancer and Leukemia Group B (Richard L. Schilsky, Chairman).
Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer
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Samowitz WS, Albertsen H, Herrick J, Levin TR, Sweeney C, Mur-taugh MA, Wolff RK, Slattery ML. Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer. Gastroenterology 2005;129:837– 845.
Evaluation of a large, population-based sample supports a CpG island methylator phenotype in colon cancer
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Distinct genetic profiles in colorectal tumors with or without the CpG island methylator phenotype
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CpG island methylation in sporadic colorectal cancers and its relationship to microsatellite instability
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CpG island methylator phenotypes in aging and cancer
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Cancer epigenetics comes of age
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A National Cancer Institute Workshop on Microsatellite Instability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer
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Concordant CpG island methylation in hyperplastic polyposis
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