Aberrant Methylation Of CpG Islands Research Articles

Tissue factor pathway inhibitor 2 ( TFPI2) is frequently silenced by aberrant promoter hypermethylation in gastric cancer

Aberrant methylation of promoter CpG islands is associated with transcriptional inactivation of tumor-suppressor genes in cancer. TFPI2, a Kunitz-type serine proteinase inhibitor, has been identified as a putative tumor-suppressor gene from genome-wide screening for aberrant methylation, using a microarray combined with the methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dCyd) in various types of tumors. We assessed the methylation status of TFPI2 and investigated its expression pattern in human primary gastric cancer (GC) tissues and in GC cell lines. Hypermethylation of the promoter CpG island, which was observed in more or less all of GC cell lines, was prevalent in a high proportion of primary GC tissues (15/18, or 83%), compared with noncancerous (4/18, or 22%) or normal (0/3, or 0%) stomach tissues, and expression of TFPI2 mRNA was reduced in 7 of the 17 primary GC tissues (41%). Moreover, immunohistochemical analyses showed decreased levels of TFPI-2 protein, compared with adjacent noncancerous tissues in 8 of the 20 primary GC tissues examined (40%). TFPI2 mRNA expression was restored in gene-silenced GC cells after treatment with 5-aza-dCyd. Aberrant methylation of TFPI2 promoter CpG island occurred not only in GC cells but also in primary GC tissues at a high frequency, suggesting that epigenetic silencing of TFPI2 may contribute to gastric carcinogenesis.

Promoter methylation status ofhMLH1,MGMT, andCDKN2A/p16in colorectal adenomas

To investigate aberrant DNA methylation of CpG islands and subsequent low- or high-level DNA microsatellite instability (MSI) which is assumed to drive colon carcinogenesis. DNA of healthy individuals, adenoma (tubular or villous/tubulovillous) patients, and colorectal carcinoma patients who underwent colonoscopy was used for assessing the prevalence of aberrant DNA methylation of human DNA mismatch repair gene mutator L homologue 1 (hMLH1), Cyclin-dependent kinase inhibitor 2A (CDKN2A/p16), and O-6-methylguanine DNA methyltransferase (MGMT), as well as their relation to MSI. The frequency of promoter methylation for each locus increased in the sequence healthy tissue/adenoma/carcinoma. MGMT showed the highest frequency in each group. MGMT and CDKN2A/p16 presented a statistically significant increase in promoter methylation between the less and more tumorigenic forms of colorectal adenomas (tubular vs tubullovillous and villous adenomas). All patients with tubulovillous/villous adenomas, as well as all colorectal cancer patients, showed promoter methylation in at least one of the examined loci. These findings suggest a potentially crucial role for methylation in the polyp/adenoma to cancer progression in colorectal carcinogenesis. MSI and methylation seem to be interdependent, as simultaneous hMLH1, CDKN2A/p16, and MGMT promoter methylation was present in 8/9 colorectal cancer patients showing the MSI phenotype. Methylation analysis of hMLH1, CDKN2A/p16, and MGMT revealed specific methylation profiles for tubular adenomas, tubulovillous/villous adenomas, and colorectal cancers, supporting the use of these alterations in assessment of colorectal tumorigenesis.

Methylation of p16 and E-cadherin in ameloblastoma

Introduction: Ameloblastic carcinoma is a rare malignant lesion, and may arise from either carcinoma ex-ameloblastoma or de novo carcinoma. Aberrant promoter hypermethylation of the tumor-associated genes leading to their inactivation is a common event in many cancer types. The p16/CDKN2/INK4A gene and p16 5 protein are involved directly in regulating the cell cycles. Cadherins are cell adhesion molecules that modulate the epithelial phenotype and regulate tumor invasion. The aim of this study was to evaluate the roles of p16 and E-cadherin methylation and loss of p16 and E-cadherin expression in the malignant transformation of an ameloblastoma. Materials and Methods: Eight cases of ameloblastoma, including 4 benign ameloblastomas without recurrence, 2 benign ameloblastomas with recurrence and 2 carcinoma ex-ameloblastomas, were examined. The promoter hypermethylation profile of the p16 and E-cadherin genes was studied using methylation-specific polymerase chain reaction (MSP) and immunohistochemical staining for p16 and E-cadherin expression. Results: 1) Aberrant CpG island methylation of the p16 gene was detected in 3 of the 4 benign ameloblastomas without recurrence and 1 of the 2 benign ameloblastomas with recurrence. 2) Aberrant CpG island methylation of the E-cadherin gene was found in 1 of the 4 benign ameloblastomas without recurrence. 3) A loss of p16 expression was noted in 1 of 4 benign ameloblastomas without recurrence and 1 of 2 carcinoma ex-ameloblastomas. 4) A loss of E-cadherin expression was noted in 2 of the 4 benign ameloblastomas without recurrence, 1 of the 2 benign ameloblastomas with recurrence and 2 of the 2 carcinoma ex-ameloblastomas. 5) A loss of p16 expression was observed in 1 of the 4 cases showing aberrant methylation of the p16 gene. 6) A loss of E-cadherin expression was observed in 3 benign ameloblastoma case showing aberrant methylation of the E-cadherin gene. Conclusion: These results suggest that loss of E-cadherin expression related to the other genetic pathway (not methylation) might be an adjuvant indicator predicting the malignant transformation of an ameloblastoma. However, the number of samples in this study was too small and the relationship between the treatment methods and clinical course were not defined. Therefore, further study will be needed.

Multi-Step Aberrant CpG Island Hyper-Methylation Is Associated with the Progression of Adult T–Cell Leukemia/Lymphoma

Aberrant CpG island methylation contributes to the pathogenesis of various malignancies. However, little is known about the association of epigenetic abnormalities with multistep tumorigenic events in adult T cell leukemia/lymphoma (ATLL). To determine whether epigenetic abnormalities induce the progression of ATLL, we analyzed the methylation profiles of the SHP1, p15, p16, p73, HCAD, DAPK, hMLH-1, and MGMT genes by methylation specific PCR assay in 65 cases with ATLL patients. The number of CpG island methylated genes increased with disease progression and aberrant hypermethylation in specific genes was detected even in HTLV-1 carriers and correlated with progression to ATLL. The CpG island methylator phenotype (CIMP) was observed most frequently in lymphoma type ATLL and was also closely associated with the progression and crisis of ATLL. The high number of methylated genes and increase of CIMP incidence were shown to be unfavorable prognostic factors and correlated with a shorter overall survival by Kaplan-Meyer analysis. The present findings strongly suggest that the multistep accumulation of aberrant CpG methylation in specific target genes and the presence of CIMP are deeply involved in the crisis, progression, and prognosis of ATLL, as well as indicate the value of CpG methylation and CIMP for new diagnostic and prognostic biomarkers.

Methylation profiling of tumor suppressor genes and oncogenes in hepatitis virus-related hepatocellular carcinoma in northern India

Hepatocellular carcinoma (HCC) is the fifth most common cancer in India, and hepatitis B virus and hepatitis C virus infections are major risk factors. DNA methylation alterations have been linked to various carcinomas in different populations. Aberrant CpG island methylation of genes has been recognized in HCC, information is limited for hepatitis virus–related hepatocarcinogenesis. HCC risk has not previously been associated with gene-specific DNA methylation in India. Promoter region methylation of a panel of six tumor suppressor genes ( CDKN2A, CDKN2B, CDH1, GSTP1, SOCS1, and APC) and three oncogenes ( MYC, HRAS, and KRAS) was determined by methylation-specific PCR among 23 HCC samples and 20 control hepatitis samples. CDKN2B methylation frequency in HCC was double that for hepatitis, and methylation allele density of APC, GSTP1, and CDKN2B increased 2.2-, 2.3-, and 7.6-fold, respectively. Epigenetic silencing of tumor suppressor genes starts during viral infection and progresses toward HCC with the chronicity of the disease. Findings of altered methylation status support involvement of these tumor suppressor genes in HCC. MYC showed decreased methylation in HCC, relative to hepatitis. These observations on DNA methylation suggest the involvement of CDKN2B, SOCS1, CDH1, GSTP1, and MYC in pathogenesis of HCC in India and implicate altered DNA methylation in the molecular pathogenesis.

Hypermethylation Status of Cancer-Associated Genes in Pediatric Acute Lymphoblastic Leukemia (ALL): Incidence and Potential Implications in Therapy.

Abstract 4422 IntroductionAcute Lymphoblastic Leukemia (ALL) is the most common malignancy diagnosed in children, representing nearly one third of all pediatric cancers. Aberrant methylation of CpG island of the promoter region of genes causes gene silencing and could be critical in the initiation and progression ALL. Patients and MethodsThe study included a group of 10 de novo pediatric cases of ALL and 18 healthy control children. The cases were treated according to the University Children Hospital protocol and followed-up for 28 days. In the present study we assessed the methylation frequency of p14ARF, p15CDKN2B, p16CDKN2A, MLH1, CTNNB1, and APAF1 genes before cases started therapy (Day 0) and after completing the induction phase at Day 28. DNA was extracted from peripheral blood cells from cases and controls. Methylation status was performed using the MethyLight technique. The methylation index (MI; ratio between the number of genes methylated and the number of genes analyzed) was calculated and results were correlated to minimal residual disease (MRD) status of the cases. ResultsThe gene most frequently methylated was p15CDKN2B (90% of cases on Day 0). Frequencies of p16CDKN2A, MLH1, CTNNB1 gene methylation were 80%, 70%, and 10% respectively. A coexistence of p15CDKN2B, p16CDKN2A and MLH1 gene methylation was observed. No patient showed methylation in p14ARF and APAF1 genes. The methylation index ranged from 0 to 0.67 with a median of 0.5. After induction therapy was completed (Day 28) the most frequently methylated gene was p15CDKN2B (80% of cases on Day 28). Frequencies of MLH1, p16CDKN2A, p14ARF and CTNNB1 gene methylation were 40%, 30%, 20% and 10% respectively. No patient showed methylation of the APAF1 genes on Day 28. The methylation index ranged from 0 to 0.67 with a median of 0.17 on Day 28. We found that after the induction treatment methylation of p15CDKN2B, p16CDKN2A, and MLH1 is a frequent event. Interestingly methylation of p14ARF was detected after induction. No significant differences in the frequencies of gene methylation and presence of minimal residual disease between patients with and without aberrant methylation, respectively, were found. We found that the methylation status was not associated with patient age at diagnosis, sex, FAB classification and cytogenetic changes. ConclusionsOur findings suggest that aberrant methylation of p15CDKN2B gene is a frequent event in this pathology. The relationship between methylation of p15CDKN2B and leukemia has been reported previously. It appears that methylation of p15CDKN2B is an early event in ALL and continue to be present even after patients completed the induction treatment. Simultaneously, our data would confirm that, in our cohort, the methylation of p16CDKN2A and MLH1 gene promoters is a frequent event in pediatric ALL. However, to assess the impact of promoter methylation of these tumor suppressor genes on disease prognosis longer follow-up and a larger patient population is warranted. Disclosures:No relevant conflicts of interest to declare.

Two-stage case–control study of DNMT-1 and DNMT-3B gene variants and breast cancer risk

Aberrant DNA methylation of CpG islands is a common epigenetic alteration found in cancers. DNA methylation is typically mediated by DNA methyltransferases (DNMTs). Only two studies have evaluated DNMT-1 and/or DNMT-3B gene polymorphisms in relation to breast cancer risk, and results have been inconsistent. We comprehensively evaluated genetic variations in the DNMT-1 and DNMT-3B genes with breast cancer risk among the participants of the Shanghai Breast Cancer Study, a large-scale, two-stage, case-control study. Of the 25 SNPs in the DNMT-1 and DNMT-3B genes analyzed, only one (rs8101866) reached a normal significance level (P = 0.042). This association, however, was no longer statistically significant after adjustment for multiple comparisons. Our data suggest that there is no apparent association of common DNMT-1 and DNMT-3B polymorphisms with the risk of breast cancer among Chinese women.

DNA methyltransferase expression differs with proliferation in childhood acute lymphoblastic leukemia

DNA methylation is involved in genomic imprinting, tissue and stage specific gene regulation, X chromosome inactivation and especially necessary in normal mammalian development [1]. Methylation of DNA at cytosine base occurs at most CpG islands in the mammalian genome, with exception of CpG islands of gene promoters which are usually unmethylated. Methylation of promoter CpG islands inhibits the activity of the gene by inhibiting the association of some DNA-binding factors with methylated DNA sequences or by silencing transcription via methyl-CpG binding proteins with co-repressors and chromatin modifiers [2]. Cancer is known as a genetic disease, in which epigenetic alterations play important roles. Cancer cells show global genomic hypomethylation, but the CpG islands of the promoters, especially the promoters of the tumour suppressor genes are hypermethylated [3]. Aberrant methylation of CpG islands is a major epigenetic mechanism of gene expression in human cancers. Global hypomethylation is important in tumour formation by different ways which include chromosomal and genomic instability, increased mutation rate and recombination frequency [4]. Hypermethylation of tumour suppressor genes causes gene inactivation, furthermore aberrant DNA methylation facilitates gene mutation, because deamination of 5-methylcytosine leads to the formation of thymine which is not repaired by uracil glycosylases, instead of the formation of uracil by cytosine deamination [5]. Acute lymphoblastic leukemia (ALL), is the most frequent cancer of childhood (25%). The blockage of lymhpoid cell development at any stage, leads to ALL. Chromosomal aberrations as well as epigenetic changes are important in it’s development. E-cadherin, DAP-kinase, p73 and p15 gene promoters are some of the gene promoters that are known to be hypermethylated in childhood ALL [6–8]. DNA methyltransferases (DNMT’s) are the enzymes that methylate DNA. In mammalians, there are five different DNMT’s: DNMT1, DNMT2, DNMT3A, DNMT3B and DNMT3L. All of the DNMT’s, except DNMT3L, are catalitically active. All have a catalytic carboxy terminal and a regulator amino terminal, except DNMT2. The activity of DNMTs are greatly regulated by their amino terminal domain which interacts with other molecules. DNMT2, contains only the catalytic domain and participates scarcely to the formation of DNA methylation pattern although it covalently binds to DNA [9–11]. DNMT1 targets the replication fork, methylates preferentially hemimethylated DNA, and is responsible for the Isik Bokesoy—Retired Professor.

Detection of methylation in the CpG islands of the RASSF1A and RAR2b gene promoters in breast cancer (BC)

e14632 Background: Aberrant methylation of CpG islands of cancer-related genes has emerged as an important epigenetic mechanism during carcinogenesis. We examined the methylation of RASSF1A (Ras-association domain family 1, isoform A) and RAR2b (Retinoic Acid Receptor 2b) genes in BC. The knowledge of their role in BC is limited and confused to date. Methods: Promoter methylation was measured in 37 pts, 26 with BC and 11 with benign lesions. The specimens were obtained from archive formalin-fixed paraffin-embedded tumors. After DNA extraction, the methylation was determined by chemical modification of DNA with sodium bisulfite and subsequent double “hot start” Methylation-Specific PCR (MSP), followed by detection on agarose gel. Results: Methylation of at least one of the genes was observed in 18/26 pts (p<0.05). Methylation of RASSF1A gene was observed in 15/26 and RAR2b in 11/26 pts. Both genes were methylated in 8/26 pts. Correlation between methylation and clinicopathological features revealed an association of the RASSF1A gene with T2 tumors (12/15 pts, p<0.05) and ER (+) status (12/15 pts, p<0.05). T2 tumors and ER (+) status presented together in 9/15 pts. The methylation of RAR2b gene was not associated with any known clinicopathological features. In benign lesions methylation of at least one of the genes was observed in 8/11 pts (p<0.05). Methylation of RASSF1A gene was observed in 5/11 pts and RAR2b in 7/11 pts. Both genes were methylated in 4/11 pts. Conclusions: Both genes are frequently methylated in both benign and malignant breast lesions. The association of methylation of RASSF1A gene with tumor size and ER status is noteworthy. The small number of pts does not allow us to confirm the exact role of gene methylation in BC yet. Larger studies are required in order to assess if these epigenetic alterations point out new BC markers, which could be helpful for BC control. No significant financial relationships to disclose.

Methylation-sensitive Regulation of TMS1/ASC by the Ets Factor, GA-binding Protein-α

Epigenetic silencing involving the aberrant DNA methylation of promoter-associated CpG islands is one mechanism leading to the inactivation of tumor suppressor genes in human cancers. However, the molecular mechanisms underlying this event remains poorly understood. TMS1/ASC is a novel proapoptotic signaling factor that is subject to epigenetic silencing in human breast and other cancers. The TMS1 promoter is embedded within a CpG island that is unmethylated in normal cells and is spanned by three DNase I-hypersensitive sites (HS). Silencing of TMS1 in cancer cells is accompanied by local alterations in histone modification, remodeling of the HS, and hypermethylation of DNA. In this study, we probed the functional significance of the CpG island-specific HS. We identified a methylation-sensitive complex that bound a 55-bp intronic element corresponding to HS2. Affinity chromatography and mass spectrometry identified a component of this complex to be the GA-binding protein (GABP) alpha. Supershift analysis indicated that the GABPalpha binding partner, GABPbeta1, was also present in the complex. The HS2 element conferred a 3-fold enhancement in TMS1 promoter activity, which was dependent on both intact tandem ets binding sites and the presence of GABPalpha/beta1 in trans. GABPalpha was selectively enriched at HS2 in human cells, and its occupancy was inversely correlated with CpG island methylation. Down-regulation of GABPalpha led to a concomitant decrease in TMS1 expression. These data indicate that the intronic HS2 element acts in cis to maintain transcriptional competency at the TMS1 locus and that this activity is mediated by the ets transcription factor, GABPalpha.

T1913 Effects of Helicobacter pylori Infection On Aberrant CpG Island Methylation Status and Cellular Phenotype in Columnar-Lined Esophagus in a Japanese Population

T1913 Effects of Helicobacter pylori Infection On Aberrant CpG Island Methylation Status and Cellular Phenotype in Columnar-Lined Esophagus in a Japanese Population

SALL3 Interacts with DNMT3A and Shows the Ability To Inhibit CpG Island Methylation in Hepatocellular Carcinoma

The mechanisms of aberrant CpG island methylation in oncogenesis are not fully characterized. In particular, little is known about the mechanisms of inhibition of CpG island methylation. Here we show that sal-like 3 (SALL3) is a novel inhibitory factor for DNA methyltransferase 3 alpha (DNMT3A). SALL3 binds to DNMT3A by a direct interaction between the double zinc finger motif of SALL3 and the PWWP domain of DNMT3A. SALL3 expression reduces DNMT3A-mediated CpG island methylation in cell culture and in vitro. CpG island methylation is enhanced in SALL3-depleted cells. Consistently, DNMT3A from SALL3-depleted cells increases methyltransferase activity in vitro. Binding of DNMT3A to chromatin is reduced or increased by SALL3 expression or depletion, respectively, accounting for the mechanism by which SALL3 inhibits DNMT3A-mediated CpG island methylation. We also show that SALL3 is inducible by BMP-4 and silenced by associated DNA methylation in hepatocellular carcinoma (HCC). Our results suggest that silencing of SALL3 results in acceleration of DNA methylation in HCC. This functional characterization of SALL3 sheds light on regulatory mechanisms for DNMT3A and provides new strategies to inhibit aberrant methylation in cancer.

Promoter methylation correlates with reduced NDRG2expression in advanced colon tumour

BackgroundAberrant DNA methylation of CpG islands of cancer-related genes is among the earliest and most frequent alterations in cancerogenesis and might be of value for either diagnosing cancer or evaluating recurrent disease. This mechanism usually leads to inactivation of tumour-suppressor genes. We have designed the current study to validate our previous microarray data and to identify novel hypermethylated gene promoters.MethodsThe validation assay was performed in a different set of 8 patients with colorectal cancer (CRC) by means quantitative reverse-transcriptase polymerase chain reaction analysis. The differential RNA expression profiles of three CRC cell lines before and after 5-aza-2'-deoxycytidine treatment were compared to identify the hypermethylated genes. The DNA methylation status of these genes was evaluated by means of bisulphite genomic sequencing and methylation-specific polymerase chain reaction (MSP) in the 3 cell lines and in tumour tissues from 30 patients with CRC.ResultsData from our previous genome search have received confirmation in the new set of 8 patients with CRC. In this validation set six genes showed a high induction after drug treatment in at least two of three CRC cell lines. Among them, the N-myc downstream-regulated gene 2 (NDRG2) promoter was found methylated in all CRC cell lines. NDRG2 hypermethylation was also detected in 8 out of 30 (27%) primary CRC tissues and was significantly associated with advanced AJCC stage IV. Normal colon tissues were not methylated.ConclusionThe findings highlight the usefulness of combining gene expression patterns and epigenetic data to identify tumour biomarkers, and suggest that NDRG2 silencing might bear influence on tumour invasiveness, being associated with a more advanced stage.

Methylation of homeobox genes is a frequent and early epigenetic event in breast cancer

IntroductionAberrant methylation of CpG islands is a hallmark of cancer and occurs at an early stage in breast tumorigenesis. However, its impact on tumor development is not fully determined, and its potential as a diagnostic biomarker remains to be validated. Methylation profiling of invasive breast carcinoma has been largely explored. Conversely, very little and sparse information is available on early-stage breast cancer. To gain insight into the epigenetic switches that may promote and/or contribute to the initial neoplastic events during breast carcinogenesis, we have analyzed the DNA methylation profile of ductal carcinoma in situ, a premalignant breast lesion with a great potential to progress toward invasive carcinoma.MethodsWe have utilized a comprehensive and sensitive array-based DNA mapping technique, the methylated-CpG island recovery assay, to profile the DNA methylation pattern in ductal carcinoma in situ. Differential methylation of CpG islands was compared genome-wide in tumor DNA versus normal DNA utilizing a statistical linear model in the LIMMA software package.ResultsUsing this approach, we have identified 108 significant CpG islands that undergo aberrant DNA methylation in ductal carcinoma in situ and stage I breast tumors, with methylation frequencies greater than or comparable with those of more advanced invasive carcinoma (50% to 93%). A substantial fraction of these hypermethylated CpG islands (32% of the annotated CpG islands) is associated with several homeobox genes, such as the TLX1, HOXB13, and HNF1B genes. Fifty-three percent of the genes hypermethylated in early-stage breast cancer overlap with known Polycomb targets and include homeobox genes and other developmental transcription factors.ConclusionsWe have identified a series of new potential methylation biomarkers that may help elucidate the underlying mechanisms of breast tumorigenesis. More specifically, our results are suggestive of a critical role of homeobox gene methylation in the insurgence and/or progression of breast cancer.

Promoter hypermethylation is an early event in breast carcinogenesis.

Abstract Abstract #5041 Background. Aberrant methylation of CpG islands in the promoter region of tumor suppressor genes has become established as an important epigenetic mechanism for gene silencing. Promoter hypermethyaltion in precursor lesions at risk for progression to invasive cancer may be biomarkers of cancer risk and targets for cancer chemoprevention. In breast cancer promoter hypermethylation has been described for several genes covering all aspects of cellular function. However, the methylation studies of precursor lesion of the breast are rather sparse and mostly done in a purely qualitative manner.
 Design. To evaluate the significance of alterations in promoter hypermethylation during multistage carcinogenesis of the breast, quantitative multiplex methylation-specific PCR of six genes (APC1, Cyclin D2, HIN-1, RAR-b, RASSF1A, and Twist) was performed on DNA from 15 normal breast tissues, 21 usual ductal hyperplasia (UDH), 48 ductal carcinoma in situ (DCIS), and 35 stage I invasive ductal carcinoma (IDC), not otherwise specified.
 Results. We found no to very low levels of promoter methylation in normal samples. In general UDH, DCIS, and IDC samples revealed varying levels of methylation ranging from 0 to 100%. One-way analysis of variance showed that the methylation levels of all six genes increased significantly with the progression of breast neoplasia from normal epithelium, through hyperplasia, to DCIS. However, methylation levels were not significantly different between DCIS and IDC.
 Conclusion. Our results suggest that promoter hypermethylation is an early event in breast carcinogenesis. Promoter hypermethylation in the precursor lesions of the breast cancer may be used as a target for cancer chemoprevention. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 5041.

Aberrant CpG Island Hypermethylation of the RUNX3 Gene in Osteosarcoma

Purpose: Transcriptional silencing of tumor suppressor genes by aberrant methylation of CpG islands plays a crucial role in the development of human cancers. We comprehensively examined the methylation status of several tumor suppressor genes in osteosarcoma with a special focus on the RUNX3 gene. Materials and Methods: Methylation-specific polymerase chain reaction (MSP) was performed for osteo- sarcoma tissues and their cell lines. MSP and RT-PCR for the RUNX3 gene were performed in the tumor-derived cell lines and the immortalized cell lines. The demethylating agent 5-aza-2' deoxycytidine was used in the SaOS-2 cell line to reverse the methylation status. Results: Hypermethylation of the RUNX3 gene was observed in 60% (24 of 40) of the osteosarcoma tissues, whereas other tumor suppressor genes showed very low methylation. Thirteen of 30 (43%) tumor-derived cell lines, and U-2OS and SaOS-2 showed hypermethylation of the RUNX3 gene on MSPCR. However, RUNX3 was expressed in the SaOS-2 cell line, as determined by RT-PCR, and the expression was augmented by treatment with 5-aza-2' deoxycytidine. Conclusion: Our study suggests that aberrant methylation is an important mechanism of RUNX3 down-regulation in osteosarcoma. This data may have potential significance in developing a potential therapeutic target for osteosarcoma.

Detection of Methylation in the CpG islands of the P16INK4A, RASSF 1A and Methyl-Guanine Methyl-Transferase (MGMT) gene promoters in Pancreatic Adenocarcinoma

Pancreatic cancer consists of an accumulation of genetic and epigenetic alterations. Recently, aberrant methylation of CpG islands of cancer-related genes has emerged as an important epigenetic mechanism of their transcriptional dysregulation during tumour development [1]. Therefore, new diagnostic methods, for early detection based on a better understanding of the molecular biology of pancreatic cancer, are required. We examined the methylation status of p16INK4A, RASSF 1A and methylguanine methyltransferase (MGMT) genes considered to be inactivated by promoter methylation in several tumours.The p16INK4A is an important G1/S cell cycle regulator gene [2]. RASSF 1A gene is involved in apoptotic signalling, microtubule stabilization and cell cycle progression [3]. The MGMT gene removes mutagenic and cytotoxic alkyl-adducts from the O6-position of guanine in DNA. Hypermethylation of the gene leads to the inactivation of DNA repair and to microsatellite instability [4].To date, little is known about the exact role of hypermethylation of these genes in pancreatic adenocarcinoma, as the molecular mechanisms underlying these neoplasms remain poorly understood.

CpG island methylation of TMS1/ASC and CASP8 genes in cervical cancer

BackgroundGene silencing associated with aberrant methylation of promoter region CpG islands is an acquired epigenetic alteration that serves as an alternative to genetic defects in the inactivation of tumor suppressor and other genes in human cancers.AimsThis study describes the methylation status of TMS1/ASC and CASP8 genes in cervical cancer. We also examined the prevalence of TMS1/ASC and CASP8 genes methylation in cervical cancer tissue and none - neo plastic samples in an effort to correlate with smoking habit and clinicopathological features.MethodTarget DNA was modified by sodium bisulfite, converting all unmethylated, but not methylated, cytosines to uracil, and subsequently amplified by Methylation Specific (MS) PCR with primers specific for methylated versus unmethylated DNA. The PCR product was detected by gel electrophoresis and combined with the clinical records of patients.ResultsThe methylation pattern of the TMS1/ASC and CASP8 genes in specimens of cervical cancer and adjacent normal tissues were detected [5/80 (6.2%), 3/80 (3.75%)-2/80 (2.5%), 1/80 (1.2%) respectively]. No statistical differences were seen in the extent of differentiation, invasion, pathological type and smoking habit between the methylated and unmethylated tissues (P > 0.05).ConclusionThe present study conclude that the frequency of TMS1/ASC and CASP8 genes methylation in cervical cancer are rare (< 6%), and have no any critical role in development of cervical cancer.

CpG island methylation patterns in chronic lymphocytic leukemia

Chronic lymphocytic leukemia (CLL) is the most common leukemia in Western countries. In CLL, a large number of genes affecting cancer-related pathways may be dysregulated by epigenetic silencing. We analysed by methylation-specific polymerase chain reaction the CpG island methylation status of 15 well-characterised cancer-related genes in 32 patients with CLL. Aberrant methylation in the sample of patients with CLL was shown for secreted frizzled-related protein 1 (68.8%), secreted frizzled-related protein 2 (65.6%), death-associated protein kinase 1 (50.0%), E-cadherin (21.9%), secreted frizzled-related protein 4 (15.6%), p15 (9.4%), p16 (6.3%), retinoic acid receptor β2 (3.1%), secreted frizzled-related protein 5 (3.1%) and tissue inhibitor of matrix metalloproteinases 3 (3.1%). For human Mut-L homolog 1, O6-methylguanine DNA methyltransferase, p73, suppressor of cytokine signalling 1 and tissue inhibitor of matrix metalloproteinases 2 no hypermethylation was detected. Hypermethylation of at least one gene was observed in 87.5% of the samples. Our results show that aberrant CpG island methylation affecting cancer-related pathways such as Wnt signalling, regulation of apoptosis, cell cycle control and tissue invasion is a common phenomenon in CLL. Epigenetic disturbances may be involved in the pathogenesis of CLL and thus may provide a molecular rationale for therapeutic approaches.

A Multifactorial Signature of DNA Sequence and Polycomb Binding Predicts Aberrant CpG Island Methylation

Aberrant CpG island methylation is associated with transcriptional silencing of regulatory genes in human cancer. Although most CpG islands remain unmethylated, a subset accrues aberrant methylation in cancer via unknown mechanisms. Previously, we showed that CpG islands differ in their intrinsic propensity towards hypermethylation. We developed a classifier (PatMAn) based on the frequencies of seven DNA sequence patterns that discriminated methylation-prone (MP) and methylation-resistant (MR) CpG islands. Here, we report on the genome-wide application and direct testing of PatMAn in cancer. Although trained on data from a cell culture model of de novo methylation involving the overexpression of DNMT1, PatMAn accurately predicted CpG islands at increased risk of hypermethylation in cancer cell lines and primary tumors. Analysis of CpG islands predicted to be MP revealed a strong association with embryonic targets of polycomb-repressive complex 2 (PRC2), indicating that PatMAn predicts not only aberrant methylation, but also PRC2 binding. A second classifier (SUPER-PatMAn) that integrates the seven PatMAn DNA patterns with SUZ12 enriched regions as a marker of PRC2 occupancy showed improved performance (prediction accuracy, 81-88%). In addition to many non-PRC2 targets, SUPER-PatMAn identified a subset of PRC2 targets that were more likely to be hypermethylated in cancer. Genome-wide, CpG islands predicted to be MP were enriched in genes known to undergo hypermethylation in cancer, genes functioning in transcriptional regulation, and components of developmental pathways. These findings show that hypermethylation of certain gene loci is controlled in part by an underlying susceptibility influenced by both local sequence context and trans-acting factors.