Methylation-specific Polymerase Chain Reaction Method Research Articles

Evaluation of the Effect of Delivery Mode on Methylation Changes in the Global DNA and the PTEN Gene

Objective: This study aimed to investigate the association between global DNA and PTEN gene methylation changes and the type of delivery. Material and Methods: The study included a total of 129 pregnant women at the >37th week of pregnancy who had a cesarean (CS) (n=62) or vaginal delivery (VD) (n=67) and their infant's cord blood (n=129). The 5-mC DNA ELISA method performed global DNA methylation analyses, while PTEN gene methylation change analyses were conducted using the methylation-specific polymerase chain reaction method. Results: The global DNA methylation changes in the women in the CS (Group 1) and VD (Group 2) groups and their infants were found to be CS 9.15±4.82, VD 10.6±5.09 (p=0.09); CS 11.3±6.78, and VD 11.7±5.69 (p=0.75), respectively. Based on age, when the global DNA methylation changes were examined in the pregnant women under and over 30, and their infants, the differences in both groups were statistically significant (p=0.05, p=0.015). The PTEN gene methylation rates of the pregnant women in Group 1 (22.5%) were higher than in Group 2 (13.4%). The PTEN gene methylation rates of the infants in Group 1 (17.7%) were higher than those in Group 2 (14.9%). Conclusion: In this study, a significant increase was determined in mothers and infants regarding their global DNA methylation based on age. Our study is also the first study showing gene-specific methylation changes in the PTEN gene. Our findings are believed to pioneer new studies and positively contribute to scientific research.

Validation of methylation-specific polymerase chain reaction method and evaluation of FMR1 gene pre-mutations in premature ovarian insufficiency

Background. Fragile X-associated premature ovarian insufficiency is clinically defined as a type of early ovarian failure with irregular menstrual cycles, increased follicle-stimulating hormone, premature menopause, and infertility. Genetically, the CGG trinucleotide repeat expansion in the 5'-untranslated region of the FMR1 gene is recognized as a causative factor. The aim of this study was to standardize molecular detection methods and estimate the number of repeats among patients with premature ovarian insufficiency. Methods. After obtaining a consent form and blood sampling, genomic DNA was extracted and treated with sodium bisulfite. The FMR1 gene is located on X chromosome and one allele is methylated by X-inactivation. As a result, the methylation-specific polymerase chain reaction (MS-PCR) was performed using two pairs of specific primers for methylated and non-methylated DNA yelding the products of 108+3n and 168+3n bp, respectively. Following clinical evaluations, 20 sporadic patients and two families with at least two patients were studied. Results. The mean level of follicle-stimulating hormone was 85.45±44.73UI/L in sporadic and 75.72±33.61UI/L in familial cases. Ultrasound examinations reported atrophic ovaries in sporadic and familial cases by 80% and 75%, respectively. The evaluation of the trinucleotide repeat expansions on agarose gels showed that two sporadic patients were carriers of FMR1 intermediate alleles (10%). No cases of pre-mutation or full mutation were observed in other sporadic or familial cases and the trinucleotide repeat expansions were estimated between 15 and 35. Conclusion. Due to the role of the FMR1 gene trinucleotide repeat expansion in women with premature ovarian insufficiency, a fast and cost-effective molecular detection method is of particular importance. This test will be beneficial not only in ovarian dysfunction, but also to identify pre-mutations that may expand in next generations leading to fragile X syndrome. Practical Implications. In young women, the detection of expanded CGG trinucleotide repeats in the 5'-untranslated region of the FMR1 gene along with genetic counseling will provide them to plan reproductive life.

Association of AGTR1 gene methylation and its genetic variant in Chinese farmer with hypertension: A case-control study.

The objective was to determine the potential associations of the angiotensin II receptor type 1 (AGTR1) gene polymorphism, methylation, and lipid metabolism in Chinese farmers with hypertension.A case-control study was conducted in Wuzhi county of Henan province in China in 2013 to 2014. A total of 1034 local residents (35–74 years, 386 hypertensive cases, and 648 normotensive subjects) were enrolled in this study. Triglyceride (TG), total cholesterol (TC), high-density lipoprotein, and low-density lipoprotein were measured using automatic chemistry analyzer. The AGTR1 gene promoter methylation level was measured using quantitative methylation-specific polymerase chain reaction method. The single nucleotide polymorphism rs275653 was genotyped with TaqMan probe assay at an applied biosystems platform.The gender, body mass index (BMI), TG, TC, and family history of hypertension in the hypertension group were significantly higher than those in control group (P < .05). No significant difference was observed in the distribution of AGTR1 rs275653 polymorphism in the hypertension and controls (P > .05). The AGTR1 gene methylation in subjects carrying different genotypes was not significantly observed (P > .05). The logistic regression analysis found the AGTR1 gene methylation level was negative correlation with hypertension in the present study (odds ratio, 0.946, 95% confidence interval, 0.896–0.999) through adjusting for age, gender, BMI, education, smoking, alcohol drinking, fruit and vegetable intake, pickles intake, and family history of hypertension.The association of AGTR1 gene hypomethylation and essential hypertension was observed in Chinese farmers; no significant difference was observed in the distribution of AGTR1 rs275653 polymorphism.

High Levels of Organochlorines Are Associated with Induction of ABL1 Promoter Methylation in Children with Acute Lymphoblastic Leukemia.

Exposure to organochlorines is associated with epigenetic changes, including methylation change in the promoter of tumor suppressor genes, thereby leading to cancer induction. The aim of this study was to investigate the relationship between organochlorine pesticides (OCPs) and ABL1 promoter methylation in child patients with acute lymphoblastic leukemia (ALL) and the control group. The methylation rate of the ABL1 promoter was evaluated using the methylation-specific polymerase chain reaction method, and the level of OCPs in patients with ALL and healthy children was measured using gas chromatography. ABL1 promoter hypermethylation was observed in 64% of ALL patients and 28.5% of children in the control group. The level of OCPs in children with methylated ABL1 promoters was significantly higher than that in children with nonmethylated ABL1 promoters (p < 0.05). Our findings suggest that OCPs, especially alpha-hexachlorocyclohexane, beta-hexachlorocyclohexane, gamma-hexachlorocyclohexane, 2,4 dichlorodiphenyldichloroethylene, and 4,4 dichlorodiphenyltrichloroethane may induce methylation at the ABL1 promoter level, thereby preventing the normal expression of the ABL1 gene. As a result, the reduced expression of ABL1 (a tumor suppressor) gene due to the hypermethylation of its promoter leads to the disruption of normal biological processes, thus making cells vulnerable to oncogenic factors.

The epigenetic role of breastfeeding in mammary differentiation.

Maternal milk consumption can cause changes in the mammary epithelium of the offspring that result in the expression of molecules involved in the induction of differentiation, reducing the risk of developing mammary cancer later in life. We previously showed that animals that maintained a higher intake of maternal milk had a lower incidence of mammary cancer. In the present study, we evaluated one of the possible mechanisms by which the consumption of maternal milk could modify the susceptibility to mammary carcinogenesis. We used Sprague Dawley rats reared in litters of 3 (L3), 8 (L8), or 12 (L12) pups per mother in order to generate a differential consumption of milk. Whole mounts of mammary glands were performed to analyze the changes in morphology. Using real-time polymerase chain reaction (PCR), we analyzed the expression of mammary Pinc, Tbx3, Stat6, and Gata3 genes. We use the real-time methylation-specific polymerase chain reaction method to assess the methylation status of Stat6 and Gata3 CpG sites. Our findings show an increase in the size of the epithelial tree and a smaller number of ducts called terminal end buds in L3 vs. L12. We observed an increased expression of mRNA of Stat6, Gata3, Tbx3, and a lower expression of Pinc in L3 with respect to L12. Stat6 and Gata3 are more methylated in the CpG islands of the promoter analyzed in L12 vs. L3. In conclusion, the increased consumption of maternal milk during the postnatal stage generates epigenetic and morphological changes associated with the differentiation of the mammary gland.

Promoter DNA Methylation Frequency and Clinicopathological Role of miR-129-2 Gene in Patients with Chronic Lymphocytic Leukemia.

ObjectivesChronic lymphocytic leukemia (CLL) is characterized by the accumulation of apparently mature B-type lymphocytes in the lymphohematopoietic organs. Methylation in promoters of tumor suppressor genes is one of the mechanisms that causes blood malignancy. In this study, we evaluated the promoter DNA methylation status of miR-129-2 tumor suppressor gene and its association with clinical and laboratory parameters of patients with CLL.MethodsWe studied the promoter DNA methylation frequency of the miR-129-2 gene in 50 patients with CLL and 50 healthy controls using methylation-specific polymerase chain reaction methods. Statistical analysis was performed using SPSS-18 software, and a p-value < 0.050 was considered statistically significant.ResultsThe frequency of promoter DNA methylation of the miR-129-2 gene was significantly higher in the CLL group compared with control group (38.0% vs. 0.0%, p < 0.001; χ2 = 23.457). The promoter DNA methylation frequency of miR-129-2 gene was not significantly different between the two sexes (p = 0.236). A significant but weak correlation was seen between the methylated state of the miR-129-2 gene and organomegaly (p = 0.019, r = 0.330) as well as hemoglobin levels (p = 0.020, r = -0.233). However, binary logistic regression analysis indicated organomegaly as the only clinical biomarker with a statistically significant association with the hypermethylated miR-129-2 gene state (p = 0.046).ConclusionsThe high frequency of promoter DNA methylation of the miR-129-2 gene in the CLL group compared to the control group, as well as its significant association with organomegaly, suggests the importance of this epigenetic biomarker in the pathogenesis and prognosis of CLL disease.

Investigating the expression and promoter methylation of RET gene in patients with medullary thyroid cancer with unmutated RET.

Thyroid cancer is one of the most common endocrine malignancies. Mutations in the rearranged during transfection (RET) gene, especially in exon 10, 11, and 16, as well as epigenetic modifications, constitute the major underlying molecular events leading to medullary thyroid cancer (MTC). There are few studies on the mutations and epigenetic changes of RET gene in Iranian patients with MTC. In the present study, we aimed to address this question and explore the clinical relevance of such genetic alternations in an Iranian population. Thirty-three patients with confirmed MTC who underwent thyroidectomy surgery in Imam Khomeini Hospital (Tehran, Iran) were enrolled. DNA extracted from cancerous tissues was amplified by polymerase chain reaction (PCR) and then was sequenced for identification of RET mutations. In patients with no identified mutations, the methylation status of RET promoter and its expression were further investigated using methylation-specific PCR and real-time PCR methods, respectively. In MTC patients with no RET mutations, the promoter of the proto-oncogene was hypomethylated. Furthermore, RET gene expression was elevated in patients who revealed no mutations in neither of exon 10, 11, or 16 of the RET gene. Hypomethylation of RET promoter may contribute to MTC pathogenesis. The methylation status of RET promoter could be a new potential prognostic, diagnostic and therapeutic marker in MTC.

Study of p16 promoter methylation in Egyptian colorectal cancer patients.

Many tumor-suppressor genes contain CpG islands in their promoter regions which raised the necessity of investigating the role of methylation in silencing these genes. We examined p16 methylation as a potential biomarker in the peripheral blood of colorectal cancer (CRC) patients. Using methylation-specific polymerase chain reaction method, the methylation status of p16 was investigated in the tumor tissue and blood of 65 CRC patients and blood samples from 70 healthy control individuals. Also, the relationship between p16 methylation level and the clinical-pathological findings in CRC was evaluated. The frequency of blood p16 methylation in CRC cases was significantly higher than in control (P = 0.0001). The sensitivity and specificity of p16 methylation in diagnosing CRC was 55.38% and 98.5%, respectively, with 77.7% diagnostic accuracy. There was significant association between p16 methylation and age, sex, Dukes staging, lymph node involvement, and carcinoembryonic antigen levels. Our study revealed that p16 promoter methylation could be considered as both potential diagnostic and prognostic biomarker of CRC.

Hypermethylation of MDFI promoter with NSCLC is specific for females, non-smokers and people younger than 65.

Non-small cell lung carcinoma (NSCLC) is a major subtype of lung cancer. Aberrant DNA methylation has been frequently observed in NSCLC. The aim of the present study was to investigate the role of MyoD family inhibitor (MDFI) methylation in NSCLC. Formalin-fixed paraffin-embedded tumor tissues and adjacent non-cancerous tissues were collected from a total of 111 patients with NSCLC. A methylation assay was performed using the quantitative methylation-specific polymerase chain reaction method. The percentage of methylated reference was used to represent the methylation level of the MDFI promoter. Data mining of a dataset from The Cancer Genome Atlas (TCGA) demonstrated that MDFI promoter methylation levels were significantly increased in 830 tumor tissues compared with 75 non-tumor tissues (P=0.012). However, the results on tissues obtained in the present study indicated that the MDFI promoter methylation levels in tumor tissues were not significantly different compared with those in the adjacent non-tumor tissues (P=0.159). Subsequent breakdown analysis identified that higher MDFI promoter methylation levels were significantly associated with NSCLC in females (P=0.031), but not in males (P=0.832). Age-based subgroup analysis demonstrated that higher MDFI promoter methylation levels were significantly associated with NSCLC in younger patients (≤65 years; P=0.003), but not in older patients (P=0.327). In addition, the association of MDFI methylation with NSCLC was significant in non-smokers (P=0.014), but not in smokers (P=0.832). Similar results also have been determined from subgroup analysis of the TCGA datasets. The Gene Expression Omnibus database indicated MDFI expression restoration in partial lung cancer cell lines (H1299 and Hotz) following demethylation treatment. However, it was identified that MDFI promoter hypermethylation was not significantly associated with prognosis of NSCLC (P>0.05). In conclusion, the present study indicated that the association of higher methylation of the MDFI promoter with NSCLC may be specific to females, non-smokers and people aged ≤65.

Methylation of p14ARF gene on oral squamous cell carcinoma patients with non-smoking history in Muwardi Hospital Surakarta, Central Java

Background: Oral squamous cell carcinoma (OSCC) is the sixth cancer disease in the world. Epigenetic alteration of tumour suppressor gene has been postulated as an early step of carcinogenesis. The methylation of p14ARF gene might be one type of epigenetic alteration contributing to the carcinogenesis of OSCC. Objective: The purpose of this study was to to examine the hypermethylation status of p14ARF gene. Methods: Fresh tissue sample was obtained from four patients diagnosed with OSCC. Examination with bisulfite modification and the hypermethylation status was analysed using methylation-specific polymerase chain reaction method. Findings: Methylation of p14ARF gene occurred in all of four samples of oral squamous cell carcinoma. The history of smoking actively or passively was denied by all patients. All patients were Javanese, and commonly lived in rural area with averagely less satisfactory oral hygiene. Conclusion: this study indicated that methylation in p14ARF gene play a role in oral carcinogenesis, particularly the squamous cell carcinoma. The lack of smoking history among the patients suggested that bad oral hygiene as one condition that might become a risk factor for the development of OSCC other than smoking.

Polyclonality in Sclerosing Angiomatoid Nodular Transformation of the Spleen.

Sclerosing angiomatoid nodular transformation (SANT) of the spleen is a morphologically distinctive lesion. Although the clinical course of SANT is benign, its reactive or neoplastic nature remains to be clarified. Furthermore, some investigators have suggested that SANT is related to IgG4 sclerosing lesion or inflammatory pseudotumor with stromal cells positive for Epstein-Barr virus (EBV). In this study, we assessed 22 cases of SANT derived from adult women. Clinical data and follow-up information were obtained by chart review. Immunohistochemical studies for IgG4, IgG, and CD21 stains and in situ hybridization to detect EBV-encoded small RNAs were performed. We also assessed genomic DNA extracted from paraffin-embedded tissue for human androgen-receptor α gene analysis using conventional and methylation-specific polymerase chain reaction methods. The median patient age was 41.5 years (range, 25 to 82 y). Most (77%) patients presented with a single mass that was detected incidentally (59%). The mean size of the lesions was 3.8 cm (range, 1.0 to 9.0 cm). Clinical symptoms correlated with multiple lesions (P=0.043) but not lesional size (P=0.637) or location in the spleen (hilum vs. periphery, P=0.696). None of the cases had evidence of IgG4-related disease or recurred after splenectomy. The mean number of IgG4 cells was 27.7 (range, 4 to 125), and the mean IgG4/IgG ratio was 16.4% (range, 1.6% to 55.7%) with only 2 cases being >40%. Cases with higher IgG4 cells did not correlate with inflammatory pseudotumor-like morphology. No lesions were positive for EBV-encoded small RNAs, and almost all cases with informative results (n=19) showed a polyclonal pattern. We conclude that SANT is a polyclonal, reactive lesion rather than a neoplasm.

Association of DNA methyltransferases expression with global and gene-specific DNA methylation in colorectal cancer cells.

There are conflicting reports regarding the association between DNA methyltransferases (DNMTs) expression and global or gene-specific DNA methylation in colorectal cancer (CRC) cells. To correlate DNMTs expression with DNA methylation, we quantified DNMT1, DNMT3A and DNMT3B mRNA levels in five CRC cell lines (HCT116, LS180, HT29/219, Caco2 and SW742) by real-time reverse-transcriptase polymerase chain reaction (PCR) assay. In addition, we examined the global 5-methyl cytosine levels and the methylation patterns of 12 CpG islands in these CRC cells by enzyme-linked immunosorbent assay and methylation-specific PCR methods, respectively. The average expression levels of three DNMTs in HCT116, Caco2, HT29/219 and SW742, relative to the expression level in LS180 (taken to be 1), were 90.1, 31.6, 2.66 and 1.86. Our data indicated that overall about 1.45%, 1.03%, 0.98%, 0.86% and 0.85% of the cytosines were methylated in the genome of HCT116, Caco2, HT29/219, SW742 and LS180 cells, respectively. The 5-mC percentages were positively correlated with the relative cellular DNMTs expression in five CRC cell lines as verified by Pearson correlation test. However, we found no positive correlation between mRNA expression of DNMTs and gene promoter hypermethylation in these cells. Our results suggest that cellular DNMT expression is positively correlated with global DNA methylation level but not with regional DNA hypermethylation at each locus.

CDKN2A (p14(ARF)/p16(INK4a)) and ATM promoter methylation in patients with impalpable breast lesions.

Early detection of breast cancer increases the chances of cure, but the reliable identification of impalpable lesions is still a challenge. In spite of the advances in breast cancer detection, the molecular basis of impalpable lesions and the corresponding circulating biomarkers are not well understood. Impalpable lesions, classified by radiologists according to the Breast Imaging Reporting and Data System in the categories 3 and 4, can be either benign or malignant (slow growing or aggressive). In this article, we report the DNA methylation pattern in CDKN2A (p14(ARF)/p16(INK4a)) and in ATM gene promoters from 62 impalpable lesions, 39 peripheral blood samples, and 39 saliva samples, assessed by methylation-specific polymerase chain reaction method. ATM showed the greatest percentage of methylation in DNA from lesions (benign and malignant), blood (even with p16(INK4a)), and saliva, followed by p16(INK4a) and p14(ARF). Among the malignant cases, ATM promoter was the most hypermethylated in lesion DNA and in blood and saliva DNAs, and p14(ARF), the least. The highest percentage of p16(INK4a) methylation was found in the blood. Finally, our data are relevant because they were obtained using impalpable breast lesions from patients who were carefully recruited in 2 public hospitals of Rio de Janeiro.

Monoclonality and cytogenetic abnormalities in hyaline vascular Castleman disease

Hyaline vascular Castleman disease is traditionally regarded as a reactive hyperplastic process. Occasional cases, however, have been reported with cytogenetic anomalies bringing this concept into question. In this study, we used conventional and methylation-specific polymerase chain reaction methods to assess the human androgen receptor α (HUMARA) gene in 29 female patients with hyaline vascular Castleman disease and compared the results with three cases of plasma cell Castleman disease and 20 cases of age-matched lymphoid hyperplasia. We also assessed for immunoglobulin gene and T-cell receptor gene rearrangements, and conventional cytogenetic analysis was performed in three cases of hyaline vascular Castleman disease. In cases with informative results, conventional and methylation-specific human androgen receptor α gene analyses yielded a monoclonal pattern in 10 of 19 (53%) and 17 of 23 (74%) cases of hyaline vascular Castleman disease, respectively. A monoclonal pattern was also detected in three cases of plasma cell Castleman disease but not in cases of lymphoid hyperplasia. The frequency of monoclonality was higher for lesions >5 cm in size (100%) and for the stromal-rich variant (91%). Cytogenetic abnormalities in stromal cells were revealed in two cases of hyaline vascular Castleman disease and no cases showed monoclonal immunoglobulin or T-cell receptor gene rearrangements. Follow-up data showed persistent disease in 4 of 23 (17%) patients. We conclude that hyaline vascular Castleman disease is often a monoclonal proliferation, most likely of lymph node stromal cells.

Development of a Quantitative Methylation-Specific Polymerase Chain Reaction Method for Monitoring Beta Cell Death in Type 1 Diabetes

DNA methylation is a mechanism by which cells control gene expression, and cell-specific genes often exhibit unique patterns of DNA methylation. We previously reported that the mouse insulin-2 gene (Ins2) promoter has three potential methylation (CpG) sites, all of which are unmethylated in insulin-producing cells but methylated in other tissues. In this study we examined Ins2 exon 2 and found a similar tissue-specific methylation pattern. These methylation patterns can differentiate between DNA from insulin-producing beta cells and other tissues. We hypothesized that damaged beta cells release their DNA into circulation at the onset of type 1 diabetes mellitus (T1DM) and sought to develop a quantitative methylation-specific polymerase chain reaction (qMSP) assay for circulating beta cell DNA to monitor the loss of beta cells. Methylation-specific primers were designed to interrogate two or more CpG in the same assay. The cloned mouse Ins2 gene was methylated in vitro and used for development of the qMSP assay. We found the qMSP method to be sensitive and specific to differentiate between insulin-producing cells and other tissues with a detection limit of 10 copies in the presence of non-specific genomic DNA background. We also compared different methods for data analysis and found that the Relative Expression Ratio method is the most robust method since it incorporates both a reference value to normalize day-to-day variability as well as PCR reaction efficiencies to normalize between the methylation-specific and bisulfite-specific components of the calculations. The assay was applied in the streptozotocin-treated diabetic mouse model and detected a significant increase in circulating beta cell DNA before the rise in blood glucose level. These results demonstrate that this qMSP assay can be used for monitoring circulating DNA from insulin-producing cells, which will provide the basis for development of assays to detect beta cell destruction in early T1DM.

Locked Nucleic Acids Can Enhance the Analytical Performance of Quantitative Methylation-Specific Polymerase Chain Reaction

Aberrant DNA methylation of tumor suppressor genes is a frequent epigenetic event that occurs early in tumor progression. Real-time quantitative methylation-specific polymerase chain reaction (QMSP) assays can provide accurate detection and quantitation of methylated alleles that may be potentially useful in diagnosis and risk assessment for cancer. Development of QMSP requires optimization to maximize analytical specificity and sensitivity for the detection of methylated alleles. However, in some cases challenges encountered in primer and probe design can make optimization difficult and limit assay performance. Locked nucleic acids (LNAs) demonstrate increased affinity and specificity for their cognate DNA sequences. In this proof-of-principle study, LNA residues were incorporated into primer and probe design to determine whether LNA-modified oligonucleotides could enhance the analytical performance of QMSP for IGSF4 promoter methylation in human cancer cell lines using either SYBR Green or fluorogenic probe detection methods. Use of LNA primers in QMSP with SYBR Green improved analytical specificity for methylated alleles and eliminated the formation of nonspecific products because of mispriming from unmethylated alleles. QMSP using LNA probe and primers showed an increased amplification efficiency and maximum fluorescent signal. QMSP with LNA oligonucleotides and either detection method could reliably detect five genome equivalents of methylated DNA in 1000- to 10,000-fold excess unmethylated DNA. Thus, LNA oligonucleotides can be used in QMSP optimization to enhance analytical performance.

Aberrant Methylation of Multiple Genes in Gastric Carcinomas

In this study, we examined aberrant methylation of the E-cadherin, estrogen receptor, RB1 , p16, p15, p14, and MGMT genes by the methylation-specific polymerase chain reaction method in 101 gastric carcinomas. Hypermethylation was detected in E-cadherin, estrogen receptor, RB1, p16, p14, p15, and MGMT at the rates of 27.7%, 44.6%, 44.6%, 30.7%, 19.2%, 7.7%, and 6.9%, respectively. A total of 82.2% cases had methylation in at least 1 of these genes, and 44.6% had methylation in 2 or more of these genes. Methylation of RB1 was associated with absence of lymph node metastasis. Methylation of estrogen receptor was associated with age and tumor location. Methylation of E-cadherin coincided with methylation of p16 or estrogen receptor. Moreover, loss of p16 protein was strongly associated with its gene methylation. This study indicates that aberrant methylation of multiple genes is involved in gastric carcinogenesis.

Stability of E‐cadherin methylation status in gastric mucosa associated with histology changes

We have previously shown reversal of E-cadherin methylation in gastric mucosa from patients with dyspepsia at week 6 after Helicobacter pylori-eradication therapy. But the long-term methylation status of these patients was unknown. To investigate the methylation status at E-cadherin at year 3 after H. pylori-eradication therapy. 35 patients (25 with and 10 without H. pylori eradicated) enrolled in our previous study were recruited into the present study (year 3 analysis). Methylation at E-cadherin was evaluated by methylation-specific polymerase chain reaction method. There was no difference in age and sex distribution in the two groups. Methylation at E-cadherin in patients with H. pylori eradicated at weeks 0, 6 and year 3 were 52%, 20% and 20%, respectively. Concordant methylation status at week 6 and year 3 was 92%. Methylation at E-cadherin in patients without H. pylori at weeks 0, 6 and year 3 were 50%, 60% and 60%, respectively. Concordant methylation status between week 6 and year 3 was 90%. Stability of E-cadherin methylation status was associated with histological changes. No association between E-cadherin methylation status and age was observed. The methylation pattern is stable for a long period, thus suggesting the effect of environment on methylation.

Aberrant maspin expression in human endometrial cancer

Maspin, a mammary serine protease inhibitor, was originally reported as a tumor suppressor gene in breast cancer. The purpose of the present study was to examine maspin expression and evaluate its clinicopathological significance in endometrial cancer. We examined maspin expression immunohistochemically in 41 cases with endometrioid adenocarcinoma. DNA methylation status at the maspin promoter region was determined by the methylation-specific polymerase chain reaction method. Aberrant maspin expression was observed in 27 (66%) of 41 endometrioid adenocarcinomas but not in normal endometrial glands. Maspin immunoreactivity of the tumor cells varied in incidence and density among tumors. Positive staining was correlated significantly with the presence of squamous differentiation (presence vs absence = 11/11 [100%] vs 16/30 [53%], P < 0.05), and nuclear subcellular localization of maspin protein was also significantly associated with squamous differentiation (nuclear positive vs nuclear negative = 6/11 [54%] vs 2/30 [6.7%], P < 0.05). An inverse correlation between their immunoreactivity and methylation status was observed (P < 0.01). Three of the four cell lines established from endometrioid adenocarcinomas overexpressed maspin mRNA and its protein product. In a maspin-negative cell line, maspin expression was induced by treatment with 5-aza-2'-deoxycytidine, a DNA demethylating agent. There was no significant correlation between maspin expression and any clinicopathlogical data. These findings suggest that maspin induced by DNA demethylation at the promoter region may contribute to squamous differentiation of tumor cells in endometrioid adenocarcinomas.

Quantitative analysis of promoter hypermethylation in multiple genes in osteosarcoma

Osteosarcoma is the most common solid malignant diseases of childhood, occurring in approximately 6 children per million annually; however, to the authors' knowledge to date, the cause of osteosarcoma has remained mostly unknown. Genetic alterations of genes that are specific for osteosarcoma have not been identified. Genetic alternations in the status of DNA methylation, known as epigenetic alterations, are the most common molecular alterations in human neoplasia. Aberrant methylation in the promoter region of tumor-related genes is associated closely with epigenetically mediated gene silencing, which is a common feature in human tumors. The authors analyzed CpG islands of 5 different gene loci for aberrant methylation profiles in 30 pairs of osteosarcoma and corresponding normal tissues by using the quantitative methylation-specific polymerase chain reaction method. The objectives of this study were to characterize the methylation changes in osteosarcoma more extensively and to identify epigenetic biomarkers that may be useful in the diagnosis and prevention of osteosarcoma. For the Ras effector homologue (RASSF1A), tissue inhibitor of metalloproteinase 3 (TIMP3), O-6-methylguanine DNA methyltransferase (MGMT), and death-associated protein kinase 1 (DAPK1) genes, significant differences were observed in the degree of hypermethylation between tumors and normal tissues (P < 0.01 and P < 0.001, respectively). Measurement of the cumulative multiple promoter hypermethylation revealed striking differences between tumor specimens and normal tissues (t = 7.31; P < .001). There also was a significant difference in the levels of DNA methylation between the metastatic and nonmetastatic high-grade osteosarcomas (t = 4.57; P < .01). In addition, the methylation levels were associated closely with gender (t = 6.44; P < .001). The results indicated that tumor tissues from patients with osteosarcoma had a significantly higher incidence of hypermethylation for several genes compared with corresponding normal tissues. The epigenetic changes observed in this study may have prognostic importance for patients with osteosarcoma.