• Title, Summary, Keyword: methylation-specific PCR

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Application of Multiplex Nested Methylated Specific PCR in Early Diagnosis of Epithelial Ovarian Cancer

  • Wang, Bi;Yu, Lei;Yang, Guo-Zhen;Luo, Xin;Huang, Lin
    • Asian Pacific Journal of Cancer Prevention
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    • v.16 no.7
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    • pp.3003-3007
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    • 2015
  • Objective: To explore the application of multiplex nested methylated specific polymerase chain reaction (PCR) in the early diagnosis of epithelial ovarian carcinoma (EOC). Materials and Methods: Serum and fresh tissue samples were collected from 114 EOC patients. RUNX3, TFPI2 and OPCML served as target genes. Methylation levels of tissues were assessed by multiplex nested methylated specific PCR, the results being compared with those for carcinoma antigen 125 (CA125). Results: The serum free deoxyribose nucleic acid (DNA) methylation spectrum of EOC patients was completely contained in the DNA spectrum of cancer tissues, providing an accurate reflection of tumor DNA methylation conditions. Serum levels of CA125 and free DNA methylation in the EOC group were evidently higher than those in benign lesion and control groups (p<0.05). Patients with early EOC had markedly lower serum CA125 than those with advanced EOC (p<0.05), but there was no significant difference in free DNA methylation (p>0.05). The sensitivity, specificity and positive predicative value (PPV) of multiplex nested methylated specific PCR were significantly higher for detection of all patients and those with early EOC than those for CA125 (p<0.05). In the detection of patients with advanced EOC, the PPV of CA125 detection was obviously lower than that of multiplex nested methylated specific PCR (p>0.05), but there was no significant difference in sensitivity (p>0.05). Conclusions: Serum free DNA methylation can be used as a biological marker for EOC and multiplex nested methylated specific PCR should be considered for early diagnosis since it can accurately determine tumor methylation conditions.

Hypermethylation of Suppressor of Cytokine Signaling 1 in Hepatocellular Carcinoma Patients

  • Saelee, Pensri;Chuensumran, Ubol;Wongkham, Sopit;Chariyalertsak, Sunanta;Tiwawech, Danai;Petmitr, Songsak
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.7
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    • pp.3489-3493
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    • 2012
  • Hepatocellular carcinoma (HCC), the most common primary hepatic tumor, is highly prevalent in the Asia-Pacific region, including Thailand. Many genetic and epigenetic alterations in HCC have been elucidated. The aim of this study was to determine whether aberrant methylation of the suppressor of cytokine signaling 1 gene (SOCS1) occurs in HCCs. Methylation specific-PCR assays were performed to identify the methylation status of SOCS1 in 29 tumors and their corresponding normal liver tissues. An abnormal methylation status was detected in 17 (59%), with a higher prevalence of aberrant SOCS1 methylation significantly correlating with HCC treated without chemotherapy (OR=0.04, 95%CI=0.01-0.31; P=0.001). This study suggests that epigenetic aberrant SOCS1 methylation may be a predictive marker for HCC patients.

Genetic Diagnosis of Beckwith Wiedemann Syndrome using Methylation Specific PCR-RFLP Method (Methylation Specific PCR-RFLP 방법을 이용한 Beckwith Wiedemann Syndrome의 진단)

  • Kim, Gu-Hwan;Lee, Jin-Joo;Choi, Seung-Hoon;Lee, Joo-Yeon;Lee, Beom-Hee;Yoo, Han-Wook
    • Journal of Genetic Medicine
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    • v.7 no.2
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    • pp.133-137
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    • 2010
  • Purpose: Beckwith-Wiedemann syndrome (BWS) is an overgrowth malformation syndrome caused by a methylation abnormality at chromosome 11p15, consisting of two imprinting centers, BWSIC1 (IGF2, H19) and BWSIC2 (LIT1, KvDMR). This study evaluated the applicability of a methylation-specific (MS) PCR RFLP method for the genetic diagnosis of BWS. Materials and Methods: A total of 12 patients were recruited based on clinical findings. Karyotyping was performed using peripheral blood leukocytes, and genomic DNA was treated with bisulfate and amplified using methylation-specific primers. RFLP was conducted with restriction enzymes in differentially methylated regions of LIT1, H19, and IGF2. Results: The 12 BWS patients had normal karyotypes. Abnormal methylation patterns in the BWSIC2 (LIT1) region were identified in seven patients (58.3%) using the MS-PCR RFLP method. Conclusions: The MS-PCR RFLP method is a simple, economical genetic test. It detected genetic abnormalities in 50-60% of BWS patients, suggesting that it can be used as a screening test. A more precise method is required, however, to enhance the detection rate of genetic abnormalities, especially in BWSIC1 region.

Intragenic DNA Methylation Concomitant with Repression of ATP4B and ATP4A Gene Expression in Gastric Cancer is a Potential Serum Biomarker

  • Raja, Uthandaraman Mahalinga;Gopal, Gopisetty;Rajkumar, Thangarajan
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.11
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    • pp.5563-5568
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    • 2012
  • Based on our previous report on gastric cancer which documented ATP4A and ATP4B mRNA down-regulation in gastric tumors relative to normal gastric tissues, we hypothesized that epigenetic mechanisms could be responsible. ATP4A and ATP4B mRNA expression in gastric cancer cell lines AGS, SNU638 and NUGC-3 was examined using reverse transcriptase PCR (RT-PCR). AGS cells were treated with TSA or 5'-AzaDC and methylation specific PCR (MSP) and bisulfite sequencing PCR (BSP) analysis were performed. MSP analysis was on DNA from paraffin embedded tissues sections and plasma. Expression analysis revealed downregulation of ATP4A and ATP4B genes in gastric cancer cell lines relative to normal gastric tissue, while treatment with 5'-AzaDC re-activated expression of both. Search for CpG islands in their putative promoter regions did not indicate CpG islands (CGI) but only further downstream in the bodies of the genes. Methylation specific PCR (MSP) in the exon1 of the ATP4B gene and exon7 in ATP4A indicated methylation in all the gastric cancer cell lines tested. MSP analysis in tumor tissue samples revealed methylation in the majority of tumor samples, 15/19, for ATP4B and 8/8 for ATP4A. There was concordance between ATP4B and ATP4A down-regulation and methylation status in the tumour samples tested. ATP4B methylation was detectable in cell free DNA from gastric cancer patient's plasma samples. Thus ATP4A and ATP4B down-regulation involves DNA methylation and methylated ATP4B DNA in plasma is a potential biomarker for gastric cancer.

Epithelial-Specific SHP1-P2 Methylation - a Novel Universal Tumor Marker for Detection of Colorectal Cancer Lymph Node Metastasis

  • Rattanatanyong, Prakasit;Keelawat, Somboon;Kitkumthorn, Nakarin;Mutirangura, Apiwat
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.8
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    • pp.4117-4123
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    • 2016
  • Background: Methylation of promoter 2 of the SHP1 gene is epithelial cell specific, with reported potential as a lymph node metastatic marker. Objective: To demonstrate SHP1-P2 methylation-specific quantitative PCR effectiveness in detecting colorectal cancer (CRC) DNA in lymph nodes. Materials and Methods: SHP1-P2 methylation levels were measured in lymph nodes of CRC patients and compared with pathological findings and patient prognosis. Results: Lymph nodes of CRC metastatic patients without microscopically detectable cancer cells had higher SHP1-P2 methylation levels than lymph nodes of controls (p<0.001). In addition, a higher SHP1-P2 methylation level was associated with a shorter duration until adverse disease events, metastasis, recurrence and death (r2 = 0.236 and p value = 0.048). Studying two cohorts of 74 CRC patients without microscopic lymph node metastases showed that only the cohort containing samples with high SHP1-P2 methylation levels had a significant hazard ratio of 3.8 (95%CI = 1.02 to 14.2). Conclusions: SHP1-P2 methylation PCR can detect CRC DNA in lymph nodes even if cancer cells are not visible under a microscope, confirming applicability as a potential universal lymph node metastatic marker.

A lifelong exposure to a Western-style diet, but not aging, alters global DNA methylation in mouse colon

  • Choi, Sang-Woon;Tammen, Stephanie A;Liu, Zhenhua;Friso, Simonetta
    • Nutrition Research and Practice
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    • v.9 no.4
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    • pp.358-363
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    • 2015
  • BACKGROUND/OBJECTIVES: Previous studies have indicated that when compared to young mice, old mice have lower global DNA methylation and higher p16 promoter methylation in colonic mucosa, which is a common finding in colon cancer. It is also known that a Western-style diet (WSD) high in fat and calories, and low in calcium, vitamin D, fiber, methionine and choline (based on the AIN 76A diet) is tumorigenic in colons of mice. Because DNA methylation is modifiable by diet, we investigate whether a WSD disrupts DNA methylation patterns, creating a tumorigenic environment. SUBJECTVIES/METHODS: We investigated the effects of a WSD and aging on global and p16 promoter DNA methylation in the colon. Two month old male C57BL/6 mice were fed either a WSD or a control diet (AIN76A) for 6, 12 or 17 months. Global DNA methylation, p16 promoter methylation and p16 expression were determined by LC/MS, methyl-specific PCR and real time RT-PCR, respectively. RESULTS: The WSD group demonstrated significantly decreased global DNA methylation compared with the control at 17 months (4.05 vs 4.31%, P = 0.019). While both diets did not change global DNA methylation over time, mice fed the WSD had lower global methylation relative to controls when comparing all animals (4.13 vs 4.30%, P = 0.0005). There was an increase in p16 promoter methylation from 6 to 17 months in both diet groups (P < 0.05) but no differences were observed between diet groups. Expression of p16 increased with age in both control and WSD groups. CONCLUSIONS: In this model a WSD reduces global DNA methylation, whereas aging itself has no affect. Although the epigenetic effect of aging was not strong enough to alter global DNA methylation, changes in promoter-specific methylation and gene expression occurred with aging regardless of diet, demonstrating the complexity of epigenetic patterns.

Methylation of the Mouse Dlx5 and Osx Gene Promoters Regulates Cell Type-specific Gene Expression

  • Lee, Ji Yun;Lee, Yu Mi;Kim, Mi Jin;Choi, Je Yong;Park, Eui Kyun;Kim, Shin Yoon;Lee, Sam Poong;Yang, Jae Sup;Kim, Dong Sun
    • Molecules and Cells
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    • v.22 no.2
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    • pp.182-188
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    • 2006
  • Dlx5 and Osx are master regulatory proteins essential for initiating the cascade leading to osteoblast differentiation in mammals, but the mechanism of osteoblast-specific expression is not fully understood. DNA methylation at CpG sequences is involved in tissue and cell type-specific gene expression. We investigated the methylation status of Dlx5 and Osx in osteogenic and nonosteogenic cell lines by methylationspecific PCR (MSP). The CpG dinucleotides of the Dlx5 and Osx promoter regions were unmethylated in osteogenic cell lines transcribing these genes but methylated in nonosteogenic cell lines. Treatment of C2C12 cells with 5-AzadC induced dose- and timedependent expression of Dlx5 and Osx mRNA by demethylating the corresponding promoters. Furthermore the mRNAs for the osteoblast markers ALP and OC, which were undetectable in untreated cells, gradually increased after 5-AzadC treatment. In addition, BMP-2 stimulation induced Dlx5 expression by hypomethylating its promoter. These findings suggest that DNA methylation plays an important role in cell type-specific expression of Dlx5 and Osx.

ROLE OF DCC(DELETED IN COLORECTAL CANCER) GENE IN ORAL SQUAMOUS CELL CARCINOMA (구강편평상피암종에서 DCC 유전자의 역할)

  • Ko, Seong-Kyu;Han, Se-Jin;Kim, Kyung-Wook
    • Journal of the Korean Association of Oral and Maxillofacial Surgeons
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    • v.34 no.5
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    • pp.518-524
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    • 2008
  • Chromosome 18q alteration plays a key role in colorectal tumorigenesis, and loss of heterozygosity at 18q is associated with a poor prognosis in colon cancer. DCC(Deleted in Colorectal Cancer) is a putative tumor- suppressor gene at 18q21 that encodes a transmembrane protein with structural similarity to neural cell adhesion molecule that is involved in both epithelial and neuronal cell differentiation. DCC is implicated in regulation of cell growth, survival and proliferation. Thus, tumor progression in squamous cell carcinoma, stomach cancer, colorectal cancer correlates with downregulation of DCC expression. The mechanism for DCC suppression is associated with hypermethylation of the DCC gene promoter region. Hence, the goal of this study is to identify the promoter methylation responsible for the down-regulation of DCC expression in oral squamous cell carcinoma. 12 of tissue specimens for the study are excised and gathered from 12 patients who are diagnosed as SCC in department of OMS, dental hospital, dankook university. To find expression of DCC in each tissue samples, immunohistochemical staining, RT-PCR gene analysis and methylation specific PCR are processed. The results are as follows. 1. In the DCC gene RT-PCR analysis, 5(41.6%) of 12 specimens of oral squamous cell carcinoma did not expressed DCC gene. 2. In the promoter methylation specific PCR analysis, 5(41.6%) of 12 specimens showed promoter methylation of DCC gene. 3. In the immunohistochemical staining of poor differentiated and invasive oral squamous cell carcinoma, loss of DCC expression was observed. These findings suggest that methylation of the DCC gene may play a role in loss of gene expression in invasive oral squamous cell carcinoma.

Clinicopathological Significance of BRCA1 Promoter Hypermethylation in Thai Breast Cancer Patients

  • Saelee, Pensri;Chaiwerawattana, Arkom;Ogawa, Kumiko;Cho, Young-Man;Tiwawech, Danai;Suktangman, Vimol
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.24
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    • pp.10585-10589
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    • 2015
  • Breast cancer susceptibility gene 1 (BRCA1), mapped on chromosome 17q21, is implicated in the mechanisms of cellular DNA repair. Inactivation of this gene is involved in the development of many human cancers, including breast cancer. This study aimed to investigate the prognostic value of BRCA1 promoter hypermethylation and expression in breast cancer cases. Sixty-one breast cancers were examined for BRCA1 hypermethylation by methylation-specific polymerase chain reaction (PCR), and 45 paired normal breast tissues were analyzed for altered BRCA1 mRNA levels by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR). Aberrant methylation status in BRCA1 was detected in 15 of 61 cases (24.6%), while reduced expression was found in 7 of 45 (15.6%). BRCA1 hypermethylation was statistically associated with tumor grade III (p=0.04), a high frequency of stage IIB (p=0.02), and triple-negative phenotype (OR= 3.64, 95%CI =1.1-12.3, p=0.03). Our findings indicated that BRCA1 promoter hypermethylation is a useful prognostic marker for breast cancer.

Promoter Methylation and Relative mRNA Expression of the p16 Gene in Cervical Cancer in North Indians

  • Gupta, Amita;Ahmad, Mohammad Kaleem;Mahndi, Abbas Ali;Singh, Renu;Pradeep, Yashodhara
    • Asian Pacific Journal of Cancer Prevention
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    • v.17 no.8
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    • pp.4149-4154
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    • 2016
  • Background: Cervical carcinoma is one of the main causes of mortality in women worldwide as well as in India. It occurs as a result of various molecular events that develop from the combined influences of an individual's genetic predisposition and external agents such as smoking and menstrual hygiene, for example. However, infection with human papillomavirus (HPV) is the established major risk factor. The aim of the current study was to investigate p16 CpG island methylation and establish any correlation with mRNA expression in north Indian population. Materials and Methods: We analyzed 196 woman volunteer out of which 98 were cases and 98 healthy controls. For the analysis of methylation pattern, DNA extracted from blood samples was modified with a bisulfate kit and used as template for methylation specific PCR (MSP). Quantitative real-time PCR (QRT-PCR) was performed to check mRNA expression. Results: Correlation between methylation status of p16 gene and poor menstrual hygiene was significant (p=0.006), high parity cases showed methylation of p16 gene (p=0.031) with increased risk up to 1.86 times for cervical cancer and smoking was a strong risk factor associated with cervical cancer. We analyzed methylation pattern and found 60.3% methylation in cases with low mRNA expression level (0.014) as compare to controls (1.24). It was also observed that promoter methylation of p16 gene was significantly greater in FIGO stage III. Conclusions: We conclude that p16 methylation plays an important role in cervical cancer in the north Indian population and its methylation decreases mRNA expression. It can be used as an important and consistent blood biomarker in cervical cancer patients.