Methylation-specific High Resolution Melting Research Articles

TMEM25 is a candidate biomarker methylated and down-regulated in colorectal cancer.

The identification of novel genes involved in colorectal cancerogenesis is of high clinical relevance for early diagnosis, applying new therapeutic strategies and monitoring disease recurrence, in order to reduce disease incidence and mortality. Gene silencing through CpG island hypermethylation is a major epigenetic mechanism involved in cancer development. In our study, we aimed to identify and validate novel genes with a tumour specific DNA methylation profile in colorectal cancer. We performed a whole-genome methylation scan and identified several possible candidate genes that are hypermethylated in tumour in comparison to healthy colon mucosa. Using methylation-specific high-resolution melting analysis in a set consisting of 133 colorectal cancer samples, we were able to confirm an altered CpG site in TMEM25 in 69.2% (92/133) tumours analysed. Furthermore, the expression of TMEM25 was found to be significantly lower in tumour tissue. An inverse correlation between hypermethylation of TMEM25 and TMEM25 down-regulated expression was observed.Our results suggest that epigenetic down-regulation of TMEM25 is cancer-related; we thus suggest that TMEM25 hypermethylation might play a significant role in altering expression of this gene in colorectal cancer.

HOXA4Gene Promoter Hypermethylation as an Epigenetic Mechanism Mediating Resistance to Imatinib Mesylate in Chronic Myeloid Leukemia Patients

Development of resistance to imatinib mesylate (IM) in chronic myeloid leukemia (CML) patients has emerged as a significant clinical problem. The observation that increased epigenetic silencing of potential tumor suppressor genes correlates with disease progression in some CML patients treated with IM suggests a relationship between epigenetic silencing and resistance development. We hypothesize that promoter hypermethylation of HOXA4 could be an epigenetic mechanism mediating IM resistance in CML patients. Thus a study was undertaken to investigate the promoter hypermethylation status of HOXA4 in CML patients on IM treatment and to determine its role in mediating resistance to IM. Genomic DNA was extracted from peripheral blood samples of 95 CML patients (38 good responders and 57 resistant) and 12 normal controls. All samples were bisulfite treated and analysed by methylation-specific high-resolution melt analysis. Compared to the good responders, the HOXA4 hypermethylation level was significantly higher (P = 0.002) in IM-resistant CML patients. On comparing the risk, HOXA4 hypermethylation was associated with a higher risk for IM resistance (OR 4.658; 95% CI, 1.673–12.971; P = 0.003). Thus, it is reasonable to suggest that promoter hypermethylation of HOXA4 gene could be an epigenetic mechanism mediating IM resistance in CML patients.

Aberrant methylation of the M-type phospholipase A2 receptor gene in leukemic cells

BackgroundThe M-type phospholipase A2 receptor (PLA2R1) plays a crucial role in several signaling pathways and may act as tumor-suppressor. This study examined the expression and methylation of the PLA2R1 gene in Jurkat and U937 leukemic cell lines and its methylation in patients with myelodysplastic syndrome (MDS) or acute leukemia.MethodsSites of methylation of the PLA2R1 locus were identified by sequencing bisulfite-modified DNA fragments. Methylation specific-high resolution melting (MS-HRM) analysis was then carried out to quantify PLA2R1 methylation at 5`-CpG sites identified with differences in methylation between healthy control subjects and leukemic patients using sequencing of bisulfite-modified genomic DNA.ResultsExpression of PLA2R1 was found to be completely down-regulated in Jurkat and U937 cells, accompanied by complete methylation of PLA2R1 promoter and down-stream regions; PLA2R1 was re-expressed after exposure of cells to 5-aza-2´-deoxycytidine. MS-HRM analysis of the PLA2R1 locus in patients with different types of leukemia indicated an average methylation of 28.9% ± 17.8%, compared to less than 9% in control subjects. In MDS patients the extent of PLA2R1 methylation significantly increased with disease risk. Furthermore, measurements of PLA2R1 methylation appeared useful for predicting responsiveness to the methyltransferase inhibitor, azacitidine, as a pre-emptive treatment to avoid hematological relapse in patients with high-risk MDS or acute myeloid leukemia.ConclusionsThe study shows for the first time that PLA2R1 gene sequences are a target of hypermethylation in leukemia, which may have pathophysiological relevance for disease evolution in MDS and leukemogenesis.

Abstract 4538: Semiquantitative detection of aberrant methylation as a tumor biomarker in the serum and plasma of patients with gastric cancer

Abstract Background: Epigenetic silencing of tumor-related genes, due to CpG island methylation, is considered to be an important mechanism for the development of many tumors, including gastric cancinoma (GC). DNA methylation of multiple CpG sites in promoter regions of several tumor related genes, such as hMLH1, p14, COX2, and APC has been analyzed in GC so for. Circulating tumor DNA in serum/plasma has been demonstrated to reflect the biological characteristics of tumors. Recently, the presence of gene promoter methylation in serum/plasma DNA has also been demonstrated in patients with cancers of lung, head and neck, liver, and breast. So, in the present study, we attempted to determine the feasibility and the clinical correlations of detecting tumor-associated aberrant methylation in the serum/plasma of patients with gastric cancer. Materials and Methods: We examined promoter methylation of 6 genes using methylation-specific PCR (MSP) and methylation-sensitive high-resolution melting (MS-HRM) in paired serum, plasma and tumor samples of 50 gastric cancer patients. The tumor and the paired serum/plasma were investigated for aberrant methylation in BLU, DAPK1, GADD45G, MGMT, p15 and p16. The sensitivity of the HRM analysis was tested by using dilutions of fully methylated DNA into unmethylated DNA. Results: MSP was used to assess gene methylation in tumor samples. Promoter methylation in BLU, DAPK1, GADD45G, MGMT, p15, and p16 were detected in 47%, 37%, 59%, 32%, 14%, and 43% of tumor tissues by MSP. MS-HRM was used to assess gene methylation in serum/plasma samples concurrently. In the serum/plasma of gastric cancer patients, BLU, DAPK1, GADD45G, MGMT, p15, and p16 were methylated at frequencies of 26%, 21%, 23%, 11%, 9%, and 17%, respectively. Nineteen (38%) gastric tumor samples displayed concurrent methylation in three or more tumor genes. Aberrant methylation in one or more genes was found in 74% (37/50) serum samples and 70% (35/50) plasma samples. However, there was not a significant relationship of gene methylation between gastric tumor tissues and serum/plasma samples.Conclusion: These results suggest that aberrant promoter methylation in serum/plasma can be detected in a substantial proportion of gastric cancer patients. Detection of DNA methylation in serum/plasma may be a biomarker for early detection of gastric cancer. MS-HRM is powerful technique for the analysis of promoter methylation. Application of HRM analysis to large amount of clinical samples proves to be a fast and high-throughput way to investigate the epigenetic status of genes. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4538. doi:1538-7445.AM2012-4538

Combined RASSF1A and RASSF2A Promoter Methylation Analysis as Diagnostic Biomarker for Bladder Cancer

Promoter hypermethylation, a widely studied epigenetic event known to influence gene expression levels, has been proposed as a potential biomarker in multiple types of cancer. Clinical diagnostic biomarkers are needed for reliable prediction of bladder cancer recurrence. In this paper, DNA promoter methylation of five C-terminal Ras-association family members (RASSF1A, RASSF2A, RASSF4, RASSF5, and RASSF6) was studied in 64 formalin-fixed paraffin-embedded (FFPE) bladder cancer and normal adjacent tissues using methylation-specific high-resolution melting (MS-HRM) analysis. Results showed that 73% (30/41) of transitional cell carcinoma, 100% (3/3) of squamous cell carcinoma, and 100% (4/4) of small cell carcinoma demonstrated promoter methylation of the RASSF1A or RASSF2A gene, but only 6% (1/16) of normal tissues had promoter methylation of RASSF genes. Testing positive for hypermethylation of RASSF1A or RASSF2A promoter provided 77% sensitivity and 94% specificity for identification of cancer tissues with an area under the curve of 0.854, suggesting that promoter methylation analysis of RASSF1A and RASSF2A genes has potential for use as a recurrence biomarker for bladder cancer patients.

Regulation of thrombomodulin expression in prostate cancer cells

In carcinomas the expression of thrombomodulin (TM) is inversely correlated with tumour progression and metastasis. In the present study a decreased TM expression in human prostate cancer cell lines, LNCaP, DU-145, and PC-3, in relation to normal prostate epithelial cells (PrEC) is shown. Sequencing and methylation-specific high resolution melting (MS-HRM) analyses of bisulphite-modified genomic DNA indicates a high degree of methylation in DU-145 cells and lesser degrees in PC-3 and LNCaP cells, whereas in PrEC the TM promoter is unmethylated. The expression of TM is negatively regulated by NF-κB- and GSK3-β-dependent signalling pathways and positively regulated by retinoic acid and transcription factor Sp1 in PrEC, LNCaP and PC-3 cells, but not in DU-145 cells. However, exposure of DU-145 cells to the demethylating agent, 5-aza-2′deoxycytidine, restores the TM expression and its control by retinoic acid, NF-κB- and GSK3-β-dependent signalling. In conclusion, the study establishes that in prostate cancer cell lines relative to PrEC the TM is down-regulated and that the TM promoter is hypermethylated, which seems to be responsible for the down-regulation and failed regulation of TM expression in DU-145 cells.

Methylation-specific high-resolution melting analysis (MS-HRM)-based DNA promoter profiling in paired FFPE bladder cancer samples.

315 Background: DNA methylation and histone modification are widely studied epigenetic events that can decrease gene expression levels. Promoter hypermethylation has been proposed as a potential diagnostic or prognostic biomarker in various cancers. We studied DNA promoter methylation of 5 cancer-associated genes (MRE11, APX1, ERCC1, RASSF1A and RASSF2A ) in paired FFPE bladder cancer tissues and normal adjacent tissue. The MRE11/Rad50/NBS1 complex serves as a single-strand DNA nuclease which participates in the repair of DNA double-strand breaks and replication errors. APX1 plays a key role in regulating H2O2 levels and H2O2 signaling. DNA repair machinery, ERCC1 protein levels in tumor tissue have been shown to predict response to platinum-based chemotherapy. RASSF1 is thought to be a tumor suppressor gene, while the function of RASSF2 is less well understood. Methods: 16 bladder cancer cases with available paraffin-embedded tumor and matched normal adjacent tissue specimens (32 tissue samples) were analyzed. DNA was extracted by Ambion RecoverAll Total Nucleic Acid Isolation kit. FFPE DNA bisulfite modification was performed using Zymo EZ DNA Methylation Kit. Methylation Specific-High Resolution Melting (MS-HRM) analysis was used to assess methylation status. MS-HRM monitors the melting behavior of PCR amplicons by using a DNA intercalating fluorescent dye. Results: MRE11 and APX1 promoters were not methylated in either cancer or normal adjacent samples. The ERCC1 gene was heavily methylated in 94% (30/32) of all cancer and wild type samples. RASSF1A and RASSF2A promoter methylation was significantly different between cancer and normal adjacent tissue. 50% (8/16) RASSF1A and 25% (4/16) RASSF2A had promoter methylation in cancer tissues, while only 6% (1/16) RASSF1A and 0% (0/16) RASSF2A had promoter methylation in normal adjacent tissues. 69% (11/16) of bladder cancer tissues were positive for RASSF1A or RASSF2A promotor methylation while only 1/16 normal adjacent tissue samples was positive for either promotor methylation. Conclusions: The results show that cancer and non-cancer tissue have different RASSF1A and RASSF2A promoter methylation patterns.

Abstract A159: Epigenetic silencing of the M-type phospholipase A2 receptor gene in leukemic cells.

Abstract Background: The M-type phospholipase A2 receptor (PLA2R) plays a crucial role in a number of different signaling pathways and may act as tumor-suppressor. In the current study the expression and methylation of the PLA2R gene in the myeloid U937 cell line and blood leukocytes of patients with leukemia were analyzed. Methods. Expression of PLA2R in U937 cells was studied using RT-quantitative PCR. To determine methylation levels of the PLA2R locus, bisulfite-modified DNA fragments were sequenced. Identification of different 5′-CpG methylation sites in normal and leukemic patients was followed by methylation specific-high resolution melting (MS-HRM) analysis to quantify PLA2R methylations. Results: Our data establish that expression of PLA2R is completely down-regulated in U937 cells. Simultaneously, a 100% methylation of PLA2R promoter and down-stream regions was found in this cell line; after exposure of the cells to 5-aza-2 -deoxycytidine, PLA2R was re-expressed. MS-HRM analyzes in 34 patients with different types of leukemia indicated an average PLA2R methylation of 30%±18%, whereas in 52 normal subjects methylation levels were below 10%. In a preliminary study of high-risk myelodysplastic syndrome patients (MDS), three patients had increased PLA2R methylations. In the course of treatment with azacitidine (Vidaza) as methyltransferase inhibitor, two of these patients were responders in contrast to one patient who was a non-responder with increased methylation levels in blood leukocytes during treatment. Another patient with minimal residual disease after treatment of AML underwent preemptive treatment with azacitidine to avoid hematological relapse (HR). After two azacitidine cycles a minor cell fraction with 100% methylated PLA2R was completely diminished. However, three weeks later methylation of the PLA2R promoter increased to 50%, with 9% blasts detectable in blood samples. After further azacitidine treatment cycle, blasts diminished in blood samples but the methylation of PLA2R in blood leukocytes remained at 35%. During the following seven weeks with no further azacitidine treatment blasts increased up to 44% suggesting that the treatment with azacitidine was effective but not efficient enough to prevent a HR in this patient. Conclusions: The study shows for the first time that the PLA2R promoter and down-stream regions in leukemic cells are hypermethylated and that the determination of PLA2R methylation by MS-HRM may be useful as a biomarker in the diagnosis and therapeutic treatment of high-risk MDS and AML patients. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2011 Nov 12-16; San Francisco, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2011;10(11 Suppl):Abstract nr A159.

O6-methylguanine-DNA-methyltransferase promoter methylation assessment by microdissection-assisted methylation-specific PCR and high resolution melting analysis in patients with glioblastomas

We have determined O(6)-methylguanine-DNA-methyltransferase (MGMT) promoter methylation status by methylation-specific polymerase chain reaction (MSP) in 22 paraffin-embedded specimens of glioblastoma multiforme. A MGMT methylation-specific high resolution melting (HRM) assay was performed to compare the methylation levels of the tumorous and non-tumorous portions of each sample, which were selectively collected using a microdissection technique. MGMT methylation was detected in 10 patients using MSP, while 8 patients had both methylated and unmethylated MGMT promoters. HRM assays showed that there was no difference in the level of methylation between tumorous and non-tumorous portions of each sample. In patients with MSP-positive tumors, the overall survival (median, 22 months) was longer as compared to those with MSP-negative tumors (median, 14 months). A correlation between the methylation status of the MGMT promoter and MGMT protein expression was observed in 12 samples. This study demonstrates that MGMT methylation is not restricted to glioblastoma cells. Additionally, methylation-specific HRM is a feasible approach that can be readily applied to the methylation analysis of MGMT. A further study will be needed to determine the dynamic change of MGMT methylation in the tumor environment.

Increased expressions of DNA methyltransferases contribute to CD70 promoter hypomethylation and over expression of CD70 in ITP

CD70 (TNFSF7), as a methylation susceptive immune gene, was hypomethylated in some autoimmune diseases. To investigate the status of CD70 methylation and the expressions of genes that regulated methylation in immune thrombocytopenia (ITP) patients, the expressions of CD70 mRNA and protein in CD4 + T cells from ITP and controls were measured respectively by real-time PCR and flow cytometry. Methylation specific high resolution melting (MS-HRM) technology was applied to detect CD70 promoter methylation indices. Transcription levels of DNA methyltransferases (DNMTs), methylated CpG binding protein 2 (MBD2) were measured. The results showed that CD70, DNMTs and MBD2 was over expressed and methylation indices of CD70 promoter in CD4 + T cells from ITP patients were lower than that from healthy controls. The transcription levels of CD70 showed significantly inverse correlation with methylation indices in ITP patients but significantly positive correlation with that of DNMTs. We concluded that DNMTs functioned as demethylases as MBD2, while increased DNMTs and MBD2 may cause demethylation and over expression of CD70 in CD4 + T cells, potentially contributing to the pathogenesis of ITP.

Examination of AKAP12 promoter methylation in skin cancer using methylation-sensitive high-resolution melting analysis

A kinase anchor protein 12 (AKAP12/gravin) belongs to a family of scaffold proteins and organizes protein kinase (PK)A and PKC. DNA hypermethylation in the AKAP12 promoter region has been reported in a variety of human cancers with the exception of skin cancer. Methylation-specific high-resolution melting (MS-HRM) analysis is a novel tool for analysis of promoter methylation. To use MS-HRM analysis to detect the methylation levels of the AKAP12 gene in skin samples. In total, 195 samples, including basal cell carcinoma, squamous cell carcinoma and actinic keratosis were examined. MS-HRM analysis was used to detect methylation levels of the AKAP12 gene in these samples. MS-HRM analysis successfully detected the methylation of AKAP12 in skin samples. The frequencies of AKAP12 methylation in all three types of skin abnormalities were significantly higher than in normal tissues. Application of MS-HRM analysis proved to be a fast and high-throughput method to investigate the epigenetic status of AKAP12. Methylation of AKAP12 can be detected in different skin abnormalities.

No evidence for DNA methylation of von Hippel-Lindau ubiquitin ligase complex genes in breast cancer

pVHL is the central component of an ubiquitin ligase complex that targets hypoxia-inducible factor 1α (HIF-1α) for proteasomal degradation. This complex includes four other genes, Cullin 2 (CUL2), elongin C (TCEB1), elongin B (TCEB2) and ring-box 1 (RBX1). VHL has previously been reported to be methylated in sporadic renal cell carcinoma. Since HIF-1α is frequently expressed in breast carcinomas, we evaluated DNA methylation as a possible mechanism of silencing one or more of the VHL complex genes. Methylation-specific high resolution melting (MS-HRM) was used to screen the proximal promoter CpG islands for methylation of the VHL ubiquitin ligase complex genes. We were unable to identify methylation of any of the five genes in 84 breast carcinoma samples or in a range of cancer cell lines including 13 breast cancer cell lines of various subtypes. We were able, however, to identify VHL methylation in control renal cell carcinoma samples. Epigenetic silencing by promoter DNA methylation for VHL and the complex genes, CUL2, elongin C (TCEB1), elongin B (TCEB2) and RBX1, is unlikely to play a role in HIF-1α upregulation in breast carcinomas.

Rapid determination of AKAP12 promoter methylation levels in peripheral blood using methylation-sensitive high resolution melting (MS-HRM) analysis: Application in colorectal cancer

Background Colorectal cancer is the third most common form of cancer and hypermethylation has been shown to increase the risk of developing this disease. DNA hypermethylation in the A kinase anchor protein 12 ( AKAP12/Gravin) promoter region and the accompanied underexpression of it has been noted in a variety of human cancers. Methods We applied methylation-specific high resolution melting (MS-HRM) technology to detect quantitatively A kinase anchor protein 12 ( AKAP12/Gravin) methylation in peripheral blood from 100 colorectal cancer patients and 50 healthy volunteers and in 3 colorectal cancer cell lines. Results In this study 48 of the 100 colorectal cancer samples (48%) were found to be methylated at the AKAP12 promoter region. AKAP12 methylation was significantly higher in the colorectal cancer samples with differentiation ( p = 0.03). We also compared the results generated by MS-HRM with a traditional methylation-specific PCR (MSP) assay. We found that intra-assay variability ranged from 6.14 to 9.90% and inter-assay variability ranged from 14.5 to 17.2%. The AKAP12 MS-HRM assay was able to reproducibly detect 1% methylated DNA, whereas the MSP method was unable to detect less than 5% methylation. Conclusions We demonstrate the utility of quantitative AKAP12 MS-HRM analysis of promoter methylation in peripheral blood samples. AKAP12 MS-HRM quantitative methods with excellent detection capabilities have many promising applications in the research and diagnosis of colorectal cancer.