A Pyrosequencing Assay for the Quantitative Methylation Analysis of<i>GALR1</i>in Endometrial Samples: Preliminary Results

Kottaridi, Christine; Koureas, Nikolaos; Margari, Niki; Terzakis, E; Bilirakis, Evripidis; Παππάς, Απόστολος; Chrelias, Charalampos; Spathis, Aris; Aga, Evangelia; Pouliakis, Abraham; Panayiotides, Ioannis G.; Karakitsos, Petros

doi:10.1155/2015/756359

Cited by 4 publications

(3 citation statements)

References 26 publications

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“…Previous studies have used the t-test or ANOVA 39 – 41 or the non-parametric Kruskal-Wallis test 42 – 44 to evaluate the differences of DNA methylation levels in single CpG site or the average of several sites among groups. However, the DNA methylation levels among CpG sites within a gene may be correlated 28 . Our present study also revealed that there were significant correlations among the methylation percentages of 3 CpG sites and the average of 3 CpG sites (p < 0.0001) (Table 3 ).…”

Section: Discussionmentioning

confidence: 99%

“…However, no study has used pyrosequencing to quantify DNA methylation levels of the DLGAP2 gene; in addition, no study has examined the methylation of DLGAP2 gene in TD. Furthermore, the DNA methylation levels using pyrosequencing among CpG sites within a gene may be correlated 28 . Mixed models (also known as multilevel models or hierarchical models) including both fixed effects and random effects have been developed to deal with correlated data 29 – 33 .…”

Section: Introductionmentioning

confidence: 99%

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Quantitative DNA Methylation Analysis of DLGAP2 Gene using Pyrosequencing in Schizophrenia with Tardive Dyskinesia: A Linear Mixed Model Approach

Wang

Zhang

et al. 2018

Sci Rep

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Tardive dyskinesia (TD) is a side effect of antipsychotic medications used to treat schizophrenia (SCZ) and other mental health disorders. No study has previously used pyrosequencing to quantify DNA methylation levels of the DLGAP2 gene; while the quantitative methylation levels among CpG sites within a gene may be correlated. To deal with the correlated measures among three CpG sites within the DLGAP2 gene, this study analyzed DNA methylation levels of the DLGAP2 gene using a linear mixed model (LMM) in a Chinese sample consisting of 35 SCZ patients with TD, 35 SCZ without TD (NTD) and 34 healthy controls (HCs) collected in Beijing, China. The initial analysis using the non-parametric Kruskal-Wallis test revealed that three groups (TD, NTD and HC) had significant differences in DNA methylation level for CpG site 2 (p = 0.0119). Furthermore, the average methylation levels among the three CpG sites showed strong correlations (all p values < 0.0001). In addition, using the LMM, three groups had significant differences in methylation level (p = 0.0027); while TD, NTD and TD + NTD groups showed higher average methylation levels than the HC group (p = 0.0024, 0.0151, and 0.0007, respectively). In conclusion, the LMM can accommodate a covariance structure. The findings of this study provide first evidence of DNA methylation levels in DLGAP2 associated with SCZ with TD in Chinese population. However, TD just showed borderline significant differences to NTD in this study.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Quantitative DNA Methylation Analysis of DLGAP2 Gene using Pyrosequencing in Schizophrenia with Tardive Dyskinesia: A Linear Mixed Model Approach

Wang

Zhang

et al. 2018

Sci Rep

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“…For this purpose, they combined a high-throughput procedure with a non-invasive collection technique for early diagnosis of endometrial cancer [ 35 , 36 ]. The study by Kottaridi et al has argued that pyrosequencing technology plays an important role as an indicator of malignant tumors [ 37 ]. They analyzed the mean methylation of thirteen CpG sites in the GALR1 promoter in malignant and normal endometrial specimens.…”

Section: Pyrosequencingmentioning

confidence: 99%

The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers

Jeddi,

Faghfuri,

Mehranfar

et al. 2024

Cancer Cell Int

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DNA methylation is an important molecular modification that plays a key role in the expression of cancer genes. Evaluation of epigenetic changes, hypomethylation and hypermethylation, in specific genes are applied for cancer diagnosis. Numerous studies have concentrated on describing DNA methylation patterns as biomarkers for cancer diagnosis monitoring and predicting response to cancer therapy. Various techniques for detecting DNA methylation status in cancers are based on sodium bisulfite treatment. According to the application of these methods in research and clinical studies, they have a number of advantages and disadvantages. The current review highlights sodium bisulfite treatment-based techniques, as well as, the advantages, drawbacks, and applications of these methods in the evaluation of human cancers.

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CpG islands in MyD88 and ASC/PYCARD/TMS1 promoter regions are differentially methylated in head and neck squamous cell carcinoma and primary lung squamous cell carcinoma

et al. 2021

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Background Patients with head and neck squamous cell carcinoma (HNSCC) can develop lung squamous cell carcinoma (LuSCC), which could be the second primary tumor or HNSCC metastasis. Morphologically it is difficult to distinguish metastatic HNSCC from a second primary tumor which presents a significant diagnostic challenge. Differentiation of those two malignancies is important because the recommended treatments for metastatic HNSCC and primary LuSCC differ significantly. We investigated if the quantification of the promotor methylation status in HNSCC and LuSCC differs. Methods Primary HNSCC (N = 36) and LuSCC (N = 17) were included in this study. Methylation status in the ASC/TMS1/PYCARD (apoptosis-associated speck-like protein containing a caspase recruitment domain; 8 CpG sites) and MyD88 (Myeloid differentiation primary response protein 88; 10 CpG sites) promoters was analyzed. Bisulfite converted DNA, isolated from tumor tissue was quantified using pyrosequencing. Results of pyrosequencing analysis were expressed as a percentage for each tested CpG site. Receiver-operating characteristic (ROC) curve analysis was used for the evaluation of the diagnostic properties of selected biomarkers. Results CpG sites located in the promoters of ASC/TMS1/PYCARD_CpG8 (− 65 upstream) and MyD88_CpG4 (− 278 upstream) are significantly hypermethylated in the HNSCC when compared with LuSCC (p ≤ 0.0001). By performing ROC curve analysis we showed that corresponding areas under the curve (AUC) were 85–95%, indicating that selected CpG sites are useful for a distinction between primary LuSCC and primary HNSCC. Conclusions Results of the present study indicate that there is a significant difference in the methylation status of tested genes between primary HNSCC and LuSCC. However, to prove this approach as a useful tool for distinguishing second primary LuSCC from HNSCC metastasis, it would be necessary to include a larger number of samples, and most importantly, metastatic samples.

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A Pyrosequencing Assay for the Quantitative Methylation Analysis ofGALR1in Endometrial Samples: Preliminary Results

Cited by 4 publications

References 26 publications

Quantitative DNA Methylation Analysis of DLGAP2 Gene using Pyrosequencing in Schizophrenia with Tardive Dyskinesia: A Linear Mixed Model Approach

Quantitative DNA Methylation Analysis of DLGAP2 Gene using Pyrosequencing in Schizophrenia with Tardive Dyskinesia: A Linear Mixed Model Approach

The common bisulfite-conversion-based techniques to analyze DNA methylation in human cancers

CpG islands in MyD88 and ASC/PYCARD/TMS1 promoter regions are differentially methylated in head and neck squamous cell carcinoma and primary lung squamous cell carcinoma

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