Quantitative DNA methylation analysis of selected genes in endometrial carcinogenesis

Chen, Ying-Chieh; Tsao, Chun-Ming; Kuo, Chih-Chi; Yu, Mu-Hsien; Lin, Ya-Wen; Yang, Chu-Ying; Li, Hsin-Jung; Yan, Ming‐De; Wang, Tun-Jun; Chou, Yu‐Ching; Su, Her-Young

doi:10.1016/j.tjog.2015.08.010

Cited by 25 publications

(13 citation statements)

References 19 publications

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“…These observations indicate that DNA methylation could potentially be candidate biomarkers for cancers [ 5 ]. During the past decades, a series of altered methylation genes were evaluated for the potential diagnosis of EC, such as BHLHE22 / CDO1 / CELF4 , SHP1 , TMEFF2 [ 6 7 8 ].…”

Section: Introductionmentioning

confidence: 99%

Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically

et al. 2017

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ObjectiveEndometrial cancer (EC) is a common gynecologic cancer worldwide. However, the pathogenesis of EC has not been epigenetically elucidated. Here, this study aims to describe the DNA methylation profile and identify favorable gene signatures highly associated with aberrant DNA methylation changes in EC.MethodsThe data regarding DNA methylation and gene expression were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially methylated CpG sites (DMCs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs) were identified, and the relationship between the 2 omics was further analyzed. In addition, weighted CpG site co-methylation network (WCCN) was constructed followed by an integrated analysis of DNA methylation and gene expression data.ResultsFour hundred thirty-one tumor tissues and 46 tissues adjacent tumor of EC patients were analyzed. One thousand one hundred thirty-five DMCs (merging to 10 DMRs), and 1,488 DEGs were obtained between tumor and normal groups, respectively. One hundred forty-eight DMCs-DEGs correlated pairs and 13 regional DMCs-DEGs pairs were obtained. Interestingly, we found that some hub genes in 2 modules among 8 modules of WCCN analysis were down-regulated in tumor samples. Furthermore, protocadherins (PCDHs) clusters, DDP6, TNXB, and ZNF154 were identified as novel deregulated genes with altered methylation in EC.ConclusionBased on the analysis of DNA methylation in a systematic view, the potential long-range epigenetic silencing (LRES) composed of PCDHs was reported in ECs for the first time. PCDHs clusters, DDP6, and TNXB were firstly found to be associated with tumorigenesis, and may be novel candidate biomarkers for EC.

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Section: Introductionmentioning

confidence: 99%

Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically

et al. 2017

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“…In particular, available data support the value of identi cation speci c ESCC methylation panels to enable early detection (16,33,34). COL14A1 aberrant hypermethylation has been reported in ESCC (16), as well as renal cell carcinoma, sarcomas and endometrial carcinoma (35)(36)(37), whereas hypomethylation has been shown in coronary artery disease (38). GPX3 promoter hypermethylation has been reported in ESCC and esophageal glandular lesions, including Barrett's esophagus and EA (17,18,39).…”

Section: Discussionmentioning

confidence: 81%

A DNA Methylation-based Test for Esophageal Cancer Detection

Salta

Macedo-Silva

Miranda‐Gonçalves

et al. 2020

Preprint

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Background Esophageal cancer (ECa) is the 7th most incident cancer and the 6th leading cause of cancer-related death. Most patients are diagnosed with locally advanced or metastatic disease, enduring poor survival. Biomarkers enabling early cancer detection may improve patient management, treatment effectiveness and survival are urgently needed. In this context, epigenetic-based biomarkers such as DNA methylation are potential candidates. Methods Herein, we sought to identify and validate DNA methylation-based biomarkers for early detection and prediction of response to therapy in ECa patients. Promoter methylation levels were assessed in a series of treatment-naïve ECa, post-neoadjuvant treatment ECa and normal esophagus tissues, using quantitative methylation-specific PCR for COL14A1, GPX3, and ZNF569. Results ZNF569 methylation (ZNF569me) levels significantly differed between ECa and normal samples. Moreover, COL14A1 methylation (COL14A1me) and GPX3 methylation (GPX3me) levels discriminated adenocarcinomas and squamous cell carcinomas, respectively, from normal samples. COL14A1me & ZNF569me accurately identified adenocarcinomas (82.29%) whereas GPX3me & ZNF569me identified squamous cell carcinomas with 81.73% accuracy. Furthermore, ZNF569me and GPX3me levels significantly differed between normal and pre-treated ECa. Conclusion The biomarker potential of a specific panel of methylated genes for ECa was confirmed. These might prove useful for early detection and might allow for identification of minimal residual disease after adjuvant therapy.

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“…COL14A1 aberrant methylation has been reported in ESCC (16), as well as in renal cell carcinoma, sarcomas, and endometrial carcinoma (28,31,32), whereas hypomethylation has been shown in coronary artery disease (33). GPX3 promoter methylation has been shown in ESCC and esophageal glandular lesions, including Barrett's esophagus and EA (30,34,35).…”

Section: Discussionmentioning

confidence: 99%

A DNA Methylation-based Test for Esophageal Cancer Detection

Salta

Macedo-Silva

Miranda‐Gonçalves

et al. 2020

Preprint

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Background: Esophageal cancer (ECa) is the 7 th most incident cancer and the 6 th leading cause of cancer-related death. Most patients are diagnosed with locally advanced or metastatic disease, enduring poor survival. Biomarkers enabling early cancer detection may improve patient management, treatment effectiveness, and survival, are urgently needed. In this context, epigenetic-based biomarkers such as DNA methylation are potential candidates. Methods: Herein, we sought to identify and validate DNA methylation-based biomarkers for early detection and prediction of response to therapy in ECa patients. Promoter methylation levels were assessed in a series of treatment-naïve ECa, post-neoadjuvant treatment ECa, and normal esophagus tissues, using quantitative methylation-specific PCR for COL14A1 , GPX3, and ZNF569 . Results: ZNF569 methylation ( ZNF569me) levels significantly differed between ECa and normal samples ( p <0.001). Moreover, COL14A1 methylation ( COL14A1me) and GPX3 methylation ( GPX3me) levels discriminated adenocarcinomas and squamous cell carcinomas, respectively, from normal samples ( p =0.002 and p =0.009, respectively). COL14A1me & ZNF569me accurately identified adenocarcinomas (82.29%) whereas GPX3me & ZNF569me identified squamous cell carcinomas with 81.73% accuracy. Furthermore, ZNF569me and GPX3me levels significantly differed between normal and pre-treated ECa. Conclusion: The biomarker potential of a specific panel of methylated genes for ECa was confirmed. These might prove useful for early detection and might allow for the identification of minimal residual disease after adjuvant therapy.

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Quantitative DNA methylation analysis of selected genes in endometrial carcinogenesis

Abstract: Promoter methylation of ZNF177, COL14A1, HOXA9, DPYSL4, and TMEFF2 genes is a frequent epigenetic event in EC. Furthermore, the epigenetic hypermethylation of TMEFF2 may be a valuable marker for identifying undetected EC within endometrial hyperplasia.

Cited by 25 publications

References 19 publications

Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically

Identification of DNA methylation associated gene signatures in endometrial cancer via integrated analysis of DNA methylation and gene expression systematically

A DNA Methylation-based Test for Esophageal Cancer Detection

A DNA Methylation-based Test for Esophageal Cancer Detection

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