Methylomics analysis identifies epigenetically silenced genes and implies an activation of β-catenin signaling in cervical cancer

Yu Chih Chen, Rui Lan Huang, Yung Kai Huang, Yu Ping Liao, Po Hsuan Su, Hui Chen Wang, Cheng Chang Chang, Ya Wen Lin, Mu Hsien Yu, Tang Yuan Chu, Hung Cheng Lai

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

Using DNA methylation biomarkers in cancer detection is a potential direction in clinical testing. Some methylated genes have been proposed for cervical cancer detection; however, more reliable methylation markers are needed. To identify new hypermethylated genes in the discovery phase, we compared the methylome between a pool of DNA from normal cervical epithelium (n = 19) and a pool of DNA from cervical cancer tissues (n = 38) using a methylation bead array. We integrated the differentially methylated genes with public gene expression databases, which resulted in 91 candidate genes. Based on gene expression after demethylation treatment in cell lines, we confirmed 61 genes for further validation. In the validation phase, quantitative MSP and bisulfite pyrosequencing were used to examine their methylation level in an independent set of clinical samples. Fourteen genes, including ADRA1D, AJAP1, COL6A2, EDN3, EPO, HS3ST2, MAGI2, POU4F3, PTGDR, SOX8, SOX17, ST6GAL2, SYT9, and ZNF614, were significantly hypermethylated in CIN3+ lesions. The sensitivity, specificity, and accuracy of POU4F3 for detecting CIN3+ lesions were 0.88, 0.82, and 0.85, respectively. A bioinformatics function analysis revealed that AJAP1, EDN3, EPO, MAGI2, and SOX17 were potentially implicated in β-catenin signaling, suggesting the epigenetic dysregulation of this signaling pathway during cervical cancer development. The concurrent methylation of multiple genes in cancers and in subsets of precancerous lesions suggests the presence of a driver of methylation phenotype in cervical carcinogenesis. Further validation of these new genes as biomarkers for cervical cancer screening in a larger population-based study is warranted. What's New? The identification of novel genes that are hypermethylated in cancer and precancerous lesions is needed in order to achieve a better sensitivity and specificity in cervical cancer screening. Using a genome-wide approach, here the authors identified 14 genes that were frequently hypermethylated in CIN3+ and might thus become useful biomarkers in future molecular cervical cancer screening. A bioinformatics function analysis revealed that five of these genes were potentially implicated in β-catenin signaling, suggesting the epigenetic dysregulation of Wnt signaling during cervical cancer development. The concurrent hypermethylation of multiple genes also suggests the involvement of a CpG island methylator phenotype.

Original languageEnglish
Pages (from-to)117-127
Number of pages11
JournalInternational Journal of Cancer
Volume135
Issue number1
DOIs
Publication statusPublished - Jul 1 2014

Fingerprint

Catenins
Uterine Cervical Neoplasms
Transcriptional Activation
Methylation
Genes
Early Detection of Cancer
Computational Biology
Epigenomics
Biomarkers
Phenotype
Gene Expression
Sensitivity and Specificity
CpG Islands
Neoplasm Genes
DNA
Genetic Association Studies
DNA Methylation
Tumor Biomarkers
Carcinogenesis
Epithelium

Keywords

  • biomarkers
  • cervical cancer
  • CIN
  • DNA methylation

ASJC Scopus subject areas

  • Cancer Research
  • Oncology

Cite this

Methylomics analysis identifies epigenetically silenced genes and implies an activation of β-catenin signaling in cervical cancer. / Chen, Yu Chih; Huang, Rui Lan; Huang, Yung Kai; Liao, Yu Ping; Su, Po Hsuan; Wang, Hui Chen; Chang, Cheng Chang; Lin, Ya Wen; Yu, Mu Hsien; Chu, Tang Yuan; Lai, Hung Cheng.

In: International Journal of Cancer, Vol. 135, No. 1, 01.07.2014, p. 117-127.

Research output: Contribution to journalArticle

Chen, Yu Chih ; Huang, Rui Lan ; Huang, Yung Kai ; Liao, Yu Ping ; Su, Po Hsuan ; Wang, Hui Chen ; Chang, Cheng Chang ; Lin, Ya Wen ; Yu, Mu Hsien ; Chu, Tang Yuan ; Lai, Hung Cheng. / Methylomics analysis identifies epigenetically silenced genes and implies an activation of β-catenin signaling in cervical cancer. In: International Journal of Cancer. 2014 ; Vol. 135, No. 1. pp. 117-127.
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