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| Status |
Public on Jun 26, 2014 |
| Title |
Methylomic analysis identifies epigenetically silenced genes and implies an activation of β-catenin signal in cervical cancer |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Using the pools of DNA from squamous cervical carcinomas (SCC) and DNA from normal scraping cells discovered the abnormal changes of genomic wide methylation by methylation BeadChip. The 61 genes were selected to validate by quantitative methylation specific PCR (qMSP) and bisulfite pyrosequencing in further processes. A CpG islands methylator phenotype (CIMP) was confirmed at 14 candidates in an independent set contained a spectrum of scraping cells form abnormal cervical lesions. In addition, we found among of 7 genes were announced to imply to potentially biological functions of β-catenin signal.
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| Overall design |
A pool DNA collected from equal amount of DNA of 38 SCC, and the other pool collected from equal amount of DNA of 19 normal cervical scraping cells. Based on 40 percent of different methylation in two pools of samples, we selected 91 genes showed abnormal methylation in SCC. After the confirmation of gene restored expression in cervical cell lines, there 61 genes showed upregulation in the treatment with demethylating drug. In addition, gel based of MSP were contributed to confirm in a small size of samples, and quantitative MSP was contributed to validated in an independent set. The methylation status of qMSP was also confirmed by bisulfite pyrosequence. Finally, we selected 14 genes demonstrated clinical relevance in the high methylation of CIMP associated to a risk factor in cervical intraepithelial neoplasia grade 3 (CIN3) and worse lesions. isk factor in cervical intraepithelial neoplasia grade 3 (CIN3) and worse lesions.
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| Contributor(s) |
Chen YC, Huang RL, Laio YP, Su PH, Wang HC, Lai HC, Huang YK |
| Citation(s) |
24310984 |
| Submission date |
May 24, 2013 |
| Last update date |
Jan 02, 2015 |
| Contact name |
Hung-Cheng Lai |
| E-mail(s) |
hclai30656@gmail.com
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| Organization name |
Taipei Medical University
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| Department |
Department of Obstetrics and Gynecology, School of Medicine, College of Medicine,
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| Street address |
No.250, Wuxing St.
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| City |
Taipei |
| ZIP/Postal code |
11031 |
| Country |
Taiwan |
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| Platforms (1) |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
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| Samples (2) |
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| Relations |
| BioProject |
PRJNA205245 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47351_RAW.tar |
5.8 Mb |
(http)(custom) |
TAR |
| GSE47351_non-normalized.txt.gz |
488.9 Kb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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