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Updated: May 21, 2026
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Genome-wide screening for methylation-silenced genes in colorectal cancer
Ahmed Khamas1, Toshiaki Ishikawa, Kaoru Mogushi
1Department of Surgical Oncology, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan.
Abstract:
Identification of methylation-silenced genes in colorectal cancer (CRC) is of great importance. We employed oligonucleotide microarrays to identify differences in global gene expression of five CRC cell lines (HCT116, RKO, Colo320, SW480 and HT29) that were analyzed before and after treatment with 5-aza-2'-deoxycitidine. Selected candidates were subjected to methylation-specific PCR and real-time quantitative reverse transcription-PCR using 15 CRC cell lines and 23 paired tumor and normal samples from CRC patients. After 5-aza-2'-deoxycitidine treatment, 139 genes were re-expressed in all 5 CRC cell lines collectively with a fold change of more than 1.5 in at least one cell line. These genes include known methylated and silenced genes in CRC. After applying study selection criteria we identified 20 candidates. The GADD45B and THSD1 genes were selected for further analysis. Among 15 colon cancer cell lines, methylation was only identified in THSD1 (27%). THSD1 methylation was subsequently investigated in 23 colorectal tumors and methylation was detected in 9% of the analyzed samples; the observed promoter hypermethylation was cancer-specific. THSD1 mRNA down-regulation was observed in tumor tissues. This genome-wide screening led to the identification of genes putatively affected by methylation in CRC. The THSD1 gene may play a role in the tumorigenesis of CRC.
Insights
Identifying methylation-silenced genes in colorectal cancer (CRC) is crucial. This study found THSD1 gene promoter hypermethylation in CRC, suggesting its role in tumor development.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Aberrant gene methylation is a hallmark of cancer, particularly colorectal cancer (CRC).
- Identifying methylation-silenced genes is critical for understanding CRC pathogenesis and developing targeted therapies.
Purpose of the Study:
- To identify novel genes silenced by promoter hypermethylation in colorectal cancer (CRC).
- To investigate the role of the identified genes, specifically THSD1, in CRC tumorigenesis.
Main Methods:
- Genome-wide gene expression analysis using oligonucleotide microarrays in CRC cell lines before and after 5-aza-2'-deoxycytidine treatment.
- Validation of candidate genes using methylation-specific PCR and real-time quantitative reverse transcription-PCR in CRC cell lines and patient samples.
- Analysis of THSD1 promoter hypermethylation and mRNA expression in colorectal tumors.
Main Results:
- 139 genes were re-expressed in CRC cell lines after demethylation treatment, with 20 selected as candidates.
- THSD1 promoter hypermethylation was detected in 27% of CRC cell lines and 9% of tumor samples, showing cancer-specific patterns.
- THSD1 mRNA down-regulation was observed in tumor tissues compared to normal samples.
Conclusions:
- This study identified potential methylation-silenced genes in CRC through a genome-wide screening approach.
- THSD1 promoter hypermethylation and subsequent down-regulation suggest its potential role in colorectal cancer development.
