Related Experiment Video
Updated: Jul 10, 2026
Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
Identification of methylation-silenced genes in colorectal cancer cell lines: genomic screening using oligonucleotide
Satoshi Fukutomi1, Naohiko Seki, Keiji Koda
1Department of General Surgery, Chiba University Graduate School of Medicine, Chuoh-ku, Chiba, Japan.
Objective:
Aberrant methylation of promoter CpG islands is associated with the loss of expression of tumor suppressor genes in human cancers. The purpose of this study was to examine methylation-silenced genes in colorectal cancer (CRC) cell lines.
Material And Methods:
Using an oligonucleotide array, we undertook a genome-wide search for genes upregulated following treatment with a demethylating agent (5-aza-2'-deoxycytidine) in two CRC cell lines, DLD-1 and HT29. Promoter methylation status was determined in 12 CRC cell lines and 11 CRC tissues by methylation-specific polymerase chain reaction (MSP).
Results:
After treatment, 350 genes were up-regulated 1.5-fold or more. Six genes (PAGE-5, VCX, MAEL, GAGED2, UCHL1, and GAGE7), which contained putative 5' CpG islands in their promoter regions, were confirmed to be silenced in CRC cell lines. UCHL1 (also known as PGP9.5) is involved in regulation of cellular ubiquitin levels, and its promoter methylation was detected in 10 out of 12 CRC cell lines. The level of methylation of UCHL1 was significantly higher in tumors than in corresponding normal mucosae (p = 0.005).
Conclusions:
Chemical genomic screening led to the identification of a specific promoter subject to hypermethylation in CRC. These results suggest that aberrant promoter methylation is the primary mechanism of transcriptional silencing of the UCHL1 gene and that methylation of the UCHL1 gene promoter increases during the development and progression of CRC.
Insights
Aberrant promoter methylation silences tumor suppressor genes in colorectal cancer (CRC). Researchers identified UCHL1 as a key gene silenced by hypermethylation, which increases during CRC progression.
Area of Science:
- Oncology
- Molecular Biology
- Epigenetics
Background:
- Aberrant promoter methylation of CpG islands silences tumor suppressor genes in human cancers.
- Understanding gene silencing mechanisms is crucial for cancer research.
Purpose of the Study:
- To investigate methylation-silenced genes in colorectal cancer (CRC) cell lines.
- To identify specific genes affected by aberrant promoter methylation in CRC.
Main Methods:
- Genome-wide screening using oligonucleotide arrays to identify upregulated genes after demethylating agent treatment (5-aza-2'-deoxycytidine) in CRC cell lines.
- Methylation-specific polymerase chain reaction (MSP) to determine promoter methylation status in CRC cell lines and tissues.
Main Results:
- 350 genes were upregulated post-treatment; six genes (PAGE-5, VCX, MAEL, GAGED2, UCHL1, GAGE7) with promoter CpG islands were confirmed silenced in CRC.
- UCHL1 (PGP9.5) promoter methylation was detected in 10/12 CRC cell lines and was significantly higher in tumors versus normal mucosa (p = 0.005).
Conclusions:
- Chemical genomic screening identified UCHL1 as a specific promoter subject to hypermethylation in CRC.
- Aberrant promoter methylation is the primary mechanism for UCHL1 transcriptional silencing in CRC.
- UCHL1 promoter methylation increases during colorectal cancer development and progression.
