Genome-wide screening for methylation-silenced genes in colorectal cancer

Ahmed Khamas, Toshiaki Ishikawa, Kaoru Mogushi, Satoru Iida, Megumi Ishiguro, Hiroshi Tanaka, Hiroyuki Uetake, Kenichi Sugihara

Research output: Contribution to journalArticlepeer-review

15 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)490-496
Number of pages7
JournalInternational journal of oncology
Issue number2
Publication statusPublished - 2012 Aug


  • 5-aza-2′- deoxycitidine
  • Colorectal cancer
  • CpG island
  • Methylation
  • Oligonucleotide microarray

ASJC Scopus subject areas

  • Oncology
  • Cancer Research


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