Identification of genes epigenetically silenced by CpG methylation in human gastric carcinoma.
To identify novel methylation-silenced genes in gastric cancer, we carried out a genome-wide search for genes that are up-regulated after treatment with the demethylating agent, 5-aza-2'-deoxycytidine (5Aza-dC). When three gastric cancer cell lines (SNU-1,-601, and -719) were treated with 5Aza-dC, 143 genes were found to be upregulated by twofold or more using oligonucleotide microarrays. Six of these genes, i.e. TFPI2, GPX3, GPX1, IGFBP6, IRF7 and DMRT1, showed promoter hypermethylation in one or more gastric cancer cell lines, but were unmethylated in normal gastric mucosa by bisulphite sequencing and methylation-specific PCR analysis. The following percentages of these genes were found to be aberrantly methylated in gastric cancer samples; TFPI2 (80.9%), GPX3 (30.1%), DMRT1 (46.9%), GPX1 (16.7%), IGFBP6 (22.6%) and IRF7 (32.1%). Interestingly, the survival of patients possessing methylated alleles of TFPI2 (123/152, 80.9%) was poorer than that of patients with unmethylated alleles (p=0.023). Multivariate analysis confirmed that TFPI2 methylation is a significant and independent prognostic factor in gastric carcinoma. Furthermore, altered TFPI2 expression, as demonstrated by immunohistochemistry in 566 consecutive gastric cancer tissues, was found to be significantly associated with sex (p=0.003), WHO classification (p<0.001), and a mixed subtype by Lauren's classification (p<0.001). Thus, the present study identified several novel genes, which were methylated in gastric cancer and among them, methylation of TFPI2 was an unfavourable prognostic marker.
Jee
Chang Do
CD
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Kim
Min A
MA
Department of Pathology, Seoul National University College of Medicine, 28 Yeongeon-dong, Seoul 110-799, Republic of Korea.
Jung
Eun Ji
EJ
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Kim
Jin
J
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea.
Kim
Woo Ho
WH
Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea; Department of Pathology, Seoul National University College of Medicine, 28 Yeongeon-dong, Seoul 110-799, Republic of Korea. Electronic address: woohokim@snu.ac.kr.
D014408:Biomarkers, Tumor / Q000235:genetics* / Q000378:metabolism; D002277:Carcinoma / Q000235:genetics / Q000378:metabolism / Q000401:mortality; D045744:Cell Line, Tumor; D018899:CpG Islands; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D020868:Gene Silencing; D006023:Glycoproteins / Q000235:genetics / Q000378:metabolism; D006801:Humans; D007150:Immunohistochemistry; D008297:Male; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic; D016016:Proportional Hazards Models; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013274:Stomach Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000401:mortality
D014408:Biomarkers, Tumor; D006023:Glycoproteins; C021240:tissue-factor-pathway inhibitor 2