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| Status |
Public on Jan 04, 2012 |
| Title |
Aberrant DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer [Illumina Methylation] |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by array
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| Summary |
Aberrant promoter methylation is known to be deeply involved in human gastric carcinogenesis, while association of Epstein-Barr virus (EBV) to the aberrant methylation has not been fully clarified. We analyzed promoter methylation in clinical gastric cancer cases using illumina's Infinium beadarray, and hierarchical clustering analysis classified gastric cancer into three subgroups: low and high methylation epigenotypes in EBV-negative cases, and markedly higher methylation epigenotype that was completely matched to EBV-positive cases. Three epigenotypes were characterized by three groups of genes: genes methylated specifically in the EBV-positive epigenotype (EBV(+)-markers, e.g. CXXC4, TIMP2, PLXND1), genes methylated both in EBV-positive and high epigenotypes (High-markers, e.g. COL9A2, EYA1, ZNF365), and genes methylated all in EBV-positive, high and low epigenotypes of gastric cancer (Common-markers, e.g. AMPH, SORCS3, AJAP1). Polycomb repressive complex (PRC)-target genes in ES cells were significantly enriched in High- and Common-markers (P=2x10-15 and 2x10-34, respectively), but not in EBV(+)-markers (P=0.2), suggesting a different cause for EBV(+)-marker methylation. Recombinant EBV was infected to low epigenotype gastric cancer cell, MKN7. In all the three independently established clones, DNA methylation was induced in High- and EBV(+)-markers after 18 weeks, demonstrating that EBV-positive epigenotype should involve methylation of Common-, High-, and EBV(+)-markers simultaneously. The de novo methylated genes were overlapped well among the three clones, and the methylation caused gene repression. In summary, gastric cancer was classified into three DNA methylation epigenotypes, EBV-positive gastric cancer showed markedly high methylation epigenotype expanding to non-PRC target genes, and EBV infection per se could induce the EBV-positive epigenotype.
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| Overall design |
51 clinical gastric cancer samples including 11 EBV(+) gastric cancer cases, 2 normal gastric mucosa samples and 2 peripheral blood cells were analyzed by Infinium to epigenotype gastric cancer (55 samples). In addition, 3 gastric cancer cell lines, 1 gastric cancer xenograft, and 5 methylation control samples were analyzed (9 samples). Moreover, two gastric cancer cell lines MKN7 and AGS were infected with recombinant EBV. 3 EBV(+) clones and 1 mock clone of MKN7, and 3 EBV(+) clones and 1 mock clone of AGS were analyzed (8 samples).
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| Contributor(s) |
Matsusaka K, Kaneda A, Nagae G, Ushiku T, Kikuchi Y, Uozaki H, Seto Y, Takada K, Aburatani H, Fukayama M |
| Citation(s) |
21990320, 28903418 |
| Submission date |
Aug 31, 2011 |
| Last update date |
Oct 11, 2019 |
| Contact name |
Atsushi Kaneda |
| E-mail(s) |
kaneda@genome.rcast.u-tokyo.ac.jp
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| Organization name |
The University of Tokyo
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| Department |
RCAST
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| Lab |
Genome Science Division
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| Street address |
4-6-1 Komaba
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| City |
Meguro-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
153-8904 |
| Country |
Japan |
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| Platforms (1) |
| GPL8490 |
Illumina HumanMethylation27 BeadChip (HumanMethylation27_270596_v.1.2) |
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| Samples (80)
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| This SubSeries is part of SuperSeries: |
| GSE31789 |
DNA methylation epigenotype expanding to non-polycomb target genes, induced by Epstein-Barr virus infection in human gastric cancer |
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| Relations |
| BioProject |
PRJNA155059 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE31788_RAW.tar |
5.8 Mb |
(http)(custom) |
TAR |
| GSE31788_raw_data.txt.gz |
11.3 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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