Gene Set: WATANABE_COLON_CANCER_MSI_VS_MSS_DN

Standard name WATANABE_COLON_CANCER_MSI_VS_MSS_DN
Systematic name M8976
Brief description Down-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers.
Full description or abstract Promoter methylation of the mismatch repair gene plays a key role in sporadic microsatellite instability (MSI) colorectal cancers. However, promoter methylation often occurs in proximal colon cancers, and molecular phenotypes underlying MSI cancers in distal colon have not been fully clarified. Our goal was to clarify the difference between MSI and microsatellite stability (MSS) cancers and, furthermore, to determine distinct characteristics of proximal and distal MSI cancers. By DNA microarray analysis of 84 cancers (33 MSI and 51 MSS), we identified discriminating genes (177 probe sets), which predicted MSI status with a high accuracy rate (97.6%). These genes were related to phenotypic characteristics of MSI cancers. Next, we identified 24 probe sets that were differentially expressed in proximal and distal MSI cancers. These genes included promoter methylation-mediated genes, whose expression was significantly down-regulated in proximal MSI cancers. Among discriminating genes between MSI and MSS, nine methylation-mediated genes showed down-regulation in MSI cancers. Of these, 7 (77.8%) showed down-regulation in proximal MSI cancers. Furthermore, methylation-specific PCR confirmed that frequency of hMLH1 promoter methylation was significantly higher in proximal MSI cancers (P = 0.0317). These results suggested that there is a difference between proximal and distal MSI cancers in methylation-mediated influence on gene silencing. In conclusion, using DNA microarray, we could distinguish MSI and MSS cancers. We also showed distinct characteristics of proximal and distal MSI cancers. The inactivation form of hMLH, per se, differed between proximal and distal MSI cancers. These results suggested that distal MSI cancers constitute a distinct subgroup of sporadic MSI cancers.
Collection C2: curated gene sets
      CGP: chemical and genetic perturbations
Source publication Pubmed 17047040   Authors: Watanabe T,Kobunai T,Toda E,Yamamoto Y,Kanazawa T,Kazama Y,Tanaka J,Tanaka T,Konishi T,Okayama Y,Sugimoto Y,Oka T,Sasaki S,Muto T,Nagawa H
Exact source Table 2S
Related gene sets (show 1 additional gene sets from the source publication)

(show 19 gene sets from the same authors)
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Organism Homo sapiens
Contributed by Leona Saunders (Broad Institute)
Source platform HG-U133_Plus_2
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 3.0: First introduced

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