Aberrant DNA methylation associated with aggressiveness of gastrointestinal stromal tumour

Yasuyuki Okamoto, Akira Sawaki, Seiji Ito, Toshirou Nishida, Tsuyoshi Takahashi, Minoru Toyota, Hiromu Suzuki, Yasuhisa Shinomura, Ichiro Takeuchi, Keiko Shinjo, Byonggu An, Hidemi Ito, Kenji Yamao, Makiko Fujii, Hideki Murakami, Hirotaka Osada, Hiromi Kataoka, Takashi Joh, Yoshitaka Sekido, Yutaka Kondo

Research output: Contribution to journalArticlepeer-review

55 Citations (Scopus)


Background and aims: The majority of gastrointestinal stromal tumors (GISTs) have KIT mutations; however, epigenetic abnormalities that could conceivably potentiate the aggressiveness of GISTs are largely unidentified. Our aim was to establish epigenetic profiles associated with the malignant transformation of GISTs. Methods: Methylation of four tumor suppressor genes, RASSF1A, p16, CDH1, and MGMT was analyzed in GISTs. Additionally, genome-wide DNA methylation profiles were compared between small, malignant-prone, and malignant GISTs using methylated GpG island amplification microarrays (MCAM) in a training set (n=40). Relationships between the methylation status of genes identified by MCAM and clinical features of the disease were tested in a validation set (n=75). Results: Methylation of RASSF1A progressively increased from small to malignant GISTs. p16 was specifically methylated in malignant-prone and malignant GISTs. MCAM analysis showed that more genes were methylated in advanced than in small GISTs (average of 473 genes vs 360 genes, respectively, P=0.012). Interestingly, the methylation profile of malignant GISTs was prominently affected by their location. Two genes, REC8 and PAX3, which were newly-identified via MCAM analysis, were differentially methylated in small and malignant GISTs in the training and validation sets. Patients with methylation of at least REC8, PAX3, or p16 had a significantly poorer prognosis (P=0.034). Conclusion: Our results suggest that GIST is not, in epigenetic terms, a uniform disease and that DNA methylation in a set of genes is associated with aggressive clinical behavior and unfavorable prognosis. The genes identified may potentially serve as biomarkers for predicting aggressive GISTs with poor survivability.

Original languageEnglish
Pages (from-to)392-401
Number of pages10
Issue number3
Publication statusPublished - 03-2012

All Science Journal Classification (ASJC) codes

  • Gastroenterology


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