Transcriptomics

Dataset Information

5

Array CGH analysis of human gastrointestinal stromal tumors


ABSTRACT: Gastrointestinal stromal tumors (GISTs) are the most important mesenchymal tumors of the gastrointestinal tract. The vast majority of GISTs exhibit activating mutations of KIT or PDGFRA, but epigenetic alteration of GISTs is largely unknown. In this study, we aimed to clarify the involvement of DNA methylation in GIST malignancy. A total of 25 GIST specimens were studied using Human Genome CGH Microarray Kit 105A (G4412A, Agilent). Levels of LINE-1 methylation were analyzed using bisulfite-pyrosequencing. LINE-1 hypomethylation was correlated with risk grade, and high-risk GISTs exhibited lower levels of LINE-1 methylation than low- or intermediate-risk GISTs. Array CGH analysis revealed a significant correlation between LINE-1 hypomethylation and chromosomal aberrations. Our data suggest that LINE-1 hypomethylation correlates with the aggressiveness of GISTs. Hypomethylation may increase the malignant potential of GISTs by inducing accumulation of chromosomal aberrations. A total of 25 surgically obtained human gastrointestinal stromal tumors (GISTs) was analyzed using Agilent CGH microarray. Copy number aberration was compared with clinicopathological features and DNA methylation status.

ORGANISM(S): Homo sapiens  

SUBMITTER: Hiromu Suzuki   Minoru Toyota 

PROVIDER: E-GEOD-22185 | ArrayExpress | 2010-06-20

SECONDARY ACCESSION(S): GSE22185PRJNA128819

REPOSITORIES: GEO, ArrayExpress

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Publications

A novel correlation between LINE-1 hypomethylation and the malignancy of gastrointestinal stromal tumors.

Igarashi Shinichi S   Suzuki Hiromu H   Niinuma Takeshi T   Shimizu Haruo H   Nojima Masanori M   Iwaki Hiroyuki H   Nobuoka Takayuki T   Nishida Toshirou T   Miyazaki Yasuaki Y   Takamaru Hiroyuki H   Yamamoto Eiichiro E   Yamamoto Hiroyuki H   Tokino Takashi T   Hasegawa Tadashi T   Hirata Koichi K   Imai Kohzoh K   Toyota Minoru M   Shinomura Yasuhisa Y  

Clinical cancer research : an official journal of the American Association for Cancer Research 20101026 21


PURPOSE: Gastrointestinal stromal tumors (GIST) are the most important mesenchymal tumors of the gastrointestinal tract. The vast majority of GISTs exhibit activating mutations of KIT or PDGFRA, but epigenetic alteration of GISTs is largely unknown. In this study, we aimed to clarify the involvement of DNA methylation in GIST malignancy. EXPERIMENTAL DESIGN: A total of 106 GIST specimens were studied. Levels of LINE-1 methylation were analyzed using bisulfite pyrosequencing. In addition, methyla  ...[more]

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