Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human gastrointestinal stromal tumor (GIST) reveals gene expression determined distinct classes.

ABSTRACT: GIST is considered to invariably arise through gain-of-function KIT or PDGFRA mutation of the interstitial cells of Cajal (ICC). However, the genetic basis of the malignant progression of GIST is poorly understood. We analysed the expression levels of 54,613 probe sets in 32 surgical samples of untreated GIST of the stomach and small intestine with GeneChip Human Genome U133 Plus 2.0 arrays. Experiment Overall Design: Total RNA was extracted from 32 fresh frozen tumour specimens. We analysed the global gene exprssion profiles of these GIST cases in order to clarify the genomic basis behind the malignant progression of this tumor

ORGANISM(S): Homo sapiens

SUBMITTER: Umio Yamaguchi

PROVIDER: E-GEOD-8167 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

Distinct gene expression-defined classes of gastrointestinal stromal tumor.

Yamaguchi Umio U Nakayama Robert R Honda Kazufumi K Ichikawa Hitoshi H Hasegawa Tadashi T Shitashige Miki M Ono Masaya M Shoji Ayako A Sakuma Tomohiro T Kuwabara Hideya H Shimada Yasuhiro Y Sasako Mitsuru M Shimoda Tadakazu T Kawai Akira A Hirohashi Setsuo S Yamada Tesshi T

Journal of clinical oncology : official journal of the American Society of Clinical Oncology 20080901 25

<h4>Purpose</h4>The majority of gastrointestinal stromal tumors (GIST) can be cured by surgery alone, but relapse occurs in 20% to 40% of cases. GISTs are considered to invariably arise through gain of function KIT or PDGFA mutation of the interstitial cells of Cajal (ICC). However, the genetic basis of the malignant progression of GISTs are poorly understood.<h4>Patients and methods</h4>The expression levels of 54,613 probe sets in 32 surgical samples of untreated GISTs of the stomach and small ...[more]

PMID: 18757323

Similar Datasets

Project description:Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Studies in organotypic cultures of intact gastric muscular wall tissues identified Kit(low)Cd44(+)Cd34(+)Insr(+)Igf1r(+) cells as local ICC progenitors (Lorincz et al., Gastroenterology 2008;134:1083-1093). Subsequently, conditionally immortalized Kit(low)Cd34(+) cells were isolated by immunomagnetic and fluorescent cell sorting and serial cloning from the gastric muscular wall of homozygous, 14-day-old H-2Kb-tsA58 mice and shown to share other phenotypic characteristics with in-situ ICC precursors (2xSCS70 cells; Bardsley et al., Gastroenterology 2010;139:942-952). 2xSCS70 cells were also found to express the ICC marker Ano1, to be able to extensively self-renew in the absence of the SV40 tsA58-TAg when cultured in NeuroCultÂ® Neural Stem Cell Proliferation Medium (NSCPM; STEMCELL Technologies) and to differentiate into Kit(+) ICC both in vitro and in vivo. Wild-type cells with Kit(low)Ano1(+)Cd44(+)Cd34(+)Insr(+)Igf1r(+) phenotype (2xSCS2F10 cells) were prospectively isolated from primary cultures of dissociated gastric muscular wall tissues from 7-day-old C57BL/6J mice by serial cloning following 150-day expansion in NSCPM containing 5% cell-free chick embryo extract (CEE; Accurate Chemical). Long-term culturing of both cell lines was associated with further decline in Kit expression while expression of Ano1 and other markers of ICC precursors was maintained. Following spontaneous transformation, both 2xSCS70 and 2xSCS2F10 cells grafted into nude mice gave rise to tumors containing Kit(+)cells and otherwise resembling gastrointestinal stromal tumors (GIST), which originate from the ICC lineage (Bardsley et al., Gastroenterology 2010;139:942-952). This study utilized RNA-sequencing to complement the companion microarray study in non-transformed 2xSCS70 and 2xSCS2F10 cells. Libraries were made from total RNA isolated from ICC progenitor cell lines using the Illumina TruSeq mRNA Sample Preparation Kit v2 and sequenced on the Illumina HiSeq 2000 platform.

Dataset Information

Transcription profiling of human gastrointestinal stromal tumor (GIST) reveals gene expression determined distinct classes.

Publications

Distinct gene expression-defined classes of gastrointestinal stromal tumor.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets