Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

BMC Cancer
Jerzy OstrowskiLucjan S Wyrwicz

Abstract

Gastrointestinal stromal tumours (GISTs) represent a heterogeneous group of tumours of mesenchymal origin characterized by gain-of-function mutations in KIT or PDGFRA of the type III receptor tyrosine kinase family. Although mutations in either receptor are thought to drive an early oncogenic event through similar pathways, two previous studies reported the mutation-specific gene expression profiles. However, their further conclusions were rather discordant. To clarify the molecular characteristics of differentially expressed genes according to GIST receptor mutations, we combined microarray-based analysis with detailed functional annotations. Total RNA was isolated from 29 frozen gastric GISTs and processed for hybridization on GENECHIP HG-U133 Plus 2.0 microarrays (Affymetrix). KIT and PDGFRA were analyzed by sequencing, while related mRNA levels were analyzed by quantitative RT-PCR. Fifteen and eleven tumours possessed mutations in KIT and PDGFRA, respectively; no mutation was found in three tumours. Gene expression analysis identified no discriminative profiles associated with clinical or pathological parameters, even though expression of hundreds of genes differentiated tumour receptor mutation and expression status. Funct...Continue Reading

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Methods Mentioned

BETA
surgical resection
PCR
electrophoresis
PCA

Software Mentioned

FLUSH
MathWorks
Affymetrix
MATLAB
GOstats
MAS5
Primer Express
gcrma
Bioconductor
annotate

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