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

Abstract

Background: 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.

Methods: 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.

Results: 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. Functional features of genes differentially expressed between the two groups of GISTs suggested alterations in angiogenesis and G-protein-related and calcium signalling.

Conclusion: Our study has identified novel molecular elements likely to be involved in receptor-dependent GIST development and allowed confirmation of previously published results. These elements may be potential therapeutic targets and novel markers of KIT mutation status.

Figure 1

Unsupervised hierarchical clustering for the selection of differentially expressed genes in GIST tumours according to KIT mutation. Across the top, individual tumour samples are arrayed in a column (upper: blue - KIT mutation; red - PDGFRA mutation; gray- no mutation found; lower: green - low KIT expression/high PDGFRA expression; yellow- high KIT expression/low PDGFRA expression; dark gray- high KIT/PDGFRA expression); on the left side, 311 individual probe sets differentiating tumours in accordance with the mutation are shown in rows. The colour in each cell reflects the level of expression of the corresponding probe set in the corresponding array sample relative to its mean level of expression estimated for the entire set of samples. Red indicates expression levels greater than the mean, and green indicates lower than the mean.

Figure 2

Relative mRNA expression of KIT (left panel) and PDGFRA (right panel) in GIST tumours according to sample mutation status. Black circles - KIT mutations; gray circles - PDGFRA mutations