High density DNA array analysis reveals distinct genomic profiles in a subset of gastrointestinal stromal tumors

Abstract

Gastrointestinal stromal tumors (GISTs) generally harbor activating mutations in KIT or platelet-derived growth facter receptor (PDGFRA). Mutations in these receptor tyrosine kinases lead to dysregulation of downstream signaling pathways that contribute to GIST pathogenesis. GISTs with KIT or PDGFRA mutations also undergo secondary cytogenetic alterations that may indicate the involvement of additional genes important in tumor progression. Approximately 10-15% of adult and 85% of pediatric GISTs do not have mutations in KIT or in PDGFRA. Most mutant adult GISTs display large-scale genomic alterations, but little is known about the mutation-negative tumors. Using genome-wide DNA arrays, we investigated genomic imbalances in a set of 31 GISTs, including 10 KIT/PDGFRA mutation-negative tumors from nine adults and one pediatric case and 21 mutant tumors. Although all 21 mutant GISTs exhibited multiple copy number aberrations, notably losses, eight of the 10 KIT/PDGFRA mutation-negative GISTs exhibited few or no genomic alterations. One KIT/PDGFRA mutation-negative tumor exhibiting numerous genomic changes was found to harbor an alternate activating mutation, in the serine-threonine kinase BRAF. The only other mutation-negative GIST with significant chromosomal imbalances was a recurrent metastatic tumor found to harbor a homozygous deletion in chromosome arm 9p. Similar findings in several KIT-mutant GISTs identified a minimal overlapping region of deletion of approximately 0.28 Mbp in 9p21.3 that includes only the CDKN2A/2B genes, which encode inhibitors of cell-cycle kinases. These results suggest that GISTs without activating kinase mutations, whether pediatric or adult, generally exhibit a much lower level of cytogenetic progression than that observed in mutant GISTs.

Figure 1

Immunohistochemical staining showing KIT expression in KIT/PDGFRA mutation-negative samples #15–17 (A–C).

Figure 2

Genome-wide plots of SNP CN copy data (A, B) and frequency plots of CN alterations (C, D) for samples analyzed with the Affymetrix GeneChip® Human Mapping 50K Xba Array. (A) KIT-mutant GIST #8. (B) KIT/PDGFRA-mutation-negative GIST #15. Copy-number values (0–8) are indicated to the left of each panel, chromosome labels and ideograms are shown at the top and bottom of each panel, respectively. Green and red arrows indicate selected regions of CN loss and gain, respectively, that are discussed in the text. (C) Frequency plots of CN alterations in 14 mutant GISTs. (D) Frequency plots of CN alterations in 3 mutation-negative GISTs. Chromosome labels are shown at the bottom of each panel, frequency values to the left of the panel. Determination of CN gains (red) and losses (green) was done using the ACE algorithm (Analysis of Copy Error, CGH-Explorer, University of Oslo, Norway), which was used with a False Discovery Rate (FDR) of 0.0001.

Figure 3

Heat map (log₂ ratios of SNP CN) for GIST cases #18–31 analyzed by Affymetrix Genome-Wide Human SNP Array 6.0. Heat maps were created in Affymetrix Genotyping Console 3.0 and exported as portable network graphics files. For ease of visualization, image brightness and contrast were adjusted simultaneously for heat maps and scale. The color scale ranges from bright red (CN loss) to white to bright blue (CN gain). Case numbers and mutation status are indicated at the top. Chromosome numbers are shown to the left of the figure, p and q arms are separated by hash marks. The red arrow indicates the position of the chromosome 9p homozygous deletion identified in mutation-negative sample #26 and mutant samples #18, 20, and 22.