Integrated genomic study of quadruple-WT GIST (KIT/PDGFRA/SDH/RAS pathway wild-type GIST)

BACKGROUND: About 10-15% of adult gastrointestinal stromal tumors (GIST) and the vast majority of pediatric GIST do not harbour KIT or platelet-derived growth factor receptor alpha (PDGFRA) mutations (J Clin Oncol 22:3813–3825, 2004; Hematol Oncol Clin North Am 23:15–34, 2009). The molecular biology of these GIST, originally defined as KIT/PDGFRA wild-type (WT), is complex due to the existence of different subgroups with distinct molecular hallmarks, including defects in the succinate dehydrogenase (SDH) complex and mutations of neurofibromatosis type 1 (NF1), BRAF, or KRAS genes (RAS-pathway or RAS-P). In this extremely heterogeneous landscape, the clinical profile and molecular abnormalities of the small subgroup of WT GIST suitably referred to as quadruple wild-type GIST (quadruple(WT) or KIT(WT)/PDGFRA(WT)/SDH(WT)/RAS-P(WT)) remains undefined. The aim of this study is to investigate the genomic profile of KIT(WT)/PDGFRA(WT)/SDH(WT)/RAS-P(WT) GIST, by using a massively parallel sequencing and microarray approach, and compare it with the genomic profile of other GIST subtypes. METHODS: We performed a whole genome analysis using a massively parallel sequencing approach on a total of 16 GIST cases (2 KIT(WT)/PDGFRA(WT)/SDH(WT) and SDHB(IHC+)/SDHA(IHC+), 2 KIT(WT)/PDGFRA(WT)/SDHA(mut) and SDHB(IHC-)/SDHA(IHC-) and 12 cases of KIT(mut) or PDGFRA(mut) GIST). To confirm and extend the results, whole-genome gene expression analysis by microarray was performed on 9 out 16 patients analyzed by RNAseq and an additional 20 GIST patients (1 KIT(WT)/PDGFRA(WT)SDHA(mut) GIST and 19 KIT(mut) or PDGFRA(mut) GIST). The most impressive data were validated by quantitave PCR and Western Blot analysis. RESULTS: We found that both cases of quadruple(WT) GIST had a genomic profile profoundly different from both either KIT/PDGFRA mutated or SDHA-mutated GIST. In particular, the quadruple(WT) GIST tumors are characterized by the overexpression of molecular markers (CALCRL and COL22A1) and of specific oncogenes including tyrosine and cyclin- dependent kinases (NTRK2 and CDK6) and one member of the ETS-transcription factor family (ERG). CONCLUSION: We report for the first time an integrated genomic picture of KIT(WT)/PDGFRA(WT)/SDH(WT)/RAS-P(WT) GIST, using massively parallel sequencing and gene expression analyses, and found that quadruple(WT) GIST have an expression signature that is distinct from SDH-mutant GIST as well as GIST harbouring mutations in KIT or PDGFRA. Our findings suggest that quadruple(WT) GIST represent another unique group within the family of gastrointestintal stromal tumors. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2407-14-685) contains supplementary material, which is available to authorized users.