Published in:
Open Access 01-12-2014 | Research article
Integrated genomic study of quadruple-WT GIST (KIT/PDGFRA/SDH/RAS pathway wild-type GIST)
Published in: BMC Cancer | Issue 1/2014
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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.