KIT gene deletions at the intron 10-exon 11 boundary in GI stromal tumors

Abstract

Most gastrointestinal stromal tumors (GISTs) harbor oncogenic mutations in the KIT gene, and the majority of these mutations affect the juxtamembrane domain of the kinase encoded by exon 11. Screening GISTs for KIT gene mutations is important for translational research studies and for providing prognostic information on the likelihood of tumor response to treatment with the kinase inhibitor imatinib mesylate (Gleevec). In a series of GISTs analyzed in our laboratory by a combination of denaturing HPLC and direct DNA sequencing, we identified 19 cases with KIT exon 11 deletions that included from 1 to 14 bp of intron 10 sequence and resulted in loss of the normal splice acceptor site at the beginning of exon 11. Predicted use of the next potential splice-acceptor site was confirmed by cDNA sequencing in 4 cases. Thus, the resulting mutant isoform, deletion KPMYEVQWK 550-558, was the same in all 19 cases. Only two other examples of deletions across the intron 10-exon 11 boundary have been reported, yet among 722 GISTs analyzed in our laboratories these deletions were not uncommon, accounting for 3.9% of exon 11 mutations and 2.6% of all tumors. Loss of KIT intron 10 sequences may be under-recognized if the forward primer is too close to exon 11, or if cases are examined exclusively at the cDNA level. Laboratories that offer clinical screening for KIT mutations in GI stromal tumors should be aware of this class of mutations.

Figures

Figure 1

Genomic deletions that include the intron 10–exon 11 boundary. Sequence from the end of intron 10, beginning at nucleotide 75631, and the beginning of exon 11 is shown, with the deletions of all 19 cases indicated in gray. Predicted splice acceptor sites are boxed. Wild-type sequence and amino acid codons are shown at the bottom of the figure for comparison. Note that in cases 6 and 8 the deletion was accompanied by a single nucleotide substitution at the 5′ end (underlined). A separate single nucleotide polymorphism is underlined in the intron 10 sequence of case 1.

Figure 2

cDNA sequences. The cDNA sequences from cases 1, 5, 11, and 15 all showed the identical deletion, as predicted from the genomic analyses.