Identification of an actionable mutation of KIT in extraskeletal myxoid chondrosarcoma (EMC)

Background: EMC is an extremely rare soft tissue sarcoma, marked by a translocation involving NR4A3 gene. EMC are usually indolent and generally are moderately sensitive to anthracycline-based chemotherapy; we reported on the therapeutic activity of sunitinib in a series of EMC cases, however the molecular target of sunitinib in EMC is unknown. In addition, there is still the need to identify alternative therapeutic strategies. To better characterize the molecular background of this disease we performed whole transcriptome sequencing (WTS) in a small series of EMC identifying a case carrying an activating KIT mutation. Methods: Five EMC, positive for EWSR1-NR4A3 in FISH, were collected for WTS analysis. KIT phosphorylation was evaluated through Western Blot. KIT hotspot exons were sequenced through Sanger method in these cases and in an additional cohort of 15 EMC FFPE samples. Results: Presence of the chimeric EWSR1-NR4A3 mRNA was confirmed in all cases by WTS and no additional fusion event was identified. In concordance with previous reports, exon12/exon3 EWSR1-NR4A3 fusion was the most frequent breakpoint detected (sample #2, #3 and #5). While exon7/exon2 and exon13/exon3 were detected respectively in sample #1 and #4. Pathogenic SNV and INDEL were searched starting from WTS data. Peculiarly, in sample #1 an in-frame deletion (c.1735_1737delGAT p.D579del) was identified in exon 11 of KIT. The deletion was somatic and heterozygous and was validated both at DNA and mRNA level. Sample #1 showed a marked high expression of KIT at mRNA level (9.8 fold greater than in the other 4 cases) and a mild phosphorylation of the receptor. KIT p.D579del is known to predict response to TKI treatment in GIST. However, Sanger sequencing of KIT in additional 15 FFPE EMC did not show any other mutated cases. Conclusions: Exon 11 KIT mutation has been detected in one out of 20 EMC cases analyzed, indicating that KIT alteration is not a recurrent event in EMC and thus it could not explain the sensitivity of these tumors to sunitinib. Its role in the pathogenesis of EMC is left to be determined. No additional unknown fusion and/or mutation were detected.