Human Cancer Biology IdentificationofKIF5B-RETandGOPC-ROS1Fusions in Lung Adenocarcinomas through a Comprehensive mRNA-Based Screen for Tyrosine Kinase Fusions

Background: The mutually exclusive pattern of the major driver oncogenes in lung cancer suggests that other mutually exclusive oncogenes exist. We conducted a systematic search for tyrosine kinase fusions by screening all tyrosine kinases for aberrantly high RNA expression levels of the 30 kinase domain (KD) exons relative to more 50 exons. Methods: We studied 69 patients (including five never smokers and 64 current or former smokers) with lungadenocarcinomanegative for allmajormutations inKRAS,EGFR,BRAF,MEK1,HER2, and forALK fusions (termed "pan-negative"). ANanoString-based assaywas designed to query the transcripts of 90 tyrosine kinases at two points: 50 to the KD and within the KD or 30 to it. Tumor RNAs were hybridized to the NanoString probes and analyzed for outlier 30 to 50 expression ratios. Presumed novel fusion events were studied by rapid amplification of cDNA ends (RACE) and confirmatory reverse transcriptase PCR (RT-PCR) and FISH. Results:We identified one case each of aberrant 30 to 50 ratios in ROS1 and RET. RACE isolated a GOPCROS1 (FIG-ROS1) fusion in the former and aKIF5B-RET fusion in the latter, both confirmedbyRT-PCR. The RET rearrangement was also confirmed by FISH. The KIF5B-RET patient was one of only five never smokers