Identification of KIF5B-RET and GOPC-ROS1 fusions 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 3' kinase domain (KD) exons relative to more 5' exons.


METHODS
We studied 69 patients (including five never smokers and 64 current or former smokers) with lung adenocarcinoma negative for all major mutations in KRAS, EGFR, BRAF, MEK1, HER2, and for ALK fusions (termed "pan-negative"). A NanoString-based assay was designed to query the transcripts of 90 tyrosine kinases at two points: 5' to the KD and within the KD or 3' to it. Tumor RNAs were hybridized to the NanoString probes and analyzed for outlier 3' to 5' 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 3' to 5' ratios in ROS1 and RET. RACE isolated a GOPC-ROS1 (FIG-ROS1) fusion in the former and a KIF5B-RET fusion in the latter, both confirmed by RT-PCR. The RET rearrangement was also confirmed by FISH. The KIF5B-RET patient was one of only five never smokers in this cohort.


CONCLUSIONS
The KIF5B-RET fusion defines an additional subset of lung cancer with a potentially targetable driver oncogene enriched in never smokers with "pan-negative" lung adenocarcinomas. We also report in lung cancer the GOPC-ROS1 fusion originally discovered and characterized in a glioma cell line.
Departments of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York 10065, USA.
Yoshiyuki
Y
Suehara
Maria
M
Arcila
Lu
L
Wang
Adnan
A
Hasanovic
Daphne
D
Ang
Tatsuo
T
Ito
Yuki
Y
Kimura
Alexander
A
Drilon
Udayan
U
Guha
Valerie
V
Rusch
Mark G
MG
Kris
Maureen F
MF
Zakowski
Naiyer
N
Rizvi
Raya
R
Khanin
Marc
M
Ladanyi
D048868:Adaptor Proteins, Signal Transducing; D000230:Adenocarcinoma / Q000201:enzymology / Q000235:genetics*; D000077192:Adenocarcinoma of Lung; D000293:Adolescent; D000368:Aged; D000369:Aged, 80 and over; D000077548:Anaplastic Lymphoma Kinase; D001483:Base Sequence; D002352:Carrier Proteins / Q000235:genetics*; D020134:Catalytic Domain; D045744:Cell Line, Tumor; D005260:Female; D005820:Genetic Testing / Q000379:methods; D000077614:Golgi Matrix Proteins; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D008175:Lung Neoplasms / Q000201:enzymology / Q000235:genetics*; D008297:Male; D008565:Membrane Proteins / Q000235:genetics*; D026901:Membrane Transport Proteins; D008875:Middle Aged; D008969:Molecular Sequence Data; D015514:Oncogene Proteins, Fusion / Q000235:genetics* / Q000378:metabolism; D011505:Protein-Tyrosine Kinases / Q000235:genetics*; D011518:Proto-Oncogene Proteins / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D020794:Receptor Protein-Tyrosine Kinases / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA
D048868:Adaptor Proteins, Signal Transducing; D002352:Carrier Proteins; C522504:EML4-ALK fusion protein, human; C434484:GOPC protein, human; D000077614:Golgi Matrix Proteins; C573239:KIF5B-RET fusion protein, human; D008565:Membrane Proteins; D026901:Membrane Transport Proteins; D015514:Oncogene Proteins, Fusion; D011518:Proto-Oncogene Proteins; D012333:RNA, Messenger; C000626173:ALK protein, human; D000077548:Anaplastic Lymphoma Kinase; D011505:Protein-Tyrosine Kinases; C062333:ROS1 protein, human; D020794:Receptor Protein-Tyrosine Kinases