Identification of fusion genes in breast cancer by paired-end RNA-sequencing

Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors. Next-generation sequencing technologies provide an opportunity for systematic characterization of cancer cell transcriptomes, including expression of fusion genes resulting from underlying genomic rearrangements. We applied paired-end RNA-seq to characterize 24 novel and 3 previously known fusion genes in breast cancer cells. Supported by an improved bioinformatic approach, we had a 95% success rate of validating gene fusions initially detected by RNA-seq. Fusion partner genes were found to contribute both promoters (5'UTR), coding sequences as well as 3'UTRs. Most fusion genes (23/27) were associated with copy number transition points and were particularly common in high level DNA amplifications, including the ERBB2 amplicon, suggesting that fusion events may contribute to the selective advantage provided by amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion, were only detected as a fusion transcript, indicating activation of a dormant gene by the fusion event. A number of fusion gene partners have either been previously observed in oncogenic gene fusions, mostly in leukemias (ACACA, NOTCH1, NUP214, RARA), or otherwise reported to be oncogenic (NUP214, MCF2L). RNAi-mediated knock-down of NOTCH1-NUP214 and VAPB-IKZF3 fusion genes indicated that both may be necessary for cancer cell growth and survival in the cell lines harboring these fusions. In summary, using RNA-sequencing coupled with improved bioinformatics, we have identified numerous novel fusion genes in breast cancer, including ones with potential significance in cancer pathogenesis.