Abstract
BackgroundUntil 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 the discovery of expressed fusion genes resulting from underlying genomic rearrangements.ResultsWe applied paired-end RNA-seq to identify 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 promoters (5' UTR), coding sequences and 3' UTRs. Most fusion genes were associated with copy number transitions and were particularly common in high-level DNA amplifications. This suggests that fusion events may contribute to the selective advantage provided by DNA amplifications and deletions. Some of the fusion partner genes, such as GSDMB in the TATDN1-GSDMB fusion and IKZF3 in the VAPB-IKZF3 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, or otherwise reported to be oncogenic. RNA interference-mediated knock-down of the VAPB-IKZF3 fusion gene indicated that it may be necessary for cancer cell growth and survival.ConclusionsIn summary, using RNA-sequencing and improved bioinformatic stratification, we have discovered a number of novel fusion genes in breast cancer, and identified VAPB-IKZF3 as a potential fusion gene with importance for the growth and survival of breast cancer cells.
Highlights
Until recently, chromosomal translocations and fusion genes have been an underappreciated class of mutations in solid tumors
Criteria for identification of fusion gene candidates To detect fusion genes in breast cancer, we performed paired-end RNA-seq using cDNA prepared from four well-characterized cell line models, as well as normal breast, which was used as a control
Here, we present a large number of previously unknown gene fusions in breast cancer cells, whose identification was facilitated by the development of an improved bioinformatic procedure for detecting gene fusions from RNA-seq data
Summary
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 the discovery of expressed fusion genes resulting from underlying genomic rearrangements. The recent identification of recurrent ETS-family translocations in prostate cancer [3] and EML4-ALK in lung cancer [4] suggests that fusion genes may play an important role in the development of epithelial cancers. The reason why they were not previously detected was the lack of suitable techniques to identify balanced recurrent chromosomal. RNA-seq directly identifies only those fusion genes that are expressed, providing an efficient tool to identify candidate oncogenic fusions
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