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Research Solutions: Gene Fusions

Gene fusions resulting from chromosomal translocations have been well recognized as key drivers of oncogenic pathways in hematological cancers and sarcomas for decades. The archetypical example is the BCR-ABL gene fusion present in almost all chronic myeloid leukemia (CML), which is the result of a reciprocal translocation between chromosome 9 and 22 [t(9;22)(q34;q11)]. The BCR-ABL fusion gene, located in the translocation-derived shorter chromosome (Philadelphia chromosome), makes a fusion protein with constitutively active ABL tyrosine kinase activity, which in turn activates downstream signaling pathways leading to transformation of hematopoetic cells. The identification of the BCR-ABL fusion as a critical driver of CML leads to one of the best examples of “precision medicine”–imatinib (Gleevec®)—a tyrosine kinase inhibitor specifically targeting tumor cells harboring the BCR-ABL fusion.

The discovery of recurrent fusions between TMPRSS3 and ETS transcription factor genes in prostate cancer provides the first indication that oncogenic gene fusions are not unique to blood cancers and play a similarly important role in solid tumors. Indeed, a more recent example of precision medicine—crizotinib (Xalkori®)—targets the EML4-ALK fusion present in approximately 3-5% non-small-cell lung cancer (NSCLC). The EML4-ALK fusion results in over-expression of the ALK tyrosine kinase, which is specifically inhibited by crizotinib. With the advent of next-gen sequencing technologies, a large number of novel gene fusions have been discovered in diverse cancer types, setting the stage for a new wave of treatment options for cancers previously considered untreatable.

Current diagnostic techniques for gene fusion detection is mainly based on fluorescent in situ hybridization (FISH) detecting the translocation events at the DNA level. However, development of DNA FISH assays is time consuming and may be difficult or impossible for events involving subtle genomic alterations. The RNAscope® in situ hybridization technology provides a universal assay format for directly detecting gene fusions at the RNA level. In a typical assay design, two probes are designed to hybridize to the two partner gene sequences of the fused transcripts in a duplex fluorescence format. In wild type cells, the signals from the two probes will be distinct and rarely co-localize. However, in cells harboring the gene fusion, the two probes will hybridize to the same fusion transcripts, and the two signals will co-localize and can be detected as merged fluorescent dots.

Like other RNAscope® assays, a new gene fusion RNAscope® in situ assay can be developed and validated rapidly (< 2 weeks). The RNAscope® in situ hybridization technology provides a uniform platform enabling rapid validation and clinical translation for any newly discovered gene fusions.

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