Unearthing novel fusions as therapeutic targets in solid tumors using targeted RNA sequencing

Detection of oncogenic fusion genes in cancers, particularly in the diagnosis of uncertain tumors, is crucial for determining effective therapeutic strategies. Although novel fusion genes have been discovered through sequencing, verifying their oncogenic potential remain difficult. Therefore, researchers at the Sungkyunkwan University have evaluated the utility of targeted RNA sequencing in 165 tumor samples by identifying known and unknown fusions. Additionally, by applying additional criteria, the researchers have discovered eight novel fusion genes that are expected to process oncogenicity. Among the novel fusion genes, RAF1 fusion genes were detected in two cases. PTPRG-RAF1 fusion led to an increase in cell growth; while dabrafenib, a BRAF inhibitor, reduced the growth of cells expressing RAF1. This study demonstrated the utility of RNA panel sequencing as a theragnostic tool and established criteria for identifying oncogenic fusion genes during post-sequencing analysis.

Gene fusion detection workflow

If the fusions are expected to be present in cancers whose exact cause is not determined using the existing diagnostic methods, RNA was extracted from the tissues and targeted sequencing was conducted. The sequencing data were first analyzed using the Archer pipeline. Candidate fusions were subsequently filtered further by gene distance, gene function, frame, and read count. Additional analyses were conducted, including checking for intact functional protein domains and the expression of parent genes in the tumor. Finally, a fusion expression plasmid was produced to conduct in vitro and in vivo experiments.