PATH-13. A novel C19orf47-AKT2 chimeric RNA generated by cis-splicing of adjacent genes is associated with glioblastoma prognosis

Abstract Gliomas are the most prevalent and aggressive primary brain tumors in adults, characterized by rapid progression, therapeutic resistance, and a dismal prognosis. The discovery of targetable fusion genes in cancer has spurred interest in detecting chimeric RNAs for precision treatments. This study identified and validated a novel C19orf47-AKT2 fusion in glioma, including an out-of-frame C19orf47e9-AKT2e2 and an in-frame C19orf47e9-AKT2e3 variant, via RNA sequencing and Sanger sequencing. These chimeric RNAs were undetectable in all five non-tumorous brain tissue samples from epilepsy patients but were present in a significant proportion of glioma samples, indicating tumor specificity. Specifically, they were detected in 88.9% (144/162) of glioma core tissues, higher than that in peritumoral tissues (65.2%, 30/46, p<0.001). Quantitative analysis revealed no significant expression difference between these variants in peritumoral tissues. However, in tumor core tissues, the C19orf47e9-AKT2e2 variant was significantly more abundant (p<0.001). High expression of this variant was associated with poor prognosis in glioblastoma patients (p<0.05). Further analysis revealed that C19orf47-AKT2 chimeras arise from cis-splicing of adjacent genes, involving intergenic pre-mRNA splicing without DNA rearrangement. The in-frame variant is predicted to encode a fusion protein containing domains from both parent genes, and this coding potential was validated by transfecting an expression plasmid into 293T cells. However, no endogenous fusion protein was detected in GBM tissues or patient-derived GBM cells, even after proteasome inhibition, implying that the C19orf47-AKT2 fusion may not function through protein translation. We therefore knocked down the expression of C19orf47-AKT2 chimeras via RNA interference techniques. The subsequent CCK-8 assays revealed that the proliferative capacity of GBM primary cells was significantly inhibited following the down-regulation of these chimeric RNAs. In conclusion, this study identifies novel C19orf47-AKT2 chimeras, generated through cis-splicing, that might function as non-coding RNAs to promote glioblastoma proliferation. These chimeras represent potential prognostic markers and therapeutic targets for gliomas.