The alternative splicing landscape of FET-translocated sarcomas

Gene fusions are common mutations in cancer that can lead to the formation of transcripts that subsequently encode chimeric proteins harboring domains from unrelated parent proteins. Specific genes are more prone than others to participate in gene fusions. Among them, genes encoding FET proteins (FUS, EWSR1 and TAF15), a conserved family of RNA-binding proteins, are regularly involved in chromosomal aberrations leading to gene fusions. FET fusions are pathognomonic of over twenty sarcoma and leukemia subtypes. The partner gene of these fusions is always fused in 3’ and encodes transcription factors. The resulting chimeric protein systematically contains an intrinsically disordered trans-activation domain from the N-terminal part of the FET protein and a DNA-binding domain from the C-terminal part of the transcription factor. This organization has led to the speculation that FET oncoproteins act as aberrant transcription factors by dysregulating transcription to trigger the oncogenic transformation. However, emerging evidence suggest that FET fusions could carry key post-transcriptional functions to rewire the gene expression landscape of cancer cells. By focusing on a representative subset of FET fusions, we have shown that their specific depletion in sarcoma cell lines leads to major transcriptome-wide perturbations at both transcriptional and post-transcriptional levels. We further identified that FET fusion depletion leads to hundreds of differential pre-mRNA splicing events. In order to confirm the splicing potential of these proteins, we have demonstrated that their recruitment on reporter minigenes can promote exon inclusion. Surprisingly, this novel function seems to rely mostly on the C-terminal domain for most FET oncoproteins. Finally, we have shown that FET fusions can be found in the chromatin-associated RNA fraction of these cancer cells. Together, our results point to a novel function of FET family of oncoproteins in pre-mRNA alternative splicing.