Hijacking of alternative splicing regulatory networks by FET fusion oncoproteins

Oncogenesis arises from the disruption of gene expression programs as a consequence of somatic mutations. Gene fusions, which result from chromosomal rearrangements that juxtapose two distinct genes, represent a major class of such alterations and frequently act as oncogenic drivers. Many of these driver fusions involve transcription factors (TFs), which play central roles in coordinating gene expression pathways, and therefore provide powerful models to study oncogenic transformation in simplified genetic contexts.
Fusions involving members of the FET family, which comprises the FUS, EWSR1 and TAF15 genes, are recurrent in multiple sarcoma and leukemia subtypes. These rearrangements consistently encode chimeric proteins that combine the aminoterminal low-complexity domain of FET proteins with the DNA-binding domain of various transcription factors. Owing to this domain organization, FET fusions have been almost exclusively characterized as aberrant transcriptional regulators. However, accumulating evidence suggests that their functions may extend beyond transcriptional control.
In this work, we investigated the role of FET fusion oncoproteins in the regulation of alternative splicing. Transcriptome-wide analyses of sarcoma cells following the knockdown of their respective driver fusions revealed widespread alterations in splicing patterns. These changes affected thousands of events enriched in cancer-associated biological processes. Importantly, we show that these splicing changes occur largely independently of transcriptional regulation, and may thus represent a novel and conserved molecular function for FET fusions. Mechanistically, we demonstrate that FET fusions can directly modulate exon inclusion levels when recruited onto pre-mRNA. Although they lack canonical RNA-binding domains, FET fusions associate with target transcripts through multivalent interactions with RNA-binding proteins (RBPs). These RBPs form complex regulatory networks on pre-mRNAs, through which FET fusions reorganize ribonucleoprotein composition and redistribute splicing factors along transcripts to alter splicing decisions. Furthermore, we provide evidence that this activity is dependent on the ability of FET fusions to promote the formation of biomolecular condensates. Finally, we establish the clinical relevance of this mechanism in Ewing sarcoma, where fusion-dependent splicing programs are associated with patient survival.
All in all, this study identifies a previously uncharacterized molecular mechanism through which FET fusion oncoproteins regulate gene expression at the post-transcriptional level. These findings further establish a functional link between oncogenic transcription factors and RBP networks in cancer, and highlight the relevance of alternative splicing as an underappreciated dimension of fusion-driven oncogenesis.