Contribution of mRNA degradation to the oncogenic functions of a fusion transcription factor

Gene fusions are an important class of somatic alterations in cancer. In many well-known cases, they encode aberrant fusion transcription factors (TFs) with neomorphic DNA-binding preferences. FET::ETS fusions represent a notable family of TFs. They result from the juxtaposition of a member of the FET (FUS/EWSR1/TAF15) family of RNA-binding proteins to
a member of the ETS superfamily of TFs (e.g., FLI1 and ERG). These fusions are oncogenic drivers in many sarcomas and leukemias but challenging drug targets. An important limiting factor in developing therapies for them relies in our partial understanding of their underlying pathogenic molecular mechanisms. To date, the oncogenic functions of FET::ETS fusion proteins are almost exclusively confined to the control of mRNA synthesis. Based on a growing number of studies that identified non-canonical roles in the control of mRNA decay for various non-fusion (wild-type) DNA-binding TFs in human, we investigated whether FET::ETS fusion TFs might also be involved in mRNA decay. To test this possibility, we reasoned that Ewing sarcoma might represent an attractive model for a proof-of-concept study. Ewing sarcoma is an aggressive bone and soft-tissue childhood cancer as well as a paradigm for solid tumor development after a single genetic event. In ~85% of patients, this disease is driven by the fusion protein EWSR1::FLI1 (EF). Structurally, EF is a well-defined TF containing a potent amino-terminal transactivation domain that is intrinsically-disordered and a carboxy-terminal ETS DNA-binding domain. Molecularly, EF is known to orchestrate oncogenic gene expression programs by reprogramming enhancers and promoters via phase transition and hijacking of chromatin regulators; as well as by remodeling
the 3D genome architecture. In this work, we report that EF also reprograms gene expression by affecting mRNA stability and decipher the molecular mechanisms underlying this function. We show that EF is recruited to mRNAs via interaction with the RNA-binding protein HuR (also known as ELAVL1), and promotes mRNA decay by binding to CNOT2, a component of the CCR4-NOT deadenylation complex. Interestingly, we evidence that EF antagonizes the normal mRNA protective function of HuR through its association with CCR4-NOT. Importantly, we show that EF-mediated mRNA decay supports Ewing sarcoma biology and yields a new vulnerability towards HuR inhibition. Finally, our data indicate that the control of gene expression by fusion TFs might represent a more complex scheme than anticipated, integrating mRNA synthesis and degradation, and thereby providing novel actionable molecular targets.