Oncogenic ETS factors expressed from fusion genes utilize EWSR1 to associate with the paraspeckle and regulate transcription.

Abstract

ETS family transcription factors are aberrantly expressed in prostate cancer and Ewing sarcoma due to chromosomal rearrangements resulting in fusion genes, most commonly TMPRSS2::ERG and EWSR1::FLI1, respectively. The products of these gene fusions regulate transcription together with the intrinsically disordered protein EWSR1. However, the role of EWSR1 as a transcriptional co-regulator is not fully understood. EWSR1 can undergo liquid-liquid phase separation. We found that ERG could integrate into EWSR1 phase separated droplets. We then tested the role of the paraspeckle, a nuclear membraneless organelle known to regulate transcription and include EWSR1. Both ERG and EWSR1::FLI1 associated with the paraspeckle scaffold long non-coding RNA NEAT1_2. Disruption of paraspeckles in prostate cancer and Ewing sarcoma cell lines resulted in disruption of oncogenic phenotypes mimicking the loss of oncogenic ETS factors. In Ewing sarcoma cells paraspeckle disruption promoted similar transcriptional profiles as loss of EWSR1::FLI1. Further, loss of EWSR1::FLI1 reduced the association of a paraspeckle component with EWSR1::FLI1 target genomic loci. In TMPRSS2::ERG positive prostate cancer cells paraspeckle disruption correlated with ERG-mediated transcriptional repression. These findings suggest that the paraspeckle is an important transcriptional regulator in cancers with ETS gene fusions and provides a potential target for further mechanistic understanding and drug development.