Prevalent aberrant condensates of onco-fusion transcription factors and their dissolution as potential cancer therapy

Cancer-associated chromosomal rearrangements can result in the expression of numerous pathogenic fusion proteins. The mechanisms via which the fusion proteins contribute to oncogenesis are largely unknown and effective therapies for fusion-associated cancers are lacking. Here, we comprehensively scrutinized fusion proteins found in various cancers. We found that many fusion proteins are composed of phase separation-prone domains (PS) and DNA-binding domains (DBD), and these fusions have strong correlation with aberrant gene expression patterns. Furthermore, we established a high-throughput screening method, named DropScan, to screen drugs capable of modulating aberrant condensates. One of the drugs identified via DropScan, LY2835219, effectively dissolved the condensates in reporter cells lines expressing Ewing sarcoma fusions and partially rescued the abnormal expression of target genes. Our results indicate that aberrant phase separation is likely a common mechanism for these PS-DBD fusion-related cancers, and suggest that modulating aberrant phase separation is a potential route to treat these diseases. Overall design: Wild type U2OS, U2OS integrated with mCherry-EWS-FLI1, and A673 cell lines were cultured in DMEM (HyClone) supplemented with 10% FBS (Gibco) and 100 units/mL penicillin and 100 µg/mL streptomycin (HyClone) at 37? with 5% CO2 in a humidified incubator (Above 10^7 cells in 10cm dish). Each replicate was treated with 7.5µM LY2835219 for 0(untreated), 3 and 6 hours.