Abstract / Summary
Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive sarcoma characterized by the pathognomonic EWS::WT1 fusion protein (FP), an oncogenic chimeric transcription factor (OCTF) resulting from the t(11;22)(p13;q12) translocation. Recent studies have identified “neogenes” (NGs), genes usually silent in normal tissues but transcriptionally activated by OCTFs, as potential tumor-specific markers in fusion-driven cancers. In this study, we investigated the expression and regulation of DSRCT-specific NGs (DSRCT_NGs) using multimodal data from patients, PDX, and cell lines. We demonstrate the robust ability of DSRCT_NGs to discriminate FP-detected samples consistent with fusion-calling algorithms. EWS::WT1 depletion in four cell lines consistently reduced DSRCT_NG expression. Isoform-specific ectopic expression of EWS::WT1 in LP9 and MeT-5A mesothelial cells revealed that the E–KTS isoform predominantly drives DSRCT_NG expression. Mechanistically, ChIP-seq analyses demonstrated that EWS::WT1 occupancy proximal to NG transcription start sites, coincident with active histone marks enriched. Hi-ChIP analysis showed that EWS::WT1 drives long-range looping at DSRCT_NG loci, thereby activating nearby genes. Together, these findings establish DSRCT_NGs as transcriptional outputs of the EWS::WT1 FP and implicate their loci as regulatory regions of the DSRCT transcriptome. Their fusion-dependent expression, chromatin accessibility, and chromatin loop connectivity underscore their potential utility as biomarkers and therapeutic targets. DSRCT-specific neogenes are activated by the EWS::WT1 fusion, especially the E–KTS isoform, and accurately identify fusion-positive tumors. Fusion-driven chromatin remodeling and long-range looping activate these genes, highlighting biomarker and therapeutic potential.