Abstract 3489: EWSR1::WT1 fusion oncoprotein and the androgen receptor shape the biology of desmoplastic small round cell tumors

Abstract Desmoplastic small round cell tumors (DSRCTs) are rare, aggressive sarcomas driven by the EWSR1::WT1 fusion oncoprotein (FP) and marked by poor long-term survival. Despite a relatively quiet genome with a single known oncogenic driver, DSRCTs display striking transcriptional heterogeneity and express markers from multiple lineages, epithelial, mesenchymal, myogenic, and neural. DSRCTs show a strong male predominance, suggesting a potential role for sex-specific regulatory mechanisms, including androgen receptor (AR) signaling. To investigate the molecular basis of this complexity, we generated a comprehensive, multi-modal atlas of DSRCT, integrating transcriptomic, epigenomic, and spatial omics data (10x Genomics). We focused on dissecting the regulatory architecture shaped by the EWSR1::WT1 fusion and transcription factors such as AR, aiming to uncover mechanisms of lineage specification and therapeutic vulnerabilities. We hypothesized that epigenetic regulation of the EWSR1::WT1 FP contributes to this lineage divergence. To explore FP activity, we found that neogenes (non-coding RNA FP targets) and known FP-regulated genes were more highly expressed in NE-lineage tumors, suggesting that FP affects lineage type. Spatial transcriptomic analysis revealed intratumoral heterogeneity, with distinct clusters of epithelial (AR+, cytokeratin+) and non-epithelial tumor cells. Despite phenotypic differences, all tumor cells expressed neogenes, as confirmed by RNA in situ hybridization (RNAScope). Epigenetic profiling showed enrichment of Forkhead TFs (FOXA1/2). FOXA2 was associated with NE, and AR/GRHL2 were associated with epithelial lineages. CUT Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 3489.