Abstract 2627: Integrated multi-omics analyses discovers lineage plasticity in desmoplastic small round cell tumors

Abstract Desmoplastic small round cell tumor (DSRCT) is a rare and usually incurable aggressive sarcoma subtype. Less than 20% of patients survive beyond five years with standard of care. All tumor cells harbor a pathognomonic EWS::WT1 fusion protein (FP), but FP-targeted agents are nonexistent. Given the male to female ratio of 6:1, we sought to understand androgen receptor (AR) biology and its role as a therapeutic target in DSRCT. Our preliminary data suggested that a subset of DSRCT cell’s epithelial lineage expressed AR, which is the driver of prostate cancer (PC). A separate subset of DSRCT cells exhibited neural (NE) markers without AR expression. We explored gene expression, chromatin accessibility, and protein expression using multi-omic analyses (n=9) to understand the mechanisms driving AR and NE expression in DSRCT. We identified DSRCT, fibroblasts, endothelial cells, immune cells, and smooth muscle cells in the snRNA-seq data. Using AR and NE signatures, we generated three subsets of DSRCT cells. One subset was high in AR expression, and the other was high in NE markers, but not both. The third subset appeared to exhibit both markers - implying a hybrid phenotype or a poorly differentiated phenotype. To validate protein expression, we used the Lunaphore COMET. In AR-positive tumor nests, AR was localized to the nucleus, suggesting downstream activation of this pathway, and correlated with pan-cytokeratin (Ck) expression - an epithelial marker. Tumor nests marked by neural-specific enolase (NSE), an NE marker, demonstrated little to no expression of AR or Ck. However, patient subsets that harbored a hybrid transcriptomic profile had different cell states within the tumor nests, which were AR/Ck positive or NSE positive, but not both. This suggested that tumors may harbor cells of different cell states. The ATAC-seq data found that Epithelial/AR-positive subtypes were enriched in motifs for nuclear receptors (ARE and GRE). The NE subtype lacked the ARE and GRE motifs. EMT-related motifs were associated with the NE and hybrid subtypes, such as ZEB1, SNAI1, and SNAI2 (Slug). Transcription factor binding prediction showed that ZEB1 had higher activity in the NE subtype, while AR, FOXA2, and GRHL2, a co-regulator of AR, had higher activity in the AR subtype. Although the neuroendocrine subtype in PC usually evolves in response to therapy, how the NE phenotype emerges in DSRCT remains unknown. It has yet to be discovered how transcription factors play a role in the Epithelial/AR and NE in DSRCT dimorphic states. ZEB1 and GRHL2 form a double negative feedback loop, where ZEB1 suppresses GRHL2. This suggests that there may be an interaction between the ZEB1 and AR to regulate epithelial and NE phenotype in DSRCT, which may have implications for treating DSRCT with AR inhibitors. Citation Format: Danh Truong, Emre Arslan, Veena Kochat, Roberto Cardenas, Jiaqian Fan, Clement Agyemang, Adewale A. Adebayo, Davis Ingram, Akshay Basi, Hannah C. Beird, Jared Burks, P Andrew Futreal, Alexander Lazar, Ravin Ratan, Najat C. Daw, Andrea Hayes-Dixon, Kunal Rai, Joseph Ludwig. Integrated multi-omics analyses discovers lineage plasticity in desmoplastic small round cell tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2627.