Abstract A070 Identifying therapeutic vulnerabilities in desmoplastic small round cell tumor through multi-omics analyses
Authors: Truong Danh , Arslan Emre , Kochat Veena , Krishnan Sandhya , Agyemang Clement , Divenko Margarita , Cárdenas-Zúñiga Roberto , Ingram Davis , Lazcano Rossana , Basi Akshay , Gomez Javier , Beird Hannah , Wu Chia-Chin , Burks Jared , Futreal P. Andrew , Lazar Alexander , Ratan Ravin , Daw Najat C. , Rai Kunal , Hayes Andrea , Ludwig Joseph 
Published: September 2024

Abstract
Desmoplastic small round cell tumor (DSRCT) is a rare and usually incurable aggressive sarcoma subtype affecting both adults and young adolescents. All tumor cells harbor a pathognomonic EWS::WT1 fusion protein (FP), but FP-targeted agents are nonexistent. Less than 20% of patients survive beyond five years with standard of care. Our work showed that a subset of DSRCT cells (mostly of epithelial lineage) highly express the androgen receptor (AR). On the other hand, a separate subgroup of DSRCT cells exhibited neuroendocrine (NE) markers without AR expression. Given that all the DSRCT cells share the same FP, we explore gene expression, chromatin accessibility, and proteomic analyses to understand mechanisms that may drive epithelial and NE phenotypes and present therapeutic opportunities. We studied the transcriptomic, epigenomic, and proteomic profiles of DSRCT from nine patients with matched specimens. By gene expression, three subsets of patients were identified. Two subsets were either high in AR or NE markers, but not both. The third subset appeared to exhibit both markers – implying a hybrid phenotype or a poorly differentiated phenotype. There was strong concordance between the transcriptomic and the proteomic markers as measured by multiplex immunofluorescent imaging. In AR-positive tumor nests, AR was localized to the nucleus, suggesting downstream activation of this pathway. AR expression was correlated with pan-cytokeratin expression in the tumor nests. On the other hand, tumor nests marked by neural-specific enolase, an NE marker, demonstrated little to no expression of AR. The ATAC-seq data revealed enriched motifs associated with the DSRCT subtypes. Epithelial/AR-positive subtypes were enriched in motifs for nuclear receptors (ARE and GRE) and CCAAT-enhancer-binding proteins. The NE subtype lacked the ARE and GRE motifs but was enriched for zinc finger motifs, including WT1 and the EGR family. EMT was also associated with the NE and hybrid subtypes, such as ZEB1, SNAI1, and SNAI2 (Slug). Additionally, MEF2 transcription factors were enriched in the NE and hybrid subtypes associated with muscle and neural development. Despite the male predilection, AR heterogeneity in DSRCT was an unexpected finding that may change potential treatment options. In vitro studies of AR stimulation and inhibition demonstrated that we could promote cell proliferation and inhibit cell growth, respectively. However, the emergence of the NE subtype in prostate cancer is generally in response to AR-directed therapy, which is not yet used for DSRCT patients. The motif analysis suggests that NE is associated with enriched motifs for zinc fingers, EMT, and MEF2 transcription factors. How the NE phenotype emerges in DSRCT has yet to be discovered. Ongoing research will shed light on transcription factor binding and how targeting AR may affect the epithelial/AR and NE states in DSRCT.
Citation Format: Danh Truong, Emre Arslan, Veena Kochat, Sandhya Krishnan, Clement Agyemang, Margarita Divenko, Roberto Cárdenas-Zúñiga, Davis Ingram, Rossana Lazcano, Akshay Basi, Javier Gomez, Hannah Beird, Chia-Chin Wu, Jared Burks, P. Andrew Futreal, Alexander Lazar, Ravin Ratan, Najat C. Daw, Kunal Rai, Andrea Hayes, Joseph Ludwig. Identifying therapeutic vulnerabilities in desmoplastic small round cell tumor through multi-omics analyses [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr A070.