Comprehensive Multi-Omic Profiling of Desmoplastic Small Round Cell Tumors Identifies Targetable Pathways with Therapeutic Opportunities

Abstract Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive, fusion-driven sarcoma with poor outcomes despite intensive chemotherapy. Utilization of targeted therapies in DSRCT remains limited, underscoring the need for deeper characterization of patient tumors. To address this, we performed multi-omic profiling on nine patient-derived tumor biopsies from five patients enrolled in a precision oncology program. We consistently observed elevated mRNA and protein expression of human epidermal growth factor receptor 2, androgen receptor, and DNA damage response (DDR) markers, and characterized these molecular features using an integrated assay suite including bulk and single-cell RNA sequencing, protein profiling, immunohistochemistry, immune analyses, and functional homologous recombination deficiency (HRD) testing. We define a replication stress–associated DNA damage landscape and identify functional HRD in a subset of tumors lacking genomic HRD scar signatures. Single-cell analyses reveal intratumoral and intertumoral heterogeneity, whereas longitudinal sampling uncovers treatment-dependent shifts in expression and activity that may contribute to adaptive resistance. The immune microenvironment is characterized by dysfunctional T-cell states and sparse antigen-presenting cells. Collectively, these analyses delineate recurrent, biologically targetable features and patient-specific vulnerabilities, establishing a foundation for biomarker-guided therapeutic strategies in DSRCT. These findings support the investigation of rational combination approaches informed by sensitive detection methods and functional testing to address resistance in ultra-rare cancers. Implications: Integrative multi-omic profiling combined with functional testing in DSRCTs reveals patient-specific vulnerabilities and biologically targetable receptor and DDR dependencies while defining immune states that may inform therapeutic response and rational combination strategies in this rare, fusion-driven cancer.