Evaluation of novel targeted small-molecule therapeutics in desmoplastic small round cell tumor (DSRCT) cells

Abstract Purpose Desmoplastic small round cell tumor (DSRCT) is an aggressive sarcoma associated with an extremely poor prognosis. This study evaluates the therapeutic potential of targeted, non-DNA-damaging small-molecule inhibitors in an in vitro DSRCT model. Methods We characterized the genomic architecture of the JN-DSRCT-1 cell line using fluorescence in situ hybridization (FISH) and sequencing of the tumor suppressor TP53 . In silico analysis was performed to identify shared vulnerabilities between DSRCT and Ewing sarcoma (ES). Using flow cytometry (assessing cell death, mitochondrial membrane potential loss, caspase–3 activity, and cell cycle distribution) and quantitative real-time PCR (qPCR), we systematically evaluated a small-molecule screening panel. The panel targeted chromatin acetylation (entinostat, vorinostat, tenovin-1), p53 pathway activity (RETRA, nutlin-3, RITA), receptor tyrosine kinases (imatinib), and transcription factor DNA-binding dynamics (mithramycin). Results JN-DSRCT-1 cells exhibited complex aneuploidy, and we confirmed the presence of the pathognomonic balanced EWSR1::WT1 translocation. Histone deacetylase inhibitors (entinostat, vorinostat) and nutlin-3 (an MDM2 antagonist) triggered robust intrinsic apoptosis and upregulated p53 target genes (p21, PUMA, and NOXA). Mithramycin demonstrated high cytotoxicity, whereas imatinib was ineffective. Pan-caspase inhibition using z-VAD-FMK rescued cells from entinostat-, vorinostat-, nutlin-3-, and mithramycin-induced death, but failed to protect against tenovin-1, RITA, or RETRA, indicating the activation of caspase-independent cell death pathways. Conclusion DSRCT cells display high sensitivity to histone deacetylase inhibition, p53 pathway activation, and mithramycin. Among these, histone deacetylase inhibition alone or in combination with other small molecule drugs represents a particularly promising strategy for overcoming DSRCT cell survival.