Single-cell Multiomics Profiling Reveals Heterogeneous Transcriptional Programs and Microenvironment in DSRCTs

Desmoplastic small round cell tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1::WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single -cell multi-omics on 12 samples from five patients, we find that DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism -related transcriptional programs. In vitro modeling shows that high EWSR1::WT1 DNA -binding activity associates with most lineage -related states, in contrast to glycolytic and profibrotic states. Single -cell chromatin accessibility analysis suggests that EWSR1::WT1 binding site variability may drive distinct lineage -related transcriptional programs, supporting some level of cell -intrinsic plasticity. Spatial transcriptomics reveals that glycolytic and profibrotic states specifically localize within hypoxic niches at the periphery of tumor cell islets, suggesting an additional role of tumor cell -extrinsic microenvironmental cues. We finally identify a single -cell transcriptomics-derived epithelial signature associated with improved patient survival, highlighting the clinical relevance of our findings.