Super-enhancer-driven CACNA2D2 is an EWSR1::WT1 signature gene encoding a diagnostic marker for desmoplastic small round cell tumor (DSRCT)

ABSTRACT: Desmoplastic small round cell tumor (DSRCT) is a highly aggressive cancer predominantly occurring in young male adolescents. It mainly arises at sites lined by mesothelium, such as the abdominal cavity, and is driven by the pathognomonic EWSR1::WT1 fusion oncoprotein. The dismal survival rates (5–20%) have not significantly improved since its first description in 1989, also due to a lack of comprehensive datasets that could shed new light on the biology of the disease and uncover novel diagnostic markers and therapeutic targets. Thus, we established genome-wide single-cell RNA-sequencing and bulk proteomic data of in vitro and in vivo-generated EWSR1::WT1 knockdown models and combined them with an original systems-biology-based pipeline including patient data, resulting in a rich resource for discovery analyses. This approach revealed the alpha-2/delta subunit of the voltage-dependent calcium channel complex, CACNA2D2, as a strongly overexpressed direct target of EWSR1::WT1 in DSRCTs, which is regulated by an EWSR1::WT1-bound super-enhancer. Ectopic expression of the main EWSR1::WT1 isoforms in mesothelial cells, the putative cell of origin of DSRCTs, confirmed that EWSR1::WT1 is sufficient to induce super-enhancer formation at the CACNA2D2 locus followed by robust transcription of this gene. Moreover, single-cell and bulk-level analyses on patient samples and cell line-derived xenografts highlighted CACNA2D2 as a critical mediator of the EWSR1::WT1 oncogenic signature. Based on bulk and single-cell transcriptomic data, the computed CACNA2D2 signature could be further utilized to robustly identify DSRCTs in reference sets. Finally, we show that CACNA2D2 is a highly sensitive and specific single biomarker for fast, simple, and cost-efficient diagnosis of DSRCT. Collectively, we established a freely available large-scale multi-omics dataset for this devastating disease and provide a blueprint of how such data can be used to identify a new and clinically relevant diagnostic marker, which may significantly reduce misdiagnoses, and thus improve patient care.

INSTRUMENT(S): timsTOF Pro

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Desmoplastic Small Round Cell Tumor

SUBMITTER: Stefanie Kutschmann  

LAB HEAD: Dr. Florencia Cidre-Aranaz

PROVIDER: PXD053786 | Pride | 2025-06-30

REPOSITORIES: Pride