Profiling the genomic landscape and evolutionary history of polyploid giant cancer cells in undifferentiated pleomorphic sarcomas

Polyploid giant cancer cells (PGCCs), characterised by multinucleation and atypical nuclear morphology, are a common feature of undifferentiated pleomorphic sarcomas. While PGCCs may be a critical substrate for cancer evolution, their formation pathways and genomic consequences remain underexplored. In this study, we characterise PGCCs in ten pleomorphic sarcomas and use topographic single-cell DNA sequencing (scDNA-seq) to investigate their genomic landscape. We selected PGCCs based on their nuclear morphology, including mononucleated or multinucleated bizarre, misshapen nuclei, and analysed them at single-cell resolution. Histopathological analysis showed that PGCCs were often randomly distributed throughout the tumour and did not appear in clusters, suggesting that they arise de novo rather than through clonal expansion. scDNA-seq revealed that PGCCs originate from the dominant tumour population and exhibit extensive copy number heterogeneity, either due to subsequent or ongoing chromosomal instability. Both clonal and subclonal chromothripsis-like events were identified in PGCCs, indicating that chromothripsis is a key driver of heterogeneity in these cells and is linked to multinucleation rather than mononuclear PGCC formation. FACS-based ploidy analysis of one undifferentiated pleomorphic sarcoma (UPS) revealed a twice whole-genome-duplicated population (6.2n) distinct from the bulk tumour (3.3n). This population contained all clonal, but none of the subclonal chromothripsis-like events observed in PGCCs. Our findings highlight PGCCs as a highly heterogeneous and evolutionarily dynamic component of UPSs. The recurrent chromothripsis-like events observed in PGCCs suggest ongoing genomic reshaping that may drive tumour progression and the poor clinical outcomes observed for these tumours.