Elucidating divergent biology in uterine carcinosarcoma.

Uterine carcinosarcoma (UCS) is an aggressive malignancy characterized by epithelial (C) and mesenchymal (S) components, with complex biology and poor treatment response. This study aims to enhance understanding of UCS through genomic, epigenomic, and transcriptomic analysis. Microdissected (C and S) tumor samples were processed for whole-genome sequencing (WGS), RNA-seqencing, and enzymatic methylation sequencing (EM-Seq). Multiplex immunohistochemistry (mIHC) and computational pathology techniques were employed to assess tumour microenvironment (TME). WGS and EM-seq of 18 samples from 9 patients revealed a low tumor mutation burden (TMB; median = 0.97 mutations/Mb) and no evidence of microsatellite instability (MSI). Driver mutations were identified in TP53 (94 %), PIK3CA (33 %), and PPP2R1A (22 %). Copy-number (CN) analysis revealed recurrent amplifications of MYC (67 %), PIK3CA (61 %), CCNE1 (56 %), AKT2 (44 %), and SMARCA4 (39 %). Comparative analysis of the C and S regions revealed no significant differences in mutation frequency, CN, transcriptomic and methylomic profiles. Both regions exhibited global hypomethylation, with functional enrichment for xenobiotic metabolism pathways in C and epithelial-to-mesenchymal transition pathways in S regions. Comparitive mIHC performed on 21 cases showed similar T cell and B cell densities, but a higher density of tumour-associated macrophages and PD-L1+ cells in the S component. Computational morphologic analysis showed substantial histomorphologic heterogeneity within and across UCS cases. By elucidating the complex interplay between the epithelial and mesenchymal components, this study enhances our understanding of UCS and informs the development of novel therapeutic strategies targeting both genomic alterations and the TME.