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Spatial transcriptomics of epithelial-mesenchymal transition in uterine carcinosarcoma

Uterine carcinosarcoma (UCS) is an aggressive endometrial malignancy characterized by epithelial (carcinoma) and mesenchymal (sarcoma) differentiation. To define the spatial organization of epithelial-mesenchymal transition (EMT) in UCS, we integrated microdissection-based bulk RNA sequencing with Xenium in situ spatial transcriptomics of formalin-fixed paraffin-embedded (FFPE) tumor specimens from eight patients (CS1-CS8). For bulk RNA sequencing, carcinoma and sarcoma regions identified by immunohistochemistry (AE1/AE3, CD10, vimentin and Ki-67) were separately isolated by punch-biopsy microdissection (60 micro-tissue samples in total, 4-8 sites per case) and subjected to RNA sequencing. For spatial transcriptomics, one FFPE section per case containing both carcinoma and sarcoma components was profiled on the Xenium platform (10x Genomics) using a 330-gene panel (Xenium Human Breast Gene Expression Panel plus 50 custom genes). EMT was consistently enriched in sarcomatous regions, and spatial analyses revealed continuous and segregated EMT architectures, EMT-intermediate cell states marked by HMGA1, and enrichment of MRC1-positive macrophages in mesenchymal regions. This dataset contains paired-end FASTQ files of the microdissection-based RNA-seq and Xenium output files (morphology images, decoded transcripts, cell-feature matrices, cell metadata and cell/nucleus segmentation boundaries).