Abstract Introduction: Gynecologic carcinosarcomas (GynCS) are rare, aggressive uterine and ovarian cancers with a median survival under two years. Their biology is marked by epithelial-mesenchymal transition (EMT), driving dissemination and a biphasic carcinoma-sarcoma morphology. However, the molecular drivers of intratumoral heterogeneity beyond EMT remain poorly understood. This study seeks to clarify these mechanisms by characterizing the transcriptomic landscape of GynCS. Methods: Hematoxylin-eosin-saffron (HES) slides from 35 uterine and ovarian carcinosarcomas were reviewed by a gynecologic pathologist. A total of 251 tumoral tissue sectors, including carcinoma, sarcoma and mixed components, were selected for morphological assessment and bulk RNA sequencing (RNA-seq) using the SMARTer library preparation kit. Results: Among 35 tumors included in cohort, 33 (94%) were TP53-mutated, 2 (4%) had no specific molecular profile, 1 (2%) was mismatch repair-deficient and none was POLE-mutated. EMT expression signature correlated with histological features despite 26% of histologicaly sarcomatous sectors being reclassified as epithelial based on RNAseq (WISP classifier). Gene set enrichment analysis (GSEA) in all carcinoma sectors compared to all sarcoma sectors revealed a depletion in the response to inflammation and immunity as the main mechanism alongside EMT. Both cell-type deconvolution on RNA-seq data and immunohistochemical CD3 staining on FFPE slides suggest an enrichment in T cells, particularly cytotoxic T cells, in the tumor microenvironment of carcinoma sectors compared to sarcoma sectors. Within-tumor immune gene set analysis in a subset of tumors (n=15) revealed heterogeneous microenvironmental switch across patients, with 53% of tumors (n=8) shifting from a hot-to-cold microenvironment while most others (47%; n=7) remained immune-deprived. Gene expression profiles revealed the sustained activation of non-canonical NFκB pathway by cGAS-STING as a potentially leading cause of immune exhaustion and associated with EMT. Spatial RNAseq (Visium2) of 4 representative cases confirmed inflammation response as among most spatially variable features. Conclusion: This study suggests that chromosomal instability, acting through the cGAS-STING pathway, plays a dual role in driving immune exhaustion and promoting EMT as key biological features, despite notable inter-tumor variability in this process. These findings are consistent with existing literature on the non-canonical NFκB pathway. This work highlights potential therapeutic opportunities, including the emerging STING-targeted treatments and personalized immunotherapeutic strategies tailored to the unique immune landscape of each tumor. Citation Format: Amel Kime, Julie Berthet, Juliette Renard, Antoine Gaudet Chardonnet, Pierre Laurent-Puig, Jerome Alexandre, Bruno Borghese, Guillaume Beinse. Gynecologic carcinosarcomas beyond epithelial-mesenchymal transition: Morpho-transcriptomic evidence of an immune gradient in the tumor microenvironment abstract. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 6209.
Kime et al. (2026) studied this question.