Abstract A003: Mapping the tumor microenvironment: Spatial Transcriptomic insights into ovarian cancer progression and resistance

Abstract High-grade serous ovarian cancer (HGSOC) remains the most lethal gynecologic malignancy, with a 5-year survival rate below 50%. Despite initial responsiveness to platinum-based chemotherapy and the implementation of targeted therapies such as PARP inhibitors, the majority of patients relapse and develop treatment-resistant disease. Emerging evidence suggests that the spatial organization and dynamic interactions among tumor, immune, and stromal cells within the tumor microenvironment (TME) play a critical role in therapeutic response and disease progression. However, traditional transcriptomic approaches lack the spatial context necessary to fully understand these interactions. The Xenium spatial transcriptomics (ST) platform represents an innovative technology that enables high-resolution, in situ mapping of gene expression within intact tissue architecture. By preserving the spatial relationships between cell types and molecular states, ST provides the opportunity to explore how the TME evolves under therapeutic pressure and contributes to resistance. We performed spatial transcriptomic profiling on FFPE tumor sections from three matched longitudinal pairs of HGSOC samples obtained prior to treatment and upon PARPi progression. Utilizing the Xenium 5K Plex platform from 10X Genomics, we quantified the expression of 5000 genes in over 2. 5 million cells. Cell type annotation was performed via reference mapping and marker gene expression. Differential expression and gene ontology enrichment analyses were conducted to identify key transcriptional changes in tumor clusters between paired naïve and progression samples. We furthermore describe spatial cellular neighborhoods and their changes upon development of resistance. Characterization of the tumors reveals great morphological heterogeneity between patients. Comparative analysis revealed distinct shifts in the cancer cell abundance, cancer cell area and spatial arrangement of the TME between naïve and progression samples. Progression samples exhibited increased expression of, for example, hypoxia-related genes, particularly in cancer cells. Spatial mapping identified distinct cellular neighborhoods, including niches with a high density of neutrophil- or macrophage-associated transcripts, which were notably more abundant in progression samples, suggesting a role in immune evasion and tumor progression. This study demonstrates the potential of spatial transcriptomics to elucidate the architectural and transcriptional changes of the ovarian cancer microenvironment at the single-cell level. While based on early findings, our results suggest the relevance of hypoxia, stromal remodeling, and niches with distinct cellular compositions in contributing to disease progression. These data support further investigation into spatially targeted therapeutic strategies and the use of ST as a tool for microenvironment-driven biomarker discovery. Citation Format: Sara K. Bystrup, Kathleen J. Imbach, Sergi Cervilla García, Arola Fortian Bernabeu, Daniella Grases, Eduard Porta Pardo, Jordi Barretina, Lorena Valdivieso Almeida, Pau Guillén Sentís, Adrià Bernat Peguera. Mapping the tumor microenvironment: Spatial Transcriptomic insights into ovarian cancer progression and resistance abstract. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Ovarian Cancer Research; 2025 Sep 19-21; Denver, CO. Philadelphia (PA): AACR; Cancer Res 2025;85 (18Suppl): Abstract nr A003.