Abstract 2067: Single-cell spatial whole transcriptome reveals tumor heterogeneity and stromal dynamics in invasive ductal carcinoma of the breast
Authors: Liang Zhang, Shanshan He, Michael Patrick, Stefan Rogers, Haiyan Zhai, John Lyssand, Michael Rhodes, Joseph Beechem
Journal: Cancer Research (2025)

Abstract Invasive ductal carcinoma (IDC) is the most common and aggressive form of breast cancer, characterized by tissue invasion and metastasis, contributing to significant morbidity and mortality. The tumor microenvironment (TME), composed of stromal and immune cells, plays a critical role in IDC progression and therapy resistance. However, the spatial organization and molecular heterogeneity within the IDC TME remain underexplored. Spatial transcriptomics enables the preservation of tissue architecture while revealing molecular signatures at single-cell resolution, offering new insights into cancer biology. We utilized the CosMx® Spatial Molecular Imager (SMI) platform with the CosMx Whole Transcriptome panel (approximately 19, 000 genes) to analyze a formalin-fixed, paraffin-embedded (FFPE) IDC tumor sample. The platform provides high-resolution, multiplexed RNA detection within its native tissue context. Hematoxylin and eosin (H&amp;E) staining of the same slide provided a histological reference for spatial transcriptomics. Transcriptomic data were analyzed using Uniform Manifold Approximation and Projection (UMAP) for dimensionality reduction and Leiden clustering to identify cell clusters and spatial patterns. Marker genes for each cluster were used to annotate cell types and assess their roles within the TME. Analysis identified two distinct tumor regions, each subdivided into subregions with unique and shared gene expression profiles. These tumor regions aligned with histological features observed in H&amp;E staining, validating the spatial transcriptomic findings. We observed region-specific stromal compositions, with fibroblast populations exhibiting distinct gene expression patterns. For example, one region was enriched for PIGR, CLU, and LTF, markers linked to immune response, tumor progression, and tumor-suppressive properties. These results highlight the molecular and spatial heterogeneity of IDC and the complex interactions within the TME. This study demonstrates the potential of spatial transcriptomics to uncover the molecular and spatial complexity of IDC. Integrating transcriptomic data with histological validation revealed novel insights into the TME, highlighting key gene signatures and stromal dynamics. The CosMx platform is a powerful tool for advancing precision oncology and guiding future therapeutic strategies in IDC. -Bruker Confidential- Citation Format: Liang Zhang, Shanshan He, Michael Patrick, Stefan Rogers, Haiyan Zhai, John Lyssand, Michael Rhodes, Joseph Beechem. Single-cell spatial whole transcriptome reveals tumor heterogeneity and stromal dynamics in invasive ductal carcinoma of the breast [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 2067.