Abstract 4795: Investigating HER2+ tumor cell motility and angiogenesis in FFPE breast cancer in space and at scale with CosMx and nCounter multiomics

Abstract HER2+ breast cancer’s aggressive phenotype continues to pose a major challenge despite many innovations in understanding its function and implementing treatment. Developing a deep understanding of the mechanisms of these types of invasive cancers, driven in part by disordered angiogenesis and re-modeling of the extracellular matrix, continues to be a priority in cutting edge cancer research. To better understand challenging diseases such as HER2+ breast cancer, Bruker Spatial Biology has developed workflows to measure RNA and protein on the same slide across multiple platforms, maximizing biological insight from each tissue section. The nCounter® platform is widely used today in large oncology and immunology studies, and with the addition of modular protein panels, its high-throughput multiomic workflow now enables simultaneous quantification of up to 550 proteins and 770 RNA targets spanning five orders of magnitude in dynamic range. Additionally, nCounter has an FDA approved RNA assay that enables quick and highly reproducible diagnostics. Complementing this, the CosMx® Spatial Molecular Imager (SMI) provides subcelluar, spatially resolved measurement of 19,000 mRNA targets per cell alongside a 64-plex immune-oncology protein panel. The CosMx 2.0 combined assay and software upgrade released in 2025 further improves performance, enhancing signal detection, reducing background, and increasing sensitivity by 150%. In this study, 12 FFPE breast cancer slides were pathologist-annotated for HER2 expression and serially sectioned for analysis. nCounter assay profiling identified differential expression between HER2-0 and HER2-3+ tumors, with enrichment of pathways related to cell motility and angiogenesis. To further dissect these pathways, one HER2-0 and one HER2-3+ sample were analyzed with CosMx SMI, enabling spatial pathway analysis, pseudo-time trajectory mapping, and unbiased RNA-protein correlation. These analyses revealed mechanisms that drive tumor microenvironment remodeling and angiogenic progression. Strong concordance at the bulk and pseudo-bulk scale confirmed the robustness of measurements across CosMx and nCounter platforms. At subcellular resolution, however, select targets displayed divergent correlations, emphasizing the importance of spatial context for fully resolving biological complexity. Together, these results highlight the complementary strengths of nCounter and CosMx multiomic assays, especially as they contribute to cancer research. nCounter assay enables scalable, high-throughput analysis across cohorts, allowing researchers to understand broad genetic and protein changes during the progression of HER2+ neoplasms. CosMx SMI then provides spatial and single-cell resolution to mechanistically interpret these biological processes, a crucial component in understanding tumor behavior. Citation Format: Michael Emilio Patrick, Wei Yang, Liang Zhang, Isabel Lee, Stefan-Laural Rogers, Shanshan He, Christina Bailey, John Lyssand, Joseph M. Beechem. Investigating HER2+ tumor cell motility and angiogenesis in FFPE breast cancer in space and at scale with CosMx and nCounter multiomics 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 4795.