Abstract 3100: Spatially resolved effects of oligonucleotide therapeutics on cellular phenotypes in cancer tissues

Abstract Introduction: Oligonucleotide therapeutics, such as antisense oligonucleotides (ASOs) and small interfering RNAs (siRNAs), are promising tools for targeting oncogenic pathways in cancer. However, their impact on tumor microenvironment (TME) architecture and cellular phenotypes within cancer tissues remains insufficiently understood. This study integrates oligonucleotide-based treatments with advanced spatial phenotyping to explore their effects on cancer tissues at a high-definition, single-cell scale. Methods: Cancer tissues treated with oligonucleotide therapeutics were analyzed using multiplexed immunohistochemistry (mIHC) and spatial transcriptomics. Cellular phenotypes, including immune and stromal cell populations, were characterized in situ to assess changes in the TME. High-resolution imaging and transcriptomic profiling were used to localize therapeutic effects, while computational analysis integrated phenotypic and molecular data to uncover spatially resolved mechanisms. Results: Oligonucleotide treatment led to distinct spatial alterations in the TME, including reprogramming of tumor associated macrophages and increased infiltration of cytotoxic T cells in peritumoral regions. Spatial transcriptomics revealed suppression of target oncogenes, alongside upregulation of immune activation pathways in responsive regions of the tissue. Notably, these effects were localized to specific niches, suggesting cell-type-specific and spatially restricted therapeutic responses. Conclusion: This study highlights the power of integrating oligonucleotide therapeutics with spatial phenotyping to uncover their impact on the TME in cancer tissues. The findings provide valuable insights into the spatial dynamics of oligonucleotide therapy, paving the way for more effective design and deployment of these treatments in oncology. Citation Format: Corinne Ramos, Sandra Boute, Amandine Gerstenberg, Richard Ruez. Spatially resolved effects of oligonucleotide therapeutics on cellular phenotypes in cancer tissues [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 3100.