Abstract 5302: Mapping the tumor microenvironment at single-cell resolution with Stereo-seq v1.3

Abstract Tumor cell heterogeneity and the tumor microenvironment are fundamental questions that heavily influence the process of cancer development, disease progression, and the response to treatments. Knowledge of cancer biology facilitates understanding of pharmacological effects and mechanism of action to improve clinical outcomes. Spatial transcriptomics technology, particularly Stereo-seq, makes the groundbreaking advancement in cancer research with its outstanding performance with high capture efficiency and single cell resolution. It allows scientists to visualize and analyze the complexity of tumors at an unprecedented level of detail. In this study, we mapped tumor heterogeneity and microenvironment of fresh frozen section from colorectal cancer tissue (CRC) at a single-cell resolution with Stereo-seq v1.3 kit. We identified10 cell populations using cell2location, including B cells, fibroblasts, CD4+ T cells, CD8+ T cells, dendritic cells, endothelial cells, epithelial cells, macrophages, mast cells and NK cells. In situ mapping and portion analysis of cell identification revealed a B-cell dominated area which was confirmed by H&E staining of adjacent section. To comprehensively understand the immune activities, we quantified the interactions among different cell types (by StereoSite framework), revealing biologically meaningful intercellular communications mediated by GZMA-PARD3 and CCR10- CCL28 between B cells and epithelial cells. Further pathway enrichment analysis indicated cooperated molecular activities and underlying functions in CRC, which showed interaction activities significantly associated with EGF or BMP signaling pathways. Patteren recognition method identified how functional units assocatied with pathways. Take EGF pathway as an example, results revealed CD4+ T cells and macrophages may coordinated to impact EGF pathway by communication activities. Analysis in this study showed that spatial transcriptomic data at single-cell resolution is vital for exploring intercellular communications, molecular activities, and functional units by providing spatial context. Stereo-seq possess the ability to efficiently gathering evidence of mode of action and resistance mechanims by deeply mapping the spatial profiling in TME. It paves the ways for drug development by removing uncertainties and reducing time and cost. Implementation of Stereo-seq workflow could not only offer impetus to solve unmet needs in area of oncological research, but also bring new findings from lab to patients faster. Citation Format: Jiajun Zhang, Xing Liu, Zexian Zeng, Rui Zhang, Tibby Tianbi Duan, Jing Guo, Liang Wu, Sha Liao, Ao Chen. Mapping the tumor microenvironment at single-cell resolution with Stereo-seq v1.3 [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 5302.