Abstract 5289: Mechanisms of metastasis revealed through single-cell spatial transcriptome analysis in patients with liver metastatic colorectal cancer

Abstract Background: The efficacy of treating colorectal cancer (CRC) liver metastases is hindered by significant tumor heterogeneity, both within and between tumors. This diversity stems from varied cell populations and complex interactions in the tumor microenvironment, necessitating a deeper understanding of spatial organization and cellular communication patterns. Methods: We examined 23 formalin-fixed paraffin-embedded tissue samples from 11 patients, comprising primary lesions and matched liver metastasis (6 with synchronous and 5 with metachronous metastases) using NanoString 6K CosMx Spatial Molecular Imaging (SMI). Pathologists selected optimal fields of view at tumor invasive fronts. Image processing, cell segmentation, and feature extraction utilized an in-house CosMx SMI pipeline with the Cellpose algorithm. Following quality control, the remaining cells underwent unsupervised clustering with differential gene expression analysis and cell-to-cell interaction analyses performed using the Seurat R package. Results: Analysis of 105, 624 high-quality cells revealed 23 distinct clusters, categorized as ten epithelial tumors, three cancer-associated fibroblast (CAF), two endothelial cells, five immune cells (T cell, Monocyte, Macrophage, SPP1+ Macrophage, and Plasma cell), alveolar cells, hepatocytes, and low complexity cell populations. We identified significant differences in gene expression between colon and liver CAFs, with liver CAFs displaying upregulation of 92 genes associated with epithelial-mesenchymal transition (EMT). Enhanced communication between CAFs, T cells, and macrophages was observed in liver metastases, with specific ligand-receptor pairs (SPP1-ITGA4/ITGB1, LGALS9-P4HB, LGALS9-CD44, CXCL12-CXCR4) enriched in the metastatic microenvironment. Conclusion: Our findings demonstrate distinct spatial heterogeneity and intercellular communication networks in CRC liver metastases. The identification of liver-specific CAF gene expression profiles and unique ligand-receptor interactions provides new insights into metastatic mechanisms and potential therapeutic targets. Citation Format: Jongwon Lee, Yeseul Kim, Hyo Seon Ryu, Jongmin Sim, Chungyeul Kim, Hyun Woo Kwon, Hyun Je Kim, Jong Min Park, Ah-Reum Lim, Jung Sun Kim, Hwa Jung Sung, Xingyi Guo, Jungmin Choi, Jungyoon Choi. Mechanisms of metastasis revealed through single-cell spatial transcriptome analysis in patients with liver metastatic colorectal cancer [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 5289.