Abstract 1272: Spatial profiling of human colorectal cancer brain metastasis identifies chromosomal instability with adaptive niche cellular reorganization and reprograming

Abstract Brain metastasis in colorectal cancer (mCRC) poses a significant clinical challenge with poor outcomes. Our study, the largest spatial analysis reported to date, aimed to uncover unique cellular and genomic features facilitating metastatic lesion development. Employing spatial transcriptomics on 60 patients' surgical resections, we validated our findings with single-cell RNA sequencing (scRNA-seq), whole-genome sequencing (WGS), and ex vivo functional studies in tumor slice cultures. We obtained spatially distinct gene expression profiles of metastatic tumor cells, tumor microenvironment (TME) and brain parenchymal lineages. Our analysis identified spatially heterogenous upregulation of PI3K, MAPK, EGFR, p53, and TGFβ signaling in metastatic tumor cells. Tumor cells had high levels of chromosomal instability (CIN) marked by recurrent amplifications in chromosomes 6, 7, 17, and 20. WGS from three independent cohorts revealed significantly higher CIN in mCRC brain compared to primary CRC or mCRC from other organs. Spatial neighborhood analysis identified an immune desert phenotype with lack of proximity between lymphocytes and metastatic tumor cells. However, mCRC brain contained abundant plasma cells identifying a unique TME niche feature. Significant proximity between tumor cells and endothelial cells underscored their potential role in tumor seeding and growth. Spatially aware differential expression analysis demonstrated adaptive responses in the brain parenchyma. This included increased Golgi-ER processing and Rho GTPase signaling in neurons and astrocytes adjacent to metastatic tumor cells, respectively. Macrophages were characterized by high expression of pro-fibrogenic genes. Increased SPP1 ligand expression from these macrophages interacted with corresponding receptors on spatially proximal fibroblasts, identifying a key niche reorganization feature that can promote metastatic lesion growth. To evaluate the translational potential of our findings, we examined the effects of perturbating the metastatic niche using scRNA-seq. We established a tumor slice culture from a mCRC brain surgical resection, which maintained all original cell states. Despite elevated signaling pathway activity, metastatic tumor cells were resistant to regorafenib, a multi-receptor tyrosine kinase inhibitor. In contrast, pirfenidone, an anti-fibrotic and anti-inflammatory small molecule, successfully reduced extracellular matrix-associated gene expression programs in fibroblasts in the TME. Our analysis identified distinct properties of mCRC brain that can serve as therapeutic targets, including high levels of chromosomal instability, remodeling of brain parenchyma, lymphocyte evasion, plasma cell abundance and macrophage-fibroblast interactions. Citation Format: Anuja Sathe, Aparajita Khan, Ji In Kang, Rithika Meka, Susan M. Grimes, Andrew S. Luksik, Michael Lim, Claudia Petrisch, Christopher M. Jackson, Hannes Vogel, Melanie Gephart, Summer Han, Hanlee P. Ji. Spatial profiling of human colorectal cancer brain metastasis identifies chromosomal instability with adaptive niche cellular reorganization and reprograming [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1272.