Spatial Multi-Platform Integration Reveals Distinct Tumor States and Microenvironmental Niches in Colitis-Associated Colorectal Cancer 2309487

Abstract Introduction Colitis-associated colorectal cancer (C-CRC) develops in chronic inflammatory settings, where tumor—microenvironment interactions critically influence progression. Spatial transcriptomics enables analysis of these interactions while preserving tissue architecture. We aimed to define tumor cell states and associated microenvironmental features in C-CRC. Methods Seven tissue samples from three C-CRC patients were analyzed using consecutive sections processed by 10x Xenium and 10x Visium. Single-cell spatial coordinates from Xenium were integrated with Visium spots for combined spatial transcriptomic analysis. Results Xenium profiling identified 3,506,705 cells comprising epithelial, fibroblast, and immune populations. Tumor subclustering revealed two states: proliferating tumor cells enriched for cell-cycle genes (MKI67, TOP2A) and invasive tumor cells with elevated epithelial mesenchymal transition (EMT)-associated genes (CD44, CXCL1). Spatial neighborhood analysis identified a niche unique to invasive tumor cells characterized by proximity to cancer-associated fibroblasts (CAF) and SPP1+ macrophages. Invasive regions showed enrichment of angiogenesis, hypoxia, and inflammatory pathways. Receptor—ligand analysis identified SPP1—CD44 signaling between SPP1+ macrophages and invasive tumor cells. A gene signature distinguishing invasive and proliferating tumor cells stratified TCGA sporadic colorectal cancer samples into invasive-like and proliferating-like groups, with invasive-like tumors enriched for consensus molecular subtype 4. Conclusion This integrated spatial transcriptomics study identifies two tumor populations in C-CRC with distinct microenvironmental contexts. The invasive tumor phenotype is associated with CAF and SPP1+ macrophage proximity and SPP1—CD44-mediated signaling, highlighting the tumor microenvironment as a potential therapeutic target in C-CRC. Funding Source n/a Topic Categories Tumor Immunology: Cellular Responses and Tumor Microevironment (TIME)