Profiling colon cancer architecture with spatial transcriptomics identifies clinically relevant stromal ecotypes

Abstract Despite advances in characterizing intra-tumor heterogeneity in colon cancer (CC), its spatial organization remains to be fully delineated. We generated a large spatial transcriptomic atlas of 48 stage III CC and identified recurrent, biologically relevant spatial ecosystems. Recurrence-associated analysis revealed stromal-specific upregulation of a set of genes including the regenerative/revival-stem cell (REC/RSC) marker ANXA1, together with enrichment of a YAP-TEAD program. These signals converged into a refined three-gene YAP-Rev signature (AHNAK, ANXA1, CAPN2) capturing the fetal-like state associated with relapse. Deeper dissection of the stromal compartment revealed additionally layers of heterogeneity. Further Visium HD profiling allowed spotting ANXA1-expressing tumor cells surrounded by collagen-producing cancer-associated fibroblasts (matCAFs). Finally, we translated these findings to bulk transcriptomics and demonstrated a synergistic interaction between matCAF enriched stroma derived-signature and ANXA1-REC/RSC score with strong prognostic value across three independent cohorts comprising >3,500 stage II and stage III CC patients.