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Life sciences · Journal article
Cancer Research · September 21, 2026
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Colorectal cancers (CRC) with microsatellite stability (MSS) and instability (MSI) differ in tumor microenvironment (TME) composition and clinical treatment and outcomes. While MSI CRC is considered to be sensitive to immune checkpoint blockade therapy, MSS tumors are largely resistant. Characterizing the spatial TME differences between MSS and MSI tumors could provide insights to improve immunotherapy efficacy. Here, we profiled an integrated single-cell and spatial transcriptomic atlas of MSS and MSI CRC across independent cohorts and platforms. Spatial mapping revealed subtype-specific boundary microenvironments coupled to distinct malignant epithelial states. Cancer cells in a fully mesenchymal epithelial-mesenchymal-transition (EMT) state (EMT-II subtype) were enriched near the tumor boundary in MSS, while cancer cells with metabolically active EMT programs (EMT-III subtype) and interferon states were enriched in MSI and displayed a more dispersed distribution. A boundary-proximal interaction network selectively enriched in MSS was characterized by the accumulation of glial-like and tip-like cells around tumor boundary, which preferentially co-localized with EMT-II state tumor cells. The network was linked to extracellular matrix remodeling and EMT malignant cell states. Further, development of a cross-platform classifier TiGELR, a machine learning-derived tip cell-glial cell-EMT II tumor cell ligand-receptor signature, accurately distinguished MSS from MSI and stratified immunotherapy outcomes. Together, this study characterizes the spatial heterogeneity of tumor states and TME programs in CRC and provides a translational framework for improved CRC stratification and immunotherapy guidance.