Spatial Dynamics Links PD-L1 and Tumor-Associated Macrophage–Enriched Niches to Immune and Mesenchymal States in Microsatellite Stable Colorectal Cancer

Background/Objectives: MSS-CRC comprises a heterogeneous group of tumors generally considered “immune cold” due to limited neoantigen generation and T-cell exclusion or inactivation. Current evidence indicates that the composition of T and B immune cells within the tumor microenvironment represents a prognostically relevant factor, significantly associated with both tumor expression profiles and molecular subtypes. Methods: We conducted an exploratory analysis to identify prognostically relevant immune cell components in this group of tumors and to investigate corresponding differences in RNA-based bulk expression and high-resolution spatial transcriptomic profiles. Results: A total of 254 cases of localized mismatch repair-proficient colorectal cancer cases were evaluated. Our findings revealed PD-L1 expression as a robust, independent prognostic biomarker associated with favorable outcomes in this specific population. Bulk RNA expression analysis showed that PD-L1–negative tumors exhibited an expression profile consistent with abundant cancer-associated fibroblast infiltration, increased matrix stiffness, and impaired immune activation—features aligned with tumor progression and poorer clinical outcomes. In contrast, PD-L1–positive tumors displayed stromal programs enriched in immune activation and controlled remodeling, consistent with an immunologically active microenvironment. Spatial transcriptomics added an additional layer of evidence, revealing that epithelial-to-mesenchymal transition–related programs can dominate stromal niches in PD-L1–negative tumors, particularly within macrophage-enriched stromal regions. Conclusions: Our observations suggest a crosstalk link between PD-L1 expression on immune cells and immune-activated vs mesenchymal-dominant states driven within tumor-associated macrophage-enriched stromal niches. These results provide insight into the biological mechanisms underlying disease progression and highlight tumor-associated macrophages as a potential therapeutic target to overcome immune resistance particularly in PD-L1–negative MSS-CRC tumors.