Single-cell and bulk transcriptome analyses reveal elevated amino acid metabolism promoting tumor-directed immune evasion in colorectal cancer.

Introduction: Colorectal cancer (CRC), the third most common cancer worldwide, often shows limited responsiveness to immunotherapy due to its predominantly immune-excluded phenotype. Despite increasing insights into the complex tumor microenvironment (TME), the metabolic heterogeneity of CRC cells and their interactions with tumor-infiltrating immune cells remain poorly understood. Methods: We analyzed 46,374 epithelial cells from 17 CRC patients treated with PD-1 blockade to develop an amino acid (AA) metabolism score using the AUCell algorithm. This score was applied to a separate single-cell RNA sequencing (scRNA-seq) dataset from 23 CRC patients to investigate cell-cell interactions and functions of tumor-infiltrating immune cells, revealing distinct immune TME landscapes shaped by tumor metabolism. An Results: This study identified a link between elevated amino acid metabolism in CRC epithelial cells and resistance to PD-1 blockade therapy. A 31-gene AA score was developed by intersecting differentially expressed genes between responders and non-responders to PD-1 blockade with amino acid metabolism-related genes from the Molecular Signature Database (MSigDB). Using this score, 23 additional CRC samples were classified into high and low AA score groups. Comparative analysis revealed that the low AA group exhibited a more robust immune response, characterized by a greater number and stronger cell-cell interactions. Tumor-infiltrating immune cells in this group demonstrated enhanced activation and anti-tumor functions. Furthermore, CD8 Conclusion: Our findings highlight the role of elevated epithelial amino acid metabolism in shaping an immune-suppressive microenvironment, offering insights for patient stratification and therapeutic decision-making.