An integrated bulk and single-cell transcriptomic analysis reveals stemness-driven immune regulation and therapeutic vulnerability in colorectal cancer.

Tumor stemness is increasingly recognized as a key contributor to tumor heterogeneity, immune regulation, and therapeutic resistance in colorectal cancer (CRC). In this study, we developed a stemness-based risk model using bulk transcriptomic data from The Cancer Genome Atlas and evaluated its prognostic and therapeutic relevance through integrative analyses. The proposed risk score robustly stratified patients into distinct prognostic groups and remained an independent predictor of overall survival after adjustment for clinicopathological variables. Stemness-high tumors exhibited altered immune infiltration patterns and coordinated upregulation of immune checkpoint-related genes. Although the association between stemness score and immune evasion potential was modest, its clinical relevance was supported by validation in independent immunotherapy-treated cohorts, where low-risk patients demonstrated improved survival and higher response rates. Single-cell RNA sequencing (scRNA-seq) analysis further revealed that enhanced stemness and dedifferentiation were predominantly localized within malignant epithelial cells. Together, these findings establish tumor stemness as a central determinant of prognosis, immune regulation, and therapeutic vulnerability in CRC.