The single-cell atlas of colorectal cancer reveals cellular heterogeneity and key molecular features of the tumor immune microenvironment.

BACKGROUND: Colorectal cancer (CRC) is a highly heterogeneous malignancy, with its tumor immune microenvironment (TIME) playing a crucial role in tumor progression, immune evasion, and treatment response. Despite insights from single-cell technologies, challenges such as small samples and inconsistent annotations have limited a comprehensive understanding. Thus, a large-scale, high-resolution single-cell atlas is needed to fully explore the heterogeneity of CRC TIME and guide personalized treatment. METHODS: We analyzed single-cell transcriptomic data from 100 CRC samples (371,223 cells). Immune, stromal, and epithelial cells in the TIME were clustered, annotated, and functionally analyzed. Transcription factor networks were inferred using SCENIC, differentiation states assessed with CytoTRACE, and cell-cell communication analyzed via CellPhoneDB. TIME subtypes were constructed from bulk RNA-seq data, followed by survival analysis. SCRN1 was further validated through in vitro experiments. RESULTS: This study presents a comprehensive single-cell CRC atlas, revealing significant heterogeneity in T cells, B cells, myeloid cells, fibroblasts, endothelial cells, and epithelial cells within the TIME. We defined two immune ecological subtypes: subtype 1 (enriched in metabolic and motility pathways with poor prognosis) and subtype 2 (enriched in immune response pathways, with better prognosis and greater immunotherapy potential). High SCRN1 expression in malignant epithelial cells correlated with poor prognosis and metastasis. In vitro experiments confirmed the role of SCRN1 in promoting CRC cell proliferation and migration. CONCLUSIONS: This study provides a comprehensive characterization of the CRC TIME, links TIME subtypes to prognosis, and identifies SCRN1 as a potential therapeutic target, offering insights for CRC precision subtyping and immunotherapy strategies.