Integrated single‑cell and spatial transcriptomics reveal the colorectal cancer microenvironment

Colorectal cancer (CRC) is a malignancy with high global incidence and mortality rates, necessitating innovative approaches to decipher its biological characteristics and clinical behaviors. The integration of single-cell sequencing and spatial transcriptomics has emerged as a revolutionary tool in CRC research. Single-cell sequencing uncovers tumor heterogeneity and interaction networks, while spatial transcriptomics precisely maps the cellular distribution and tissue architecture within the tumor microenvironment (TME). This integrated approach has revealed spatially organized tumor-stroma-immune networks-including immune-excluded zones characterized by CAF-mediated ECM barriers and SPP1⁺ TAMs, immune-active niches featuring T cell-myeloid cooperation, and TLS-associated domains with both activating and suppressive microenvironments. Key discoveries include MGP-high epithelial cells driving liver metastasis via NF-κB-mediated PD-L1 upregulation, SPP1⁺ CAFs forming immunosuppressive metastatic niches, and functionally validated mechanisms such as IL1R1⁺ iCAFs inducing M2 polarization and MDK-SDC4 interactions promoting Treg migration. These findings identify candidate biomarkers (e.g., TIMP1, SPP1⁺ CAFs) and potential therapeutic targets (e.g., IL1R1⁺ iCAFs, MDK-SDC4 axis) with clinical relevance. This review summarizes recent advances in the application of these integrated technologies for CRC research, discusses their prospects and challenges in characterizing tumors and advancing precision diagnostics and therapeutics, and presents a theoretical framework to guide future research and clinical practice in the study and treatment of CRC.