A Novel Prognostic Signature Composed of Autophagy and Liver Metastasis in Colorectal Cancer: Comprehensive Analysis of Bulk and Single-Cell Transcriptomic Data

Background: Colorectal cancer (CRC) is a highly aggressive malignancy prone to liver metastasis, which significantly worsens prognosis of patients. Autophagy supports tumor cell survival by meeting metabolic demands and evading programmed cell death. This study aimed to develop a prognostic risk signature for CRC patients by integrating autophagy- and metastasis-related genes and to investigate its association with the tumor immune microenvironment and implications for immunotherapy. Methods: Weighted gene co-expression network analysis (WGCNA) identified candidate genes related to autophagy and liver metastasis. Univariate Cox and LASSO regression analyses were employed to develop a risk signature in the TCGA cohort, which was subsequently validated using an independent GEO cohort. Functional enrichment, immune infiltration, the heterogeneity and dynamics of macrophages and CD8+ T cells, and cell–cell communication were analyzed. The expression patterns of key genes were confirmed through Western blotting and immunohistochemistry. Results: A prognostic risk signature incorporating six biomarkers ( SPP1 , JCHAIN , DNASE1L3 , SNAI1 , TPM1 , and FKBP10 ) was developed and confirmed. The risk signature was an independent prognosticator and outperformed traditional prognostic factors. The patients in high-risk group exhibited heightened Tumor Immune Dysfunction and Exclusion (TIDE) scores, indicating a potential for immunotherapy resistance. Furthermore, enhanced autophagy and metastatic activity were accompanied by differentiation of macrophages toward an SPP1+ M2-like phenotype and of CD8+ T cells toward an exhausted state. Experimental validation confirmed that SPP1 , SNAI1 , and FKBP10 were highly expressed in CRC tissues. Conclusion: In our study, we developed and validated a novel autophagy- and liver metastasis-associated prognostic signature for CRC. The risk signature effectively predicts alterations in the tumor immune microenvironment, immunotherapy, chemotherapy sensitivity and intercellular communication across different risk groups. Importantly, our findings reveal that autophagy and liver metastasis synergistically foster an immunosuppressive microenvironment, highlighting a potential target for therapeutic intervention. Keywords: colorectal cancer, autophagy, liver metastasis, tumor immune microenvironment, cell-cell communication