Integrated single-cell and bulk transcriptomics identify autophagy-related immune-suppressive subtypes and a prognostic signature in colorectal cancer

Background Colorectal cancer still causes many cancer deaths, and patient outcomes differ a lot. The tumor microenvironment can shape tumor growth and treatment response. Autophagy is a cell recycling process linked to tumor survival and immune control, but its cell-type pattern in colorectal cancer tissue and its clinical meaning are not clear. We mapped autophagy activity across cell types, defined autophagy-based subtypes, and tested their value for risk stratification. Methods Single-cell RNA sequencing data from colorectal cancer tumor tissues were integrated to evaluate autophagy activity across malignant, stromal, and immune cell populations. Subsequently, autophagy-related genes were curated from multiple public databases and analyzed in bulk transcriptomic cohorts obtained from The Cancer Genome Atlas and The Gene Expression Omnibus. Additionally, unsupervised consensus clustering was applied to define autophagy-based molecular subtypes. Multiple machine learning algorithms were evaluated to construct an autophagy-related prognostic model, and feature importance was assessed using explainable modeling approaches. Furthermore, immune microenvironment characteristics, genomic alterations, and stemness features were systematically analyzed. Key genes were further validated in clinical colorectal cancer specimens and through in vitro functional experiments. Results Autophagy activity varied across the tumor microenvironment. Malignant and stromal cells showed higher autophagy levels than immune cells. High-autophagy tumors showed stronger tumor–stroma interactions, weaker immune communication, and an immune-suppressive microenvironment. Using 47 prognostic autophagy-related genes, we identified four subtypes with different overall survival, genomic alteration patterns, stemness signatures, and immune landscapes. The prognostic model performed well across independent cohorts. GOLGA2 (Golgi autoantigen, golgin subfamily A member 2) was the top risk gene and was upregulated in tumor tissues. Functional assays showed that GOLGA2 promotes HCT116 cell proliferation and migration. Conclusion Autophagy is closely tied to an immune-suppressive tumor microenvironment in colorectal cancer. The autophagy-based subtypes and prognostic model support patient risk stratification. Furthermore, GOLGA2 was a top-ranked gene in the signature and showed tumor-promoting effects in vitro , so it may warrant further study as a potential target.