Abstract
BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) remains a highly aggressive malignancy with a complex tumor microenvironment. Although the class-3 semaphorin (SEMA3) gene family has been implicated in tumor progression and immune regulation, its specific role and clinical relevance in PDAC are not yet fully understood. METHODS: Multi-omics data from public cohorts (TCGA and GEO) were integrated to perform unsupervised clustering based on SEMA3 family expression. A prognostic risk model was constructed using univariate Cox and LASSO regression, and validated in an independent cohort. Immune infiltration, mutation profiling, and drug sensitivity analyses were conducted. Single-cell and spatial transcriptomic data were used to characterize the expression and spatial distribution of SEMA3 genes at cellular resolution. RESULTS: Two molecular subtypes with distinct survival outcomes were identified. A nine-gene prognostic signature was established, effectively stratifying patients into high- and low-risk groups with significant survival differences. High-risk patients exhibited an immunosuppressive microenvironment, higher tumor mutational burden, and increased KRAS mutation frequency. Drug sensitivity analysis revealed subtype-specific therapeutic vulnerabilities. Single-cell and spatial transcriptomic analyses revealed that SEMA3 family genes modulate immune cell infiltration and spatial immune heterogeneity within the tumor microenvironment. Single-cell and spatial transcriptomics highlighted SEMA3C as a key mediator highly expressed in malignant and stromal cells, with spatially restricted patterns suggesting its role in modulating cell-cell communication and immune evasion. CONCLUSION: This study underscores the prognostic and immunological significance of SEMA3 family genes in PDAC. The developed risk model and nomogram demonstrate robust predictive ability, while SEMA3C emerges as a promising therapeutic target. Our findings provide insights into the heterogeneity of PDAC and support the development of personalized treatment strategies.