Identification of ST3GAL1 as a prognostic sialyltransferase in pancreatic cancer with involvement in CA19-9 synthesis by integrative multiomics analysis

Abstract Objective: Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive malignancy with distinct tumor biology that drives rapid progression and poor therapeutic response. A prominent feature of PDAC is abnormal glycosylation, especially hypersialylation, which involves excessive sialic acid expression and contributes to tumor growth and immune evasion. Sialyltransferases (STs) mediate hypersialylation; however, the specific enzymes involved in PDAC progression remain unclear. This study aims to identify and characterize key sialyltransferases in PDAC. Methods: We integrated RNA sequencing data and clinical information from PDAC patients obtained from The Cancer Genome Atlas and Genotype-Tissue Expression databases databases. A six-gene prognostic model based on STs expression was developed using Least Absolute Shrinkage and Selection Operator regression and validated across independent PDAC cohorts. Bioinformatic analyses evaluated associations between ST expression and survival outcomes, immune infiltration, immune checkpoint expression, tumor mutational burden, and drug sensitivity. Single-cell RNA sequencing and multiplex immunofluorescence (mIHC) were employed to investigate interactions between ST-expressing tumor cells and immune cells. Functional validation was performed thourgh in vitro knockdown experiments to assess the effects of key ST on carbohydrate antigen (CA)19-9 synthesis in PDAC cells. Results: The STs-based prognostic model showed strong predictive power (area under the curve=0.797), with β-galactoside α-2,3-sialyltransferase 1 (ST3GAL1) contributing most significantly. ST3GAL1 was markedly overexpressed in PDAC compared to normal tissue and was associated with worse overall survival (hazard ratio: 1.45, P <0.001, 95% confidence interval: 1.21–1.75). High ST3GAL1 expression was linked to an immunosuppressive tumor microenvironment characterized by reduced CD8 + T cells, elevated neutrophil infiltration, and increased M2 macrophages. Single-cell analysis and mIHC confirmed a positive correlation between ST3GAL1 + tumor cells and neutrophil infiltration. Notably, ST3GAL1-driven α2,3-sialylation was critical for CA19-9 biosynthesis. Knockdown of ST3GAL1 in PDAC cell lines significantly decreased CA19-9 expression, highlighting its critical role in generating this key tumor biomarker Additionly, ST3GAL1 knockdown predominantly reduced CA19-9 expression and suppressed proliferation and migration in vivo and in vitro . Conclusion: Our integrative analysis highlights ST3GAL1 as a potential key prognostic ST in PDAC, associated with both an immunosuppressive tumor microenvironment and CA19-9 production.