Development of a Specific and Sensitive LC-MS/MS Method to Quantify Heparan Sulfate 3-O-Sulfotransferase-1 Activity

Heparan sulfate (HS) is a highly sulfated glycan that regulates diverse biological processes through specific sulfation patterns. Among these, 3-O-sulfation catalyzed by heparan sulfate 3-O-sulfotransferase-1 (3OST-1) is rare but functionally critical, influencing anticoagulation and contributing to the progression of Alzheimer's disease and cancer progression. However, direct measurement of 3OST-1 activity in biological systems has been limited by the lack of sensitive and specific assays. Here we developed a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay using a structurally defined HS hexasaccharide substrate and 13C-labeled internal standards. This method enables nanogram-level detection of 3-O-sulfated products following heparinase digestion and AMAC derivatization. The LC-MS/MS assay demonstrated 100-fold improved sensitivity compared to HPLC and successfully quantified endogenous 3OST-1 activity in HCT-116 cells and conditioned media. Using this assay, we confirmed that the 3OST-1 E86Q mutant acts as a dominant-negative inhibitor. E86Q mutant retains substrate and donor binding but abolishes catalytic activity, reducing wild-type 3OST-1-like activity by >80% in vitro and significantly decreasing 3-O-sulfated HS products in cells without affecting overall HS abundance. This assay provides the first quantitative tool for 3OST-1-like activity and establishes a dominant-negative strategy for functional studies, offering new opportunities for biomarker development and therapeutic targeting in HS-related pathologies.