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Efflux transport is a critical determinant to the pharmacokinetics of sulfate conjugates. Here we aimed to establish SULT1A3 stably transfected HEK293 cells, and to determine the contributions of BCRP and MRP transporters to excretion of chrysin and apigenin sulfates. The cDNA of SULT1A3 was stably introduced into HEK293 cells using a lentiviral vector, generating a sulfonation active cell line (i.e., SULT293 cells). Identification of sulfate transporters was achieved through chemical inhibition (using chemical inhibitors) and biological inhibition (using short-hairpin RNAs (shRNAs)) methods. Sulfated metabolites were rapidly generated and excreted upon incubation of SULT293 cells with chrysin and apigenin. Ko143 (a selective BCRP inhibitor) did not show inhibitory effects on sulfate disposition, whereas the pan-MRP inhibitor MK-571 caused significant reductions (38.5–64.3%, p < 0.001) in sulfate excretion and marked elevations (160–243%, p < 0.05) in sulfate accumulation. Further, two efflux transporters (BCRP and MRP4) expressed in the cells were knocked-down by shRNA-mediated silencing. Neither sulfate excretion nor sulfate accumulation was altered in BCRP knocked-down cells as compared to scramble cells. By contrast, MRP4 knock-down led to moderate decreases (17.1–20.6%, p < 0.05) in sulfate excretion and increases (125–135%, p < 0.05) in sulfate accumulation. In conclusion, MRP4 was identified as an exporter for chrysin and apigenin sulfates. The SULT1A3 modified HEK293 cells were an appropriate tool to study SULT1A3-mediated sulfonation and to characterize BCRP/MRP4-mediated sulfate transport.