In Vitro Functional Characterization and in Silico Prediction of Rare Genetic Variation in the Bile Acid and Drug Transporter, Na+-Taurocholate Cotransporting Polypeptide (NTCP, SLC10A1).

Na+-taurocholate cotransporting polypeptide (NTCP, SLC10A1) is a key hepatic uptake transporter for bile acids and drugs and is the main functional receptor for hepatitis B and D viruses. Next-generation sequencing has revealed that a large number of rare SLC10A1 variants exist in the population. Little data exist regarding head-to-head comparison of in silico algorithms to predict functional effects of pharmacogenetic variants when compared to direct in vitro functional assessment. This study aimed at characterizing rare SLC10A1 variants in vitro and to assess the performance of seven in silico algorithms to predict the observed functional impacts. Thirty-five previously uncharacterized, rare, missense SLC10A1 variants were transiently expressed in human embryonic kidney 293 type T (HEK293T) cells. NCTP protein expression as well as uptake of substrates taurocholic acid (TCA) and rosuvastatin were assessed. Substrate-specific effects were observed for NTCP G191R, with TCA and rosuvastatin transport observed at 89 and 8% of wild-type (WT) uptake, respectively. Significantly reduced transport of TCA and rosuvastatin was observed for 19 variants (p < 0.05), with seven variants displaying decreased protein expression and marked reduction in transport of both substrates (0-13% of WT uptake, p < 0.0001). Performance of in silico algorithms to predict in vitro uptake, assessed using the area under the receiver operating characteristic curves (AUCROC), ranged from 0.69 to 0.97 and 0.72 to 0.84 for TCA and rosuvastatin uptake, respectively. In conclusion, we identified rare variants with significantly reduced NTCP expression and function. We demonstrated that no algorithm performed robustly enough to replace functional study in vitro, particularly given the broad substrate specificity of many pharmacogenes.