A bioinformatic and cell-based study on the mutation and regulation of human nuclear receptors and their target genes
Creators: name: Liu, Ya
Publisher: name: RMIT University
Year: 2024

description: Human nuclear receptor (NR) superfamily represents an important group of regulating factors of a large number of physiologically important target genes. In this project, we hypothesized that the phenotype of non-synonymous single nucleotide polymorphisms (nsSNPs) of <i>NRs</i> and their target genes could be predicted using computational approaches and that herbal compounds regulated CYP3A4 via pregnane X receptor (PXR) mediated pathway. To test this hypothesis: <br><br>Firstly, we employed SIFT and PolyPhen to predict the impact of 442 nsSNPs in 48 human <i>NR</i> genes on NR activities and disease susceptibility. Of 442 nsSNPs, 289 (65.38%) were classified as “intolerant” by SIFT and 269 (60.86%) were classified as “probably damaging” or “possibly damaging” by PolyPhen respectively. The results from the two algorithms were in concordance. Among the 442 mutations, 229 of them have been functionally characterized. SIFT gave a correct prediction rate of 83.84%, while PolyPhen gave a prediction rate of 76.86%. These results indicate that both SIFT and PolyPhen are useful and efficient tools to predict the functional effects of nsSNPs of human <i>NR</i> genes.<br><br>Secondly, we predict the phenotypical impact of 1632 nsSNPs from human ABC transporter genes. Using the PolyPhen and SIFT, 41.8-53.6% of nsSNPs in ABC transporter genes were predicted to have an impact on protein function. The prediction accuracy was up to 63-85% when compared with known phenotypical data. Of nsSNPs predicted as deleterious, the prediction scores by SIFT and PolyPhen were significantly related to the number of nsSNPs with known phenotypes confirmed by experimental and human studies. <br><br>Finally, we investigated the effect of an array of compounds isolated from commonly used Chinese herbal medicines on the activity of PXR in transiently transfected HepG2 and Huh7 cells and on the expression of <i>PXR</i> and <i>CYP3A4</i> in human intestinal LS174T cells. The study found that praeruptorin A and C, salvianolic acid B, sodium danshensu, and protocatechuic aldehyde, cryptotanshinone, emodin, morin, and tanshinone IIA significantly transactivated the <i>CYP3A4 </i>reporter gene construct in HepG2 cells or Huh7 cells. The <i>PXR </i>mRNA expression in LS174T cells was significantly induced by physcion, protocatechuic aldehyde, salvianolic acid B, and sodium danshensu. However, epifriedelanol, morin, praeruptorin D, mulberroside A, tanshinone I, and tanshinone IIA significantly down-regulated the expression of <i>PXR</i> mRNA in LS174T cells. Furthermore, emodin, physcion, praeruptorin C and E, protocatechuic aldehyde, rhein, salvianolic acid B, and sodium danshensu significantly induced <i>CYP3A4 </i>mRNA expression in human intestinal LS174T cells.<br><br>These findings suggest that: a) predicting the phenotypic consequence of nsSNPs in human NRs and their target genes ABC transporters using computational algorithms may provide further understanding of genetic differences in susceptibility to diseases and drug response and would be useful hints for further genotype-phenotype studies; and b) herbal medicines can significantly regulate <i>PXR </i>and its target gene <i>CYP3A4</i> and this has important implication in herb-drug interactions. Further benchmarking studies are warranted to verify our prediction data for <i>NRs</i> and their target genes ABC transporters and to explore the clinical impact of herb-CYP interactions via the PXR-mediated pathway.<br>