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A methylation functional detection hepatic cell system validates correlation between DNA methylation and drug-induced liver injury


Drug-induced liver injury (DILI) is a life-threatening, adverse reaction to certain drugs. The onset and extent of DILI can vary drastically in different patients using identical drugs. Association studies suggested that subtle differences in DNA methylation may help explain the individual differences in DILI. However, there are very few experimental methods to confirm such associations. In this study, we established a novel DNA methylation functional detection system in human hepatocytes, using CRISPR/dCas9 for targeted modification of DNA methylation, and set four parameters to indicate the liver injury by cell model. Using this system, we validated the association of hypermethylation of CYP2D6 and CYP2E1 with rifampin-induced DILI. Our results revealed that, following treatment of HepaRG cells with rifampin, the methylation levels of CYP2D6 and CYP2E1 were inversely proportional to cell viability and glutathione content, and directly proportional to caspase 3/7 activity. We expect that our methylation detection system will serve as a useful tool in validating correlations between DNA methylation and DILI in other in vitro systems. Our results establish a foundation for future investigations to better understand the mechanisms underlying DILI and may aid in advancing personalized DILI medicine.

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Fig. 1: Flow chart of the construction of the functional DNA methylation detection system in human hepatic cells.
Fig. 2
Fig. 3: MS-HRM analysis of modified HepaRG cells.
Fig. 4: Representative data from the mu0ltiparametric assay in which HepaRG-D cells were treated with rifampin.
Fig. 5: Representative data from the multiparametric assay in which HepaRG-M cells were treated with rifampin.


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This work was supported by grants from the National Nature Science Foundation of China (81773818, 81273596, 30900799, and 81671326), the 863 Program (2012AA02A515, 2012AA021802), National Key Research and Development Program (2016YFC0905000, 2016YFC0905002, 2016YFC1200200, and 2016YFC0906400), the 4th Three-year Action Plan for Public Health of Shanghai (15GWZK0101), Shanghai Pujiang Program (17PJD020), Shanghai Key Laboratory of Psychotic Disorders (13dz2260500), and China Postdoctoral Science Foundation (2017M621450).

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YW and CZ conducted the experiments and drafted the paper. YG, WZ, and MW assisted in experiments and data analysis. CL helped to polish the paper. CH and SQ designed the study. All authors reviewed and approved the paper.

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Correspondence to Shengying Qin.

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Wei, Y., Huai, C., Zhou, C. et al. A methylation functional detection hepatic cell system validates correlation between DNA methylation and drug-induced liver injury. Pharmacogenomics J 20, 717–723 (2020).

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