Integrated analysis of rifampicin-induced MicroRNA and gene expression changes in human hepatocytes

Drug Metabolism and Pharmacokinetics

Volumn 29, Issue 4, 2014, Pages 333-340

  Takahashi, Kei ^a   Tatsumi, Naoyuki ^a   Fukami, Tatsuki ^a   Yokoi, Tsuyoshi ^a   Nakajima, Miki ^a  

^a KANAZAWA UNIVERSITY   (Japan)

Author keywords

Cytochrome P450; Human liver; Induction; Post transcriptional regulation; Pregnane X receptor

Indexed keywords

CYTOCHROME P450; MICRORNA; MICRORNA 143; MICRORNA 145; MICRORNA 148B; MICRORNA 15B; MICRORNA 199A 3P; MICRORNA 200A; MICRORNA 202; MICRORNA 204; MICRORNA 20B; MICRORNA 21; MICRORNA 215; MICRORNA 218; MICRORNA 22; MICRORNA 26B; MICRORNA 31; MICRORNA 328; MICRORNA 340; MICRORNA 362 3P; MICRORNA 365; MICRORNA 374B; MICRORNA 539; MICRORNA 576 3P; MICRORNA 590 5P; MICRORNA 886 5P; MICRORNA 95; PREGNANE X RECEPTOR; RIFAMPICIN; UNCLASSIFIED DRUG;

ARTICLE; CONTROLLED STUDY; DOWN REGULATION; DRUG ELIMINATION; DRUG METABOLISM; GENE; GENE EXPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; HUMAN TISSUE; LIVER CELL; MICROARRAY ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; SIGNAL TRANSDUCTION; UPREGULATION; BIOSYNTHESIS; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM;

GENE EXPRESSION REGULATION; HEPATOCYTES; HUMANS; MICRORNAS; RIFAMPIN;

EID: 84901989238     PISSN: 13474367     EISSN: 18800920     Source Type: Journal    
DOI: 10.2133/dmpk.DMPK-13-RG-114     Document Type: Article

References (33)

1. Borchert, G. M., Lanier, W. and Davidson, B. L.: RNA polymerase III transcribes human microRNAs. Nat. Struct. Mol. Biol., 13: 1097-1101 (2006).
2. Hinske, L. C., and Galante., P. A., Kuo, W. P. and Ohno-Machado, L.: A potential role for intragenic miRNAs on their hosts' interactome. BMC Genomics, 11: 533 (2010).
3. Baskerville, S. and Bartel, D. P.: Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA, 11: 241-247 (2005).
4. Davis, B. N., and Hilyard., A. C., Lagna, G. and Hata, A.: SMAD proteins control DROSHA-mediated microRNA maturation. Nature, 454: 56-61 (2008).
5. Heo, I., Joo, C., Cho, J., Ha, M., Han, J. and Kim, V. N.: Lin28 mediates the terminal uridylation of let-7 precursor MicroRNA. Mol. Cell, 32: 276-284 (2008).
6. Havens, M. A., and Reich., A. A., Duelli, D. M. and Hastings, M. L.: Biogenesis of mammalian microRNAs by a non-canonical processing pathway. Nucleic Acids Res., 40: 4626-4640 (2012).
7. Shah, Y. M., Morimura, K., Yang, Q., Tanabe, T., Takagi, M. and Gonzalez, F. J.: Peroxisome proliferator-activated receptor α regulates a microRNA-mediated signaling cascade responsible for hepatocellular proliferation. Mol. Cell. Biol., 27: 4238-4247 (2007).
8. Kuokkanen, S., Chen, B., Ojalvo, L., Benard, L., Santoro, N. and Pollard, J. W.: Genomic profiling of microRNAs and messenger RNAs reveals hormonal regulation in microRNA expression in human endometrium. Biol. Reprod., 82: 791-801 (2010).
9. Lee, J., Padhye, A., Sharma, A., Song, G., Miao, J., Mo, Y. Y., Wang, L. and Kemper, J. K.: A pathway involving farnesoid X receptor and small heterodimer partner positively regulates hepatic sirtuin 1 levels via microRNA-34a inhibition. J. Biol. Chem., 285: 12604-12611 (2010).
10. Smith, L. K., Shah, R. R. and Cidlowski, J. A.: Glucocorticoids modulate microRNA expression and processing during lymphocyte apoptosis. J. Biol. Chem., 285: 36698-36708 (2010).
11. Macias, S., Michlewski, G. and Cáceres, J. F.: Hormonal regulation of microRNA biogenesis. Mol. Cell, 36: 172-173 (2009).
12. Wada, T., Gao, J. and Xie, W.: PXR and CAR in energy metabolism. Trends Endocrinol. Metab., 20: 273-279 (2009).
13. Takagi, S., Nakajima, M., Mohri, T. and Yokoi, T.: Post-transcriptional regulation of human pregnane X receptor by micro-RNA affects the expression of cytochrome P450 3A4. J. Biol. Chem., 283: 9674-9680 (2008).
14. Okumura, H., Katoh, M., Sawada, T., Nakajima, M., Soeno, Y., Yabuuchi, H., Ikeda, T., Tateno, C., Yoshizato, K., et al.: Humanization of excretory pathway in chimeric mice with humanized liver. Toxicol. Sci., 97: 533-538 (2007).
15. Tsuchiya, Y., Nakajima, M., Kyo, S., Kanaya, T., Inoue, M. and Yokoi, T.: Human CYP1B1 is regulated by estradiol via estrogen receptor. Cancer Res., 64: 3119-3125 (2004).
16. Girard, M., Jacquemin, E., Munnich, A., Lyonnet, S. and Henrion-Caude, A.: miR-122, a paradigm for the role of microRNAs in the liver. J. Hepatol., 4: 648-656 (2008).
17. Ambros, V.: The functions of animal microRNAs. Nature, 431: 350-355 (2004).
18. Lim, L. P., and Lau., N. C., Garrett-Engele, P., Grimson, A., and Schelter., J. M., Castle, J., Bartel, D. P., Linsley, P. S. and Johnson, J. M.: Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature, 433: 769-773 (2005).
19. Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R. and Rajewsky, N.: Widespread changes in protein synthesis induced by microRNAs. Nature, 455: 58-63 (2008).
20. Rao, D. S., O'Connell, R. M., Chaudhuri, A. A., Garcia-Flores, Y., Geiger, T. L. and Baltimore, D.: MicroRNA-34a perturbs B lymphocyte development by repressing the forkhead box transcription factor Foxp1. Immunity, 33: 48-59 (2010).
21. Ribas, J., Ni, X., Haffner, M., Wentzel, E. A., and Salmasi., A. H., Chowdhury, W. H., Kudrolli, T. A., Yegnasubramanian, S., Luo, J., et al.: miR-21: an androgen receptor-regulated microRNA that promotes hormone-dependent and hormone-independent prostate cancer growth. Cancer Res., 69: 7165-7169 (2009).
22. Yauk, C. L., Jackson, K., Malowany, M. and Williams, A.: Lack of change in microRNA expression in adult mouse liver following treatment with benzo(a)pyrene despite robust mRNA transcriptional response. Mutat. Res., 722: 131-139 (2011).
23. Li, T. and Chiang, J. Y.: Mechanism of rifampicin and pregnane X receptor inhibition of human cholesterol 7α-hydroxylase gene transcription. Am. J. Physiol. Gastrointest. Liver Physiol., 288: G74-G84 (2005).
24. Kodama, S., Hosseinpour, F., Goldstein, J. A. and Negishi, M.: Liganded pregnane X receptor represses the human sulfotransferase SULT1E1 promoter through disrupting its chromatin structure. Nucleic Acids Res., 39: 8392-8403 (2011).
25. Fukuda, T., Yamagata, K., Fujiyama, S., Matsumoto, T., Koshida, I., Yoshimura, K., Mihara, M., Naitou, M., Endoh, H., et al.: DEAD-box RNA helicase subunits of the Drosha complex are required for processing of rRNA and a subset of microRNAs. Nat. Cell Biol., 9: 604-611 (2007).
26. Suzuki, H. I., Yamagata, K., Sugimoto, K., Iwamoto, T., Kato, S. and Miyazono, K.: Modulation of microRNA processing by p53. Nature, 460: 529-533 (2009).
27. Trabucchi, M., Briata, P., Garcia-Mayoral, M., Haase, A. D., Filipowicz, W., Ramos, A., Gherzi, R. and Rosenfeld, M. G.: The RNA-binding protein KSRP promotes the biogenesis of a subset of microRNAs. Nature, 459: 1010-1014 (2009).
28. Shan, G., Li, Y., Zhang, J., Li, W., and Szulwach., K. E., Duan, R., Faghihi, M. A., Khalil, A. M., Lu, L., et al.: A small molecule enhances RNA interference and promotes microRNA processing. Nat. Biotechnol., 26: 933-940 (2008).
29. Henry, J. C., and Park., J. K., Jiang, J., Kim, J. H., and Nagorney., D. M., Roberts, L. R., Banerjee, S. and Schmittgen, T. D.: miR-199a-3p targets CD44 and reduces proliferation of CD44 positive hepatocellular carcinoma cell lines. Biochem. Biophys. Res. Commun., 403: 120-125 (2010).
30. Simion, A., Laudadio, I., Prévot, P. P., Raynaud, P., Lemaigre, F. P. and Jacquemin, P.: MiR-495 and miR-218 regulate the expression of the Onecut transcription factors HNF-6 and OC-2. Biochem. Biophys. Res. Commun., 391: 293-298 (2010).
31. Cazanave, S. C., and Mott., J. L., Elmi, N. A., Bronk, S. F., and Masuoka., H. C., Charlton, M. R. and Gores, G. J.: A role for miR-296 in the regulation of lipoapoptosis by targeting PUMA. J. Lipid Res., 52: 1517-1525 (2011).
32. Liang, Z., Zhou, H., Zheng, H. and Wu, J.: Expression levels of microRNAs are not associated with their regulatory activities. Biol. Direct, 6: 43 (2011).
33. Ramamoorthy, A., Liu, Y., Philips, S., Desta, Z., Lin, H., Goswami, C., Gaedigk, A., Li, L., Flockhart, D. A., et al.: Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab. Dispos., 41: 1763-1768 (2013).