Genetic variation in the 3′-UTR of CYP1A2, CYP2B6, CYP2D6, CYP3A4, NR1I2 , and UGT2B7 : Potential effects on regulation by microRNA and pharmacogenomics relevance

Frontiers in Genetics

Volumn 5, Issue JUN, 2014, Pages

  Swart, Marelize ^a   Dandara, Collet ^a  

^a UNIVERSITY OF CAPE TOWN   (South Africa)

Author keywords

Bioinformatics prediction; Drug metabolizing enzymes; microRNA; miRSNPs; Pharmacogenomics; Polymorphisms

Indexed keywords

CYTOCHROME P450 1A2; CYTOCHROME P450 2B6; CYTOCHROME P450 2D6; CYTOCHROME P450 3A4; EFAVIRENZ; GLUCURONOSYLTRANSFERASE 2B7; MICRORNA; MICRORNA 1250-5P; MICRORNA 142-3P; MICRORNA 148B; MICRORNA 152; MICRORNA 216A; MICRORNA 371B-3P; MICRORNA 4258; MICRORNA 4707-3P; MICRORNA 508-5P; MICRORNA 510; MICRORNA 514; MICRORNA 548A; MICRORNA 548A-3P; MICRORNA 548A-5P; MICRORNA 548B-5P; MICRORNA 548C-5P; MICRORNA 548D-5P; MICRORNA 548H; MICRORNA 548I; MICRORNA 548J; MICRORNA 608; MICRORNA 671-5P; UNCLASSIFIED DRUG; UNINDEXED DRUG;

3' UNTRANSLATED REGION; ADULT; ALGORITHM; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPUTER MODEL; DNA ISOLATION; DNA SEQUENCE; FEMALE; GENE; GENE FREQUENCY; GENE TARGETING; GENETIC VARIABILITY; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; NR1I2 GENE; PHARMACOGENETICS; PHARMACOGENOMICS; POLYMERASE CHAIN REACTION; PREDICTION; RNA INTERFERENCE;

EID: 84906279761     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00167     Document Type: Article

References (72)

1. Alnouti, Y., and Klaassen, C. D. (2008). Regulation of sulfotransferase enzymes by prototypical microsomal enzyme inducers in mice. J. Pharmacol. Exp. Ther . 324, 612-621. doi: 10.1124/jpet.107.129650
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). Basic local alignment search tool. J. Mol. Biol . 215, 403-410. doi: 10.1016/S0022-2836(05)80360-2
3. Armstrong, S. C., and Cozza, K. L. (2003). Pharmacokinetic drug interactions of morphine, codeine, and their derivatives: theory and clinical reality, Part II. Psychosomatics 44, 515-520. doi: 10.1176/appi.psy.44.6.515
4. Baek, D., Villen, J., Shin, C., Camargo, F. D., Gygi, S. P., and Bartel, D. P. (2008). The impact of microRNAs on protein output. Nature 455, 64-71. doi: 10.1038/nature07242
5. Bao, L., Zhou, M., Wu, L., Lu, L., Goldowitz, D., Williams, R. W., et al. (2007). PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. Nucleic Acids Res . 35, D51-D54. doi: 10.1093/nar/gkl797
6. Batt, A. M., Magdalou, J., Vincent-Viry, M., Ouzzine, M., Fournel-Gigleux, S., Galteau, M. M., et al. (1994). Drug metabolizing enzymes related to laboratory medicine: cytochromes P-450 and UDP-glucuronosyltransferases. Clin. Chim. Acta 226, 171-190. doi: 10.1016/0009-8981(94)90214-3
7. Bhattacharya, A., Ziebarth, J. D., and Cui, Y. (2014). PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res . 42, D86-D91. doi: 10.1093/nar/gkt1028
8. Breving, K., and Esquela-Kerscher, A. (2010). The complexities of microRNA regulation: mirandering around the rules. Int. J. Biochem. Cell Biol . 42, 1316-1329. doi: 10.1016/j.biocel.2009.09.016
9. Ciccacci, C., Di Fusco, D., Marazzi, M. C., Zimba, I., Erba, F., Novelli, G., et al. (2013). Association between CYP2B6 polymorphisms and Nevirapine-induced SJS/TEN: a pharmacogenetics study. Eur. J. Clin. Pharmacol . 69, 1909-1916. doi: 10.1007/s00228-013-1549-x
10. Commandeur, J. N., Stijntjes, G. J., and Vermeulen, N. P. (1995). Enzymes and transport systems involved in the formation and disposition of glutathione S-conjugates. Role in bioactivation and detoxication mechanisms of xenobiotics. Pharmacol. Rev . 47, 271-330.
11. Dandara, C., Swart, M., Mpeta, B., Wonkam, A., and Masimirembwa, C. (2014). Cytochrome P450 pharmacogenetics in African populations: implications for public health. Expert Opin. Drug Metab. Toxicol . 10, 769-785. doi: 10.1517/17425255.2014.894020
12. Deveci, M., Catalyurek, U. V., and Toland, A. E. (2014). mrSNP: software to detect SNP effects on microRNA binding. BMC Bioinformatics 15:73. doi: 10.1186/1471-2105-15-73
13. Dluzen, D. F., Sun, D., Salzberg, A. C., Jones, N., Bushey, R. T., Robertson, G. P., et al. (2014). Regulation of UDP-glucuronosyltransferase 1A1 expression and activity by microRNA 491-3p. J. Pharmacol. Exp. Ther . 348, 465-477. doi: 10.1124/jpet.113.210658
14. Gennarino, V. A., Sardiello, M., Avellino, R., Meola, N., Maselli, V., Anand, S., et al. (2009). MicroRNA target prediction by expression analysis of host genes. Genome Res . 19, 481-490. doi: 10.1101/gr.084129.108
15. Griffiths-Jones, S., Grocock, R. J., Van Dongen, S., Bateman, A., and Enright, A. J. (2006). miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res . 34, D140-D144. doi: 10.1093/nar/gkj112
16. Grimson, A., Farh, K. K., Johnston, W. K., Garrett-Engele, P., Lim, L. P., and Bartel, D. P. (2007). MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol. Cell 27, 91-105. doi: 10.1016/j.molcel.2007.06.017
17. Guengerich, F. P. (2008). Cytochrome p450 and chemical toxicology. Chem. Res. Toxicol . 21, 70-83. doi: 10.1021/tx700079z
18. Gustafson, S., Proper, J. A., Bowie, E. J., and Sommer, S. S. (1987). Parameters affecting the yield of DNA from human blood. Anal. Biochem . 165, 294-299. doi: 10.1016/0003-2697(87)90272-7
19. Hayes, J. D., Flanagan, J. U., and Jowsey, I. R. (2005). Glutathione transferases. Annu. Rev. Pharmacol. Toxicol . 45, 51-88. doi: 10.1146/annurev.pharmtox.45.120403.095857
20. Hsu, J. B., Chiu, C. M., Hsu, S. D., Huang, W. Y., Chien, C. H., Lee, T. Y., et al. (2011). miRTar: an integrated system for identifying miRNA-target interactions in human. BMC Bioinformatics 12:300. doi: 10.1186/1471-2105-12-300
21. Huang, H. Y., Chien, C. H., Jen, K. H., and Huang, H. D. (2006). RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res . 34, W429-W434. doi: 10.1093/nar/gkl333
22. Hummel, R., Wang, T., Watson, D. I., Michael, M. Z., Van Der Hoek, M., Haier, J., et al. (2011). Chemotherapy-induced modification of microRNA expression in esophageal cancer. Oncol. Rep . 26, 1011-1017. doi: 10.3892/or.2011.1381
23. Ingelman-Sundberg, M., Sim, S. C., Gomez, A., and Rodriguez-Antona, C. (2007). Influence of cytochrome P450 polymorphisms on drug therapies: pharmacogenetic, pharmacoepigenetic and clinical aspects. Pharmacol. Ther . 116, 496-526. doi: 10.1016/j.pharmthera.2007.09.004
24. John, B., Enright, A. J., Aravin, A., Tuschl, T., Sander, C., and Marks, D. S. (2004). Human microRNA targets. PLoS Biol . 2:e363. doi: 10.1371/journal.pbio.0020363
25. Kertesz, M., Iovino, N., Unnerstall, U., Gaul, U., and Segal, E. (2007). The role of site accessibility in microRNA target recognition. Nat. Genet . 39, 1278-1284. doi: 10.1038/ng2135
26. Krek, A., Grun, D., Poy, M. N., Wolf, R., Rosenberg, L., Epstein, E. J., et al. (2005). Combinatorial microRNA target predictions. Nat. Genet . 37, 495-500. doi: 10.1038/ng1536
27. Lagos-Quintana, M., Rauhut, R., Lendeckel, W., and Tuschl, T. (2001). Identification of novel genes coding for small expressed RNAs. Science 294, 853-858. doi: 10.1126/science.1064921
28. Lewis, B. P., Shih, I. H., Jones-Rhoades, M. W., Bartel, D. P., and Burge, C. B. (2003). Prediction of mammalian microRNA targets. Cell 115, 787-798. doi: 10.1016/S0092-8674(03)01018-3
29. Liu, C., Zhang, F., Li, T., Lu, M., Wang, L., Yue, W., et al. (2012). MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs. BMC Genomics 13:661. doi: 10.1186/1471-2164-13-661
30. Lu, T. P., Lee, C. Y., Tsai, M. H., Chiu, Y. C., Hsiao, C. K., Lai, L. C., et al. (2012). miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PLoS ONE 7:e42390. doi: 10.1371/journal.pone.0042390
31. Maragkakis, M., Reczko, M., Simossis, V. A., Alexiou, P., Papadopoulos, G. L., Dalamagas, T., et al. (2009). DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res . 37, W273-W276. doi: 10.1093/nar/gkp292
32. Marin, R. M., and Vanicek, J. (2012). Optimal use of conservation and accessibility filters in microRNA target prediction. PLoS ONE 7:e32208. doi: 10.1371/journal.pone.0032208
33. Marzolini, C., Telenti, A., Decosterd, L. A., Greub, G., Biollaz, J., and Buclin, T. (2001). Efavirenz plasma levels can predict treatment failure and central nervous system side effects in HIV-1-infected patients. AIDS 15, 71-75. doi: 10.1097/00002030-200101050-00011
34. Matimba, A., Del-Favero, J., Van Broeckhoven, C., and Masimirembwa, C. (2009). Novel variants of major drug-metabolising enzyme genes in diverse African populations and their predicted functional effects. Hum. Genomics 3, 169-190. doi: 10.1186/1479-7364-3-2-169
35. McCarver, D. G., and Hines, R. N. (2002). The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms. J. Pharmacol. Exp. Ther . 300, 361-366. doi: 10.1124/jpet.300.2.361
36. Miranda, K. C., Huynh, T., Tay, Y., Ang, Y. S., Tam, W. L., Thomson, A. M., et al. (2006). A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell 126, 1203-1217. doi: 10.1016/j.cell.2006.07.031
37. Mishra, P. J. (2012). The miRNA-drug resistance connection: a new era of personalized medicine using noncoding RNA begins. Pharmacogenomics 13, 1321-1324. doi: 10.2217/pgs.12.121
38. Mishra, P. J., and Bertino, J. R. (2009). MicroRNA polymorphisms: the future of pharmacogenomics, molecular epidemiology and individualized medicine. Pharmacogenomics 10, 399-416. doi: 10.2217/14622416.10.3.399
39. Mishra, P. J., Humeniuk, R., Mishra, P. J., Longo-Sorbello, G. S., Banerjee, D., and Bertino, J. R. (2007). A miR-24 microRNA binding-site polymorphism in dihydrofolate reductase gene leads to methotrexate resistance. Proc. Natl. Acad. Sci. U.S.A . 104, 13513-13518. doi: 10.1073/pnas.0706217104
40. Mishra, P. J., Mishra, P. J., Banerjee, D., and Bertino, J. R. (2008). MiRSNPs or MiR-polymorphisms, new players in microRNA mediated regulation of the cell: introducing microRNA pharmacogenomics. Cell Cycle 7, 853-858. doi: 10.4161/cc.7.7.5666
41. Mohri, T., Nakajima, M., Fukami, T., Takamiya, M., Aoki, Y., and Yokoi, T. (2010). Human CYP2E1 is regulated by miR-378. Biochem. Pharmacol . 79, 1045-1052. doi: 10.1016/j.bcp.2009.11.015
42. Pan, Y. Z., Gao, W., and Yu, A. M. (2009). MicroRNAs regulate CYP3A4 expression via direct and indirect targeting. Drug Metab. Dispos . 37, 2112-2117. doi: 10.1124/dmd.109.027680
43. Petzinger, E., and Geyer, J. (2006). Drug transporters in pharmacokinetics. Naunyn Schmiedebergs Arch. Pharmacol . 372, 465-475. doi: 10.1007/s00210-006-0042-9
44. Qiu, C., Wang, J., and Cui, Q. (2011). miR2Gene: pattern discovery of single gene, multiple genes, and pathways by enrichment analysis of their microRNA regulators. BMC Syst. Biol . 5(Suppl. 2):S9. doi: 10.1186/1752-0509-5-S2-S9
45. Ramamoorthy, A., Liu, Y., Philips, S., Desta, Z., Lin, H., Goswami, C., et al. (2013). Regulation of microRNA expression by rifampin in human hepatocytes. Drug Metab. Dispos . 41, 1763-1768. doi: 10.1124/dmd.113.052886
46. Ramamoorthy, A., and Skaar, T. C. (2011). In silico identification of microRNAs predicted to regulate the drug metabolizing cytochrome P450 genes. Drug Metab. Lett . 5, 126-131. doi: 10.2174/187231211795305258
47. Ritchie, W., Flamant, S., and Rasko, J. E. (2010). mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets. Bioinformatics 26, 223-227. doi: 10.1093/bioinformatics/btp649
48. Rodrigues, A. C., Li, X., Radecki, L., Pan, Y. Z., Winter, J. C., Huang, M., et al. (2011). MicroRNA expression is differentially altered by xenobiotic drugs in different human cell lines. Biopharm. Drug Dispos . 32, 355-367. doi: 10.1002/bdd.764
49. Shomron, N. (2010). MicroRNAs and pharmacogenomics. Pharmacogenomics 11, 629-632. doi: 10.2217/pgs.10.26
50. Singh, D., Kashyap, A., Pandey, R. V., and Saini, K. S. (2011). Novel advances in cytochrome P450 research. Drug Discov. Today 16, 793-799. doi: 10.1016/j.drudis.2011.08.003
51. Sturm, M., Hackenberg, M., Langenberger, D., and Frishman, D. (2010). TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics 11:292. doi: 10.1186/1471-2105-11-292
52. Swart, M., Ren, Y., Smith, P., and Dandara, C. (2012a). ABCB1 4036A>G and 1236C>T polymorphisms affect plasma efavirenz levels in South African HIV/AIDS patients. Front. Genet . 3:236. doi: 10.3389/fgene.2012.00236
53. Swart, M., Skelton, M., Ren, Y., Smith, P., Takuva, S., and Dandara, C. (2013). High predictive value of CYP2B6 SNPs for steady-state plasma efavirenz levels in South African HIV/AIDS patients. Pharmacogenet. Genomics 23, 415-427. doi: 10.1097/FPC.0b013e328363176f
54. Swart, M., Skelton, M., Wonkam, A., Kannemeyer, L., Chin'ombe, N., and Dandara, C. (2012b). CYP1A2, CYP2A6, CYP2B6, CYP3A4 and CYP3A5 polymorphisms in two bantu-speaking populations from Cameroon and South Africa: implications for global pharmacogenetics. Curr. Pharmacogenomics Person. Med . 10, 43-53. doi: 10.2174/1875692111201010043
55. Swart, M., Whitehorn, H., Ren, Y., Smith, P., Ramesar, R. S., and Dandara, C. (2012c). PXR and CAR single nucleotide polymorphisms influence plasma efavirenz levels in South African HIV/AIDS patients. BMC Med. Genet . 13:112. doi: 10.1186/1471-2350-13-112
56. Takagi, S., Nakajima, M., Mohri, T., and Yokoi, T. (2008). Post-transcriptional regulation of human pregnane X receptor by micro-RNA affects the expression of cytochrome P450 3A4. J. Biol. Chem . 283, 9674-9680. doi: 10.1074/jbc.M709382200
57. Tsang, J. S., Ebert, M. S., and Van Oudenaarden, A. (2010). Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. Mol. Cell 38, 140-153. doi: 10.1016/j.molcel.2010.03.007
58. Tsuchiya, Y., Nakajima, M., Takagi, S., Taniya, T., and Yokoi, T. (2006). MicroRNA regulates the expression of human cytochrome P450 1B1. Cancer Res . 66, 9090-9098. doi: 10.1158/0008-5472.CAN-06-1403
59. Tukey, R. H., and Strassburg, C. P. (2000). Human UDP-glucuronosyltransferases: metabolism, expression, and disease. Annu. Rev. Pharmacol. Toxicol . 40, 581-616. doi: 10.1146/annurev.pharmtox.40.1.581
60. Van Rooij, E., Purcell, A. L., and Levin, A. A. (2012). Developing microRNA therapeutics. Circ. Res . 110, 496-507. doi: 10.1161/CIRCRESAHA.111.247916
61. Vardhanabhuti, S., Acosta, E. P., Ribaudo, H. J., Severe, P., Lalloo, U., Kumarasamy, N., et al. (2013). Clinical and genetic determinants of plasma nevirapine exposure following an intrapartum dose to prevent mother-to-child HIV transmission. J. Infect. Dis . 208, 662-671. doi: 10.1093/infdis/jit223
62. Vlachos, I. S., Kostoulas, N., Vergoulis, T., Georgakilas, G., Reczko, M., Maragkakis, M., et al. (2012). DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res . 40, W498-W504. doi: 10.1093/nar/gks494
63. Warnich, L., Drogemoller, B. I., Pepper, M. S., Dandara, C., and Wright, G. E. (2011). Pharmacogenomic research in South Africa: lessons learned and future opportunities in the rainbow nation. Curr. Pharmacogenomics Person. Med . 9, 191-207. doi: 10.2174/187569211796957575
64. Welsh, M., Mangravite, L., Medina, M. W., Tantisira, K., Zhang, W., Huang, R. S., et al. (2009). Pharmacogenomic discovery using cell-based models. Pharmacol. Rev . 61, 413-429. doi: 10.1124/pr.109.001461
65. Witkos, T. M., Koscianska, E., and Krzyzosiak, W. J. (2011). Practical aspects of microRNA target prediction. Curr. Mol. Med . 11, 93-109. doi: 10.2174/156652411794859250
66. Xu, C., Li, C. Y., and Kong, A. N. (2005). Induction of phase I, II and III drug metabolism/transport by xenobiotics. Arch. Pharm. Res . 28, 249-268. doi: 10.1007/BF02977789
67. Yu, A. M. (2009). Role of microRNAs in the regulation of drug metabolism and disposition. Expert Opin. Drug Metab. Toxicol . 5, 1513-1528. doi: 10.1517/17425250903307448
68. Yu, X., Dhakal, I. B., Beggs, M., Edavana, V. K., Williams, S., Zhang, X., et al. (2010). Functional genetic variants in the 3′-untranslated region of sulfotransferase isoform 1A1 (SULT1A1) and their effect on enzymatic activity. Toxicol. Sci . 118, 391-403. doi: 10.1093/toxsci/kfq296
69. Zhang, G., Wang, Q., and Xu, R. (2010). Therapeutics based on microRNA: a new approach for liver cancer. Curr. Genomics 11, 311-325. doi: 10.2174/138920210791616671
70. Zhang, W., and Dolan, M. E. (2010). The emerging role of microRNAs in drug responses. Curr. Opin. Mol. Ther . 12, 695-702.
71. Zhang, Y., and Verbeek, F. J. (2010). Comparison and integration of target prediction algorithms for microRNA studies. J. Integr. Bioinform . 7. doi: 10.2390/biecoll-jib-2010-127
72. Ziebarth, J. D., Bhattacharya, A., Chen, A., and Cui, Y. (2012). PolymiRTS Database 2.0: linking polymorphisms in microRNA target sites with human diseases and complex traits. Nucleic Acids Res . 40, D216-D221. doi: 10.1093/nar/gkr1026