Regulation of Pharmacogene Expression by microRNA in The Cancer Genome Atlas (TCGA) Research Network |
Han, Nayoung
(College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University)
Song, Yun-Kyoung (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University) Burckart, Gilbert J. (Office of Clinical Pharmacology, Office of Translational Sciences, Food and Drug Administration) Ji, Eunhee (College of Pharmacy, Gacheon University) Kim, In-Wha (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University) Oh, Jung Mi (College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University) |
1 | Agarwal, V., Bell, G. W., Nam, J. W. and Bartel, D. P. (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife 4, e05005. |
2 | Bahar, A. Y., Sayar, H., Ulasli, M., Bayraktar, R., Kirkbes, S., Sercan Simsek, S. and Arslan, A. (2017) Expression of miR-520-d-3p, miR-520b, miR-520e are significantly downregulated in locally advanced colorectal carcinoma. Tenn. Med. 2, 11. |
3 | Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Statist. Soc. B. 57, 289-300. |
4 | Chen, D. T., Hernandez, J. M., Shibata, D., McCarthy, S. M., Humphries, L. A., Clark, W., Elahi, A., Gruidl, M., Coppola, D. and Yeatman, T. (2012) Complementary strand microRNAs mediate acquisition of metastatic potential in colonic adenocarcinoma. J. Gastrointest. Surg. 16, 905-912; discussion 912-903. DOI |
5 | Chen, Y., Song, Y., Wang, Z., Yue, Z., Xu, H., Xing, C. and Liu, Z. (2010) Altered expression of MiR-148a and MiR-152 in gastrointestinal cancers and its clinical significance. J. Gastrointest. Surg. 14, 1170-1179. DOI |
6 | Koturbash, I., Tolleson, W. H., Guo, L., Yu, D., Chen, S., Hong, H., Mattes, W. and Ning, B. (2015) microRNAs as pharmacogenomic biomarkers for drug efficacy and drug safety assessment. Biomark. Med. 9, 1153-1176. DOI |
7 | Huang, R. S., Gamazon, E. R., Ziliak, D., Wen, Y., Im, H. K., Zhang, W., Wing, C., Duan, S., Bleibel, W. K., Cox, N. J. and Dolan, M. E. (2011) Population differences in microRNA expression and biological implications. RNA Biol. 8, 692-701. DOI |
8 | Kim, I. W., Han, N., Burckart, G. J. and Oh, J. M. (2014) Epigenetic changes in gene expression for drug-metabolizing enzymes and transporters. Pharmacotherapy 34, 140-150. DOI |
9 | Klein, T. E., Chang, J. T., Cho, M. K., Easton, K. L., Fergerson, R., Hewett, M., Lin, Z., Liu, Y., Liu, S., Oliver, D. E., Rubin, D. L., Shafa, F., Stuart, J. M. and Altman, R. B. (2001) Integrating genotype and phenotype information: an overview of the PharmGKB project. Pharmacogenetics Research Network and Knowledge Base. Pharmacogenomics J. 1, 167-170. DOI |
10 | Kwekel, J. C., Vijay, V., Desai, V. G., Moland, C. L. and Fuscoe, J. C. (2015) Age and sex differences in kidney microRNA expression during the life span of F344 rats. Biol. Sex Differ. 6, 1. DOI |
11 | Messingerova, L., Imrichova, D., Kavcova, H., Seres, M., Sulova, Z. and Breier, A. (2016) A decrease in cellular microRNA-27a content is involved in azacytidine-induced P-glycoprotein expression in SKM-1 cells. Toxicol. In vitro 36, 81-88. DOI |
12 | Vejnar, C. E. and Zdobnov, E. M. (2012) MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res. 40, 11673-11683. DOI |
13 | Rukov, J. L. and Shomron, N. (2011) MicroRNA pharmacogenomics: post-transcriptional regulation of drug response. Trends Mol. Med. 17, 412-423. DOI |
14 | Sayed, D. and Abdellatif, M. (2011) MicroRNAs in development and disease. Physiol. Rev. 91, 827-887. DOI |
15 | Shomron, N. (2010) MicroRNAs and pharmacogenomics. Pharmacogenomics 11, 629-632. DOI |
16 | Wang, W. C., Juan, A. H., Panebra, A. and Liggett, S. B. (2011) MicroRNA let-7 establishes expression of -adrenergic receptors and dynamically down-regulates agonist-promoted down-regulation. Proc. Natl. Acad. Sci. U.S.A. 108, 6246-6251. DOI |
17 | Djuranovic, S., Nahvi, A. and Green, R. (2012) miRNA-mediated gene silencing by translational repression followed by mRNA deadenylation and decay. Science 336, 237-240. DOI |
18 | Yu, A. M. and Pan, Y. Z. (2012) Noncoding microRNAs: Small RNAs play a big role in regulation of ADME? Acta Pharm. Sin. B 2, 93-101. DOI |
19 | Zheng, N., Yang, P., Wang, Z. and Zhou, Q. (2017) OncomicroRNAsmediated tumorigenesis: implication in cancer diagnosis and targeted therapy. Curr. Cancer Drug Targets 17, 40-47. |
20 | Dai, Y. and Zhou, X. (2010) Computational methods for the identification of microRNA targets. Open Access Bioinformatics 2, 29-39. |
21 | Dluzen, D. F. and Lazarus, P. (2015) MicroRNA regulation of the major drug-metabolizing enzymes and related transcription factors. Drug Metab. Rev. 47, 320-334. |
22 | Georgitsi, M., Zukic, B., Pavlovic, S. and Patrinos, G. P. (2011) Transcriptional regulation and pharmacogenomics. Pharmacogenomics 12, 655-673. DOI |
23 | Hsu, S. D., Chu, C. H., Tsou, A. P., Chen, S. J., Chen, H. C., Hsu, P. W., Huang, H. D. (2008) miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res. 36, D165-D169. |
24 | Huang, J., Gutierrez, F., Strachan, H. J., Dou, D., Huang, W., Smith, B., Blake, J. A., Eilbeck, K., Natale, D. A., Lin, Y., Wu, B., de Silva, N., Wang, X., Liu, Z., Borchert, G. M., Tan, M. and Ruttenberg, A. (2016) OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data. J. Biomed. Semantics. 7, 25. DOI |
25 | Betel, D., Wilson, M., Gabow, A., Marks, D. S. and Sander, C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res. 36, D149-D153. |
26 | Relling, M. V. and Evans, W. E. (2015) Pharmacogenomics in the clinic. Nature 526, 343-350. DOI |
27 | Murakami, Y., Kubo, S., Tamori, A., Itami, S., Kawamura, E., Iwaisako, K., Ikeda, K., Kawada, N., Ochiya, T. and Taguchi, Y. H. (2015) Comprehensive analysis of transcriptome and metabolome analysis in Intrahepatic Cholangiocarcinoma and Hepatocellular Carcinoma. Sci. Rep. 5, 16294. DOI |
28 | Nasr, R., Sleiman, F., Awada, Z. and Zgheib, N. K. (2016) The pharmacoepigenetics of drug metabolism and transport in breast cancer: review of the literature and in silico analysis. Pharmacogenomics 17, 1573-1585. DOI |
29 | Paraskevopoulou, M. D., Georgakilas, G., Kostoulas, N., Vlachos, I. S., Vergoulis, T., Reczko, M., Filippidis, C., Dalamagas, T. and Hatzigeorgiou, A. G. (2013) DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res. 41, W169-W173. DOI |
30 | Pasquinelli, A. E. (2012) MicroRNAs and their targets: recognition, regulation and an emerging reciprocal relationship. Nat. Rev. Genet. 13, 271-282. DOI |
31 | Rieger, J. K., Klein, K., Winter, S. and Zanger, U. M. (2013) Expression variability of absorption, distribution, metabolism, excretionrelated microRNAs in human liver: influence of nongenetic factors and association with gene expression. Drug Metab. Dispos. 41, 1752-1762. DOI |
32 | World Health Organization (2014) International Agency for Research on Cancer. World Cancer Report. |
33 | Wei, Z., Jiang, S., Zhang, Y., Wang, X., Peng, X., Meng, C., Liu, Y., Wang, H., Guo, L., Qin, S., He, L., Shao, F., Zhang, L. and Xing, Q. (2014) The effect of microRNAs in the regulation of human CYP3A4: a systematic study using a mathematical model. Sci. Rep. 4, 4283. |
34 | Weinstein, J. N., Collisson, E. A., Mills, G. B., Shaw, K. R., Ozenberger, B. A., Ellrott, K., Shmulevich, I., Sander, C. and Stuart, J. M. (2013) The Cancer Genome Atlas Pan-Cancer analysis project. Nat. Genet. 45, 1113-1120. DOI |
35 | Wienholds, E., Kloosterman, W. P., Miska, E., Alvarez-Saavedra, E., Berezikov, E., de Bruijn, E., Horvitz, H. R., Kauppinen, S. and Plasterk, R. H. (2005) MicroRNA expression in zebrafish embryonic development. Science 309, 310-311. DOI |
36 | Wilczynska, A. and Bushell, M. (2015) The complexity of miRNA-mediated repression. Cell Death Differ. 22, 22-33. DOI |
37 | Wong, N. and Wang, X. (2015) miRDB: an online resource for microRNA target prediction and functional annotations. Nucleic Acids Res. 43, D146-D152. DOI |
38 | Yang, C., Sun, C., Liang, X., Xie, S., Huang, J. and Li, D. (2016) Integrative analysis of microRNA and mRNA expression profiles in non-small-cell lung cancer. Cancer Gene Ther. 23, 90-97. DOI |
39 | Ye, B., Wang, R. and Wang, J. (2016) Correlation analysis of the mRNA and miRNA expression profiles in the nascent synthetic allotetraploid Raphanobrassica. Sci. Rep. 6, 37416. DOI |
40 | Yu, A. M., Tian, Y., Tu, M. J., Ho, P. Y. and Jilek, J. L. (2016) MicroRNA pharmacoepigenetics: posttranscriptional regulation mechanisms behind variable drug disposition and strategy to develop more effective therapy. Drug Metab. Dispos. 44, 308-319. DOI |