MiRNAs and their application in drug-induced liver injury

Biomarkers in Medicine

Volumn 8, Issue 2, 2014, Pages 161-172

  Wang, Yuping ^a   Chen, Tao ^a   Tong, Weida ^a  

^a NATIONAL CENTER FOR TOXICOLOGICAL RESEARCH   (United States)

Author keywords

drug induced liver injury; microRNA; translational biomarkers

Indexed keywords

BIOLOGICAL MARKERS; COMPUTATIONAL BIOLOGY; DRUG-INDUCED LIVER INJURY; GENE EXPRESSION PROFILING; HUMANS; MICRORNAS;

EID: 84894292092     PISSN: 17520363     EISSN: 17520371     Source Type: Journal    
DOI: 10.2217/bmm.13.147     Document Type: Review

References (106)

1. Bjornsson E, Bergmann O, Bjornsson HK et al. The frequency of drug-induced liver injury (DILI) among patients receiving potentially hepatotoxic drugs: a population based study. Hepatology 56(S1), 594A-595A (2012) (Abstract 823).
2. Grant LM, DC Rockey. Drug-induced liver injury. Curr. Opin. Gastroenterol. 28(3), 198-202 (2012).
3. Lee WM. Acetaminophen and the US Acute Liver Failure Study Group: lowering the risks of hepatic failure. Hepatology 40(1), 6-9 (2004).
4. Filipowicz W, SN Bhattacharyya, Sonenberg N. Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight? Nat. Rev. Genet. 9(2), 102-114 (2008).
5. Koturbash I, Beland FA, Pogribny IP. Role of microRNAs in the regulation of drug metabolizing and transporting genes and the response to environmental toxicants. Expert Opin. Drug Metab. Toxicol. 8(5), 597-606 (2012).
6. Lu J, Getz G, Miska EA et al. MicroRNA expression profiles classify human cancers. Nature 435(7043), 834-838 (2005).
7. Hansen TB, Jensen TI, Clausen BH et al. Natural RNA circles function as efficient microRNA sponges. Nature 495(7441), 384-388 (2013).
8. Su YW, Chen X, Jiang ZZ et al. A panel of serum microRNAs as specific biomarkers for diagnosis of compound- and herb-induced liver injury in rats. PLoS ONE 7(5), e37395 (2012).
9. Ward J, Bala S, Petrasek J, Szabo G. Plasma microRNA profiles distinguish lethal injury in acetaminophen toxicity: a research study. World J. Gastroenterol. 18(22), 2798-2804 (2012).
10. Blondal T, Jensby Nielsen S, Baker A et al. Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 59(1), S1-S6 (2012).
11. Gallego JA, Gordon ML, Claycomb K, Bhatt M, Lencz T, Malhotra AK. In vivo microRNA detection and quantitation in cerebrospinal fluid. J. Mol. Neurosci. 47(2), 243-248 (2012).
12. Alevizos I,Illei GG. MicroRNAs as biomarkers in rheumatic diseases. Nat. Rev. Rheumatol. 6(7), 391-398 (2010).
13. Frampton AE, Gall TM, Castellano L, Stebbing J, Jiao LR, Krell J. Towards a clinical use of miRNAs in pancreatic cancer biopsies. Expert Rev. Mol. Diagn. 13(1), 31-34 (2013).
14. Weber JA, Baxter DH, Zhang S et al. The microRNA spectrum in 12 body fluids. Clin. Chem. 56(11), 1733-1741 (2010).
15. Armistead D, Estep JM, Elariny H et al. Systems biology analysis of non-Alcoholic steatohepatitis related miRNA expression. Hepatology 56(S1), 266A (2012) (Abstract 147).
16. Hand NJ, Kennedy M, Le Guen CL et al. Cholestasis induces a conserved, adaptive, liver miRNA response. Hepatology 56(S1), 197A (2012) (Abstract 14).
17. Wang K, Zhang S, Marzolf B et al. Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc. Natl Acad. Sci. USA 106(11), 4402-4407 (2009).
18. Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 136(4), 642-655 (2009).
19. Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat. Cell Biol. 11(3), 228-234 (2009).
20. Du T, ZamorePD. microPrimer: the biogenesis and function of microRNA. Development 132(21), 4645-4652 (2005).
21. Feero WG, Guttmacher AE, CollinsFS. genomic medicine: genomic medicine - an updated primer. N. Eng. J. Med. 362(21), 2001-2011 (2010).
22. Zhou Q, Haupt S, Prots I et al. miRNA regulation of cell proliferation by targeting the expression of GARP. Immunology 137(S1), 74 (2012) (Abstract W30.002).
23. He JF, Luo YM, Wan XH, Jiang D. Biogenesis of miRNA-195 and its role in biogenesis, the cell cycle, and apoptosis. J. Biochem. Mol. Toxicol. 25(6), 404-408 (2011).
24. Ferraz C, Lorenz S, Wojtas B, Bornstein SR, Paschke R, Eszlinger M. Inverse correlation of miRNA and cell cycle-Associated genes suggests influence of miRNA on benign thyroid nodule tumorigenesis. Exp. Clin. Endocrinol. Diabetes 121(3), OP5-38 (2013).
25. Xu X, Fan Z, Kang L et al. Hepatitis B virus X protein represses miRNA-148a to enhance tumorigenesis. J. Clin. Invest. 123(2), 630-645 (2013).
26. Bauersachs J, Thum T. Biogenesis and regulation of cardiovascular microRNAs. Circ. Res. 109(3), 334-347 (2011).
27. Kong YW, Ferland-McCollough D, Jackson TJ, Bushell M. microRNAs in cancer management. Lancet Oncol. 13(6), e249-e258 (2012).
28. Lorenzen JM, Haller H, Thum T. MicroRNAs as mediators and therapeutic targets in chronic kidney disease. Nat. Rev. Nephrol. 7(5), 286-294 (2011).
29. Mendell JT, Olson EN. MicroRNAs in stress signaling and human disease. Cell 148(6), 1172-1187 (2012).
30. Kim VN. MicroRNA biogenesis: coordinated cropping and dicing. Nat. Rev. Mol. Cell Biol. 6(5), 376-385 (2005).
31. Barabsi AL, Gulbahce N, Loscalzo J. Network medicine: a network-based approach to human disease. Nat. Rev. Genet. 12(1), 56-68 (2011).
32. Grskovic M, Javaherian A, Strulovici B, Daley GQ. Induced pluripotent stem cells - opportunities for disease modelling and drug discovery. Nat. Rev. Drug Discov. 10(12), 915-929 (2011).
33. Cortez MA, Bueso-Ramos C, Ferdin J, Lopez- Berestein G, Sood AK, Calin GA. MicroRNAs in body fluids-The mix of hormones and biomarkers. Nat. Rev. Clin. Oncol. 8(8), 467-477 (2011).
34. Jabed A, Wagner S, McCracken J, Wells DN, Laible G. Targeted microRNA expression in dairy cattle directs production of beta-lactoglobulin-free, high-casein milk. Proc. Natl Acad. Sci. USA 109(42), 16811-16816 (2012).
35. Ogawa Y, Taketomi Y, Murakami M, Tsujimoto M, Yanoshita R. Small RNA transcriptomes of two types of exosomes in human whole saliva determined by next generation sequencing. Biol. Pharm. Bull. 36(1), 66-75 (2013).
36. Yang X, Greenhaw J, Shi Q et al. Identification of urinary microRNA profiles in rats that may diagnose hepatotoxicity. Toxicol. Sci. 125(2), 335-344 (2012).
37. Blondal T, Jensby Nielsen S, Baker A et al. Assessing sample and miRNA profile quality in serum and plasma or other biofluids. Methods 59(1), S1-S6 (2013).
38. Li Y, Kowdley KV. Method for microRNA isolation from clinical serum samples. Anal. Biochem. 431(1), 69-75 (2012).
39. Rajput SK, Dave VP, Rajput A, Pandey HP, Datta TK, Singh RK. A column-based rapid method for the simultaneous isolation of DNA, RNA, miRNA and proteins. Cell. Biol. Int. 36(9), 779-783 (2012).
40. Sharkey JW, Antoine DJ, Park BK. Validation of methods involving miRNA isolation, purification and quantification and the potential of miRNAs to be used as biomarkers of nephrotoxicity. Toxicology 290(2-3), 136-137 (2011).
41. Sourvinou IS, Markou A, Lianidou ES. Quantification of circulating miRNAs in plasma: effect of preanalytical and analytical parameters on their isolation and stability. J. Mol. Diagn. 15(6), 827-834 (2013).
42. Sharkey JW, Antoine DJ, Park BK. Validation of the isolation and quantification of kidney enriched miRNAs for use as biomarkers. Biomarkers 17(3), 231-239 (2012).
43. Turchinovich A, Weiz L, Langheinz A, Burwinkel B. Characterization of extracellular circulating microRNA. Nucleic Acids Res. 39(16), 7223-7233 (2011).
44. Lee Y, El Andaloussi S, Wood MJ. Exosomes and microvesicles: extracellular vesicles for genetic information transfer and gene therapy. Hum. Mol. Genet. 21, R125-R134 (2012).
45. Arroyo JD, Chevillet JR, Kroh EM et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc. Natl Acad. Sci. USA 108(12), 5003-5008 (2011).
46. Arroyo JD, Chevillet JR, Kroh EM et al. Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. Proc. Natl. Acad. Sci. USA 108(12), 5003-5008 (2011).
47. Wang B, Howel P, Bruheim S et al. Systematic evaluation of three microRNA profiling platforms: microarray, beads array, and quantitative real-time PCR array. PLoS ONE 6(2), e17167 (2011).
48. Kim H, Choi J, Cho M, Park H. A PNA microarray platform for miRNA expression profiling using on-chip labeling technology. Biochip J. 6(1), 25-33 (2012).
49. Wang ST, Li C, Liu L. miRNA microarray technology in miRNA profiling. Curr. Bioinform. 4(2), 141-148 (2009).
50. Hawkins RD, Hon GC, Ren B. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 11(7), 476-486 (2010).
51. Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat. Rev. Genet. 11(10), 685-696 (2010).
52. Knig J, Zarnack K, Luscombe NM, Ule J. Protein-RNA interactions: new genomic technologies and perspectives. Nat. Rev. Genet. 13(2), 77-83 (2012).
53. Gerlach D, Kriventseva EV, Rahman N, Vejnar CE, Zdobnov EM. miROrtho: computational survey of microRNA genes. Nucleic Acids Res. 37, D111-D117 (2009).
54. Thakur V, Wanchana S, Xu M et al. Characterization of statistical features for plant microRNA prediction. BMC Genomics 12, 108 (2011).
55. Lawless N, Foroushani AB, McCabe MS, OFarrelly C, Lynn DJ. Next generation sequencing reveals the expression of a unique miRNA profile in response to a Gram-positive bacterial infection. PLoS ONE 8(3), e57543 (2013).
56. Nekrutenko A, Taylor J. Next-generation sequencing data interpretation: enhancing reproducibility and accessibility. Nat. Rev. Genet. 13(9), 667-672 (2012).
57. Wang B, Xi Y. Challenges for microRNA microarray data analysis. Microarrays 2(2), 34-50 (2013).
58. Akbari Moqadam F, Pieters R, den Boer ML. The hunting of targets: challenge in miRNA research. Leukemia 27(1), 16-23 (2012).
59. Yan X, Liang H, Deng T et al. The identification of novel targets of miR-16 and characterization of their biological functions in cancer cells. Mol. Cancer 12(1), 1-11 (2013).
60. Sethupathy P, Megraw M, Hatzigeorgiou AG. A guide through present computational approaches for the identification of mammalian microRNA targets. Nat. Methods 3(11), 881-886 (2006).
61. Lewis BP, Shih IH, Jones-Rhoades MW, Bartel DP, Burge CB. Prediction of mammalian microRNA targets. Cell 115(7), 787-798 (2003).
62. Krek A, Grn D, Poy MN et al. Combinatorial microRNA target predictions. Nat. Genet. 37(5), 495-500 (2005).
63. Enright AJ, John B, Gaul U, Tuschl T, Sander C, Marks DS. MicroRNA targets in Drosophila. Genome Biol. 5(1), R12R1 (2004).
64. Jiang Q, Wang Y, Hao Y et al. miR2Disease: a manually curated database for microRNA deregulation in human disease. Nucleic Acids Res. 37(Suppl. 1), D98-D104 (2009).
65. Hindorff LA, Sethupathy P, Junkins HA et al. Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. USA 106(23), 9362-9367 (2009).
66. K Kozomara A, Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39, D152-D157 (2011).
67. Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. et al. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res. 37, D105-D110 (2009).
68. Vergoulis T, Vlachos IS, Alexiou P et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res. 40(D1), D222-D229 (2012).
69. Luo D, Wilson JM, Harvel N et al. A systematic evaluation of miRNA:mRNA interactions involved in the migration and invasion of breast cancer cells. J. Transl. Med. 11, 57 (2013).
70. Motta V, Angelici L, Nordio F et al. Integrative analysis of miRNA and inflammatory gene expression after acute particulate matter exposure. Toxicol. Sci. 132(2), 307-316 (2013).
71. Wakili R, Clau S, Kb S. Molecular mechanisms of atrial fibrillation. Potential role of microRNAs as new therapeutic targets and potential biomarkers. Herz 37(2), 166-171 (2012).
72. Samantarrai D, Dash S, Chhetri B, Mallick B. Genomic and epigenomic cross-talks in the regulatory landscape of miRNAs in breast cancer. Mol. Cancer Res. 11(4), 315-328 (2013).
73. Steinfeld I, Navon R, Ach R, Yakhini Z. miRNA target enrichment analysis reveals directly active miRNAs in health and disease. Nucleic Acids Res. 41(3), e45 (2013).
74. Van Roosbroeck K, Pollet J, Calin GA. miRNAs and long noncoding RNAs as biomarkers in human diseases. Expert Rev. Mol. Diagn. 13(2), 183-204 (2013).
75. Takahashi K, Yan I, Wen HJ, Patel T. microRNAs in liver disease: from diagnostics to therapeutics. Clin. Biochem. 46(10-11), 946-952 (2013).
76. Ji J, Shi J, Budhu A et al. MicroRNA expression, survival, and response to interferon in liver cancer. N. Eng. J. Med. 361(15), 1437-1447 (2009).
77. Szabo G, Bala S. MicroRNAs in liver disease. Nat. Rev. Gastroenterol. Hepatol. 10, 542-552 (2013).
78. Cermelli S, Ruggieri A, Marrero JA, Ioannou GN, Beretta L. Circulating microRNAs in patients with chronic hepatitis C and non-Alcoholic fatty liver disease. PLoS ONE 6(8), e23937 (2011).
79. Nunnari G, Schnell MJ. MicroRNA-122: a therapeutic target for hepatitis C virus (HCV) infection. Front. Biosci. (Schol. Ed.) 3, 1032-1037 (2011).
80. Szabo G, Bala S. MicroRNAs in liver disease. Nat. Rev. Gastroenterol. Hepatol. 10(9), 542-552 (2013).
81. Wang XW, Heegaard NH, Orum H. MicroRNAs in liver disease. Gastroenterology 142(7), 1431-1443 (2012).
82. Tarantino G, Di Minno MN, Capone D. Drug-induced liver injury: is it somehow foreseeable? World J. Gastroenterol. 15(23), 2817 (2009).
83. Reuben A, Koch DG, Lee WM; Acute Liver Failure Study Group. Drug-induced acute liver failure: results of a U.S. multicenter, prospective study. Hepatology 52(6), 2065-2076 (2010).
84. Tarantino G, Conca P, Basile V et al. A prospective study of acute drug-induced liver injury in patients suffering from non-Alcoholic fatty liver disease. Hepatol. Res. 37(6), 410-415 (2007).
85. Kaplowitz N. Avoiding idiosyncratic DILI: two is better than one. Hepatology 58(1), 15-17 (2013).
86. Chalasani N, Bjrnsson E. Risk factors for idiosyncratic drug-induced liver injury. Gastroenterology 138(7), 2246-2259 (2010).
87. Daly AK, Donaldson PT, Bhatnagar P et al. HLA-B5701 genotype is a major determinant of drug-induced liver injury due to flucloxacillin. Nat. Genet. 41(7), 816-819 (2009).
88. Tarantino G, Pezzullo MG, di Minno MN et al. Drug-induced liver injury due to natural products used for weight loss: a case report. World J. Gastroenterol. 15(19), 2414-2417 (2009).
89. Starkey Lewis PJ, Merz M, Couttet P et al. Serum microRNA biomarkers for drug-induced liver injury. Clin. Pharmacol. Ther. 92(3), 291-293 (2012).
90. Amacher DE, Schomaker SJ, Aubrecht J. Development of blood biomarkers for drug-induced liver injury: an evaluation of their potential for risk assessment and diagnostics. Mol. Diagn. Ther. 17(6), 343-354 (2013).
91. Bala S, Petrasek J, Mundkur S et al. Circulating microRNAs in exosomes indicate hepatocyte injury and inflammation in alcoholic, drug-induced, and inflammatory liver diseases. Hepatology 56(5), 1946-1957 (2012).
92. Esau C, Davis S, Murray SF et al. miR-122 regulation of lipid metabolism revealed by in vivo antisense targeting. Cell Metab. 3(2), 87-98 (2006).
93. Gatfield D, Le Martelot G, Vejnar CE et al. Integration of microRNA miR-122 in hepatic circadian gene expression. Genes Dev. 23(11), 1313-1326 (2009).
94. Castoldi M, Vujic Spasic M, Altamura S et al. The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice. J. Clin. Invest. 121(4), 1386-1396 (2011).
95. Starkey Lewis PJ, Dear J, Platt V et al. Circulating microRNAs as potential markers of human drug-induced liver injury. Hepatology 54(5), 1767-1776 (2011).
96. Su YW, Chen X, Jiang ZZ et al. A panel of serum microRNAs as specific biomarkers for diagnosis of compound-And herb-induced liver injury in rats. PLoS ONE 7(5), e37395 (2012).
97. Gracias DT, Stelekati E, Hope JL et al. The microRNA miR-155 controls CD8+ T cell responses by regulating interferon signaling. Nat. Immunol. 14(6), 593-602 (2013).
98. Bala S, Szabo G. MicroRNA signature in alcoholic liver disease. Int. J. Hematol. 2012, 1-6 (2012)
99. Eldh M, Ltvall J, Malmhll C, Ekstrm K. Importance of RNA isolation methods for analysis of exosomal RNA: evaluation of different methods. Mol. Immunol. 50(4), 278-286 (2012).
100. Dijkstra JR, Mekenkamp LJ, Teerenstra S, De Krijger I, Nagtegaal ID. MicroRNA expression in formalin-fixed paraffin embedded tissue using real time quantitative PCR: the strengths and pitfalls. J. Cell. Mol. Med. 16(4), 683-690 (2012).
101. Kolbert CP, Feddersen RM, Rakhshan F et al. Multi-platform analysis of microRNA expression measurements in RNA from fresh frozen and FFPE tissues. PLoS ONE 8(1), e52517 (2013).
102. Wang K, Yuan Y, Cho JH, McClarty S, Baxter D, Galas DJ. Comparing the MicroRNA spectrum between serum and plasma. PLoS ONE 7(7), e41561 (2012).
103. Alvarez ML, Khosroheidari M, Kanchi Ravi R, DiStefano JK. Comparison of protein, microRNA, and mRNA yields using different methods of urinary exosome isolation for the discovery of kidney disease biomarkers. Kidney Int. 82(9), 1024-1032 (2012).
104. Bala S, Petrasek J, Mundkur S et al. Circulating microRNAs in exosomes indicate hepatocyte injury and inflammation in alcoholic, drug-induced, and inflammatory liver diseases. Hepatology 56(5), 1946-1957 (2012).
105. Zhang Y, Jia Y, Zheng R et al. Plasma microRNA-122 as a biomarker for viral-, alcohol-, and chemical-related hepatic diseases. Clin. Chem. 56(12), 1830-1838 (2010).
106. Laterza OF, Lim L, Garrett-Engele PW et al. Plasma microRNAs as sensitive and specific biomarkers of tissue injury. Clin. Chem. 55(11), 1977-1983 (2009).