Abstract
MicroRNAs (miRNAs) are small noncoding RNAs (21–23 nucleotides in length) that regulate gene expression at translational or posttranslational levels. The major regulatory mechanisms include translational repression or mRNA degradation (Filipowicz et al., Curr Opin Struct Biol 15:331–341, 2005).
Aberrant expression of miRNAs has been found to be associated with a variety of human diseases such as cancers/tumors, diabetes, viral infections, cardiovascular diseases, neurodegenerative diseases, and other diseases (Wang et al., J Cell Physiol 23:25–30, 2016; Lawrie, MicroRNAs in medicine, 2013). The expression of miRNAs is tissue specific and can be used to identify tumor type and its origin (Mishra and Merlino, J Clin Invest 119:2119–2123, 2009). Many investigations suggest that the miRNA-expression profiles are novel diagnostic and prognostic biomarkers for multiple human diseases. Manipulating relevant miRNA expression or function may serve as potential therapeutic strategies for different diseases.
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References
Giraldez AJ, Mishima Y, Rihel J, Grocock RJ, Van Dongen S, Inoue K, Enright AJ, Schier AF (2006) Zebrafish miR-430 promotes deadenylation and clearance of maternal mRNAs. Science 312:75–79. doi:10.1126/science.1122689
Filipowicz W, Jaskiewicz L, Kolb FA, Pillai RS (2005) Post-transcriptional gene silencing by siRNAs and miRNAs. Curr Opin Struct Biol 15:331–341. doi:10.1016/j.sbi.2005.05.006
Wang J, Chen J, Sen S (2016) MicroRNA as biomarkers and diagnostics. J Cell Physiol 23:25–30. doi:10.1002/jcp.25056
Brennecke J, Hipfner DR, Stark A, Russell RB, Cohen SM (2003) bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell 113:25–36. doi:10.1016/S0092-8674(03)00231-9
Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297. doi:10.1016/S0092-8674(04)00045-5
Chen CZ, Li L, Lodish HF, Bartel DP (2004) MicroRNAs modulate hematopoietic lineage differentiation. Science 303:83–86. doi:10.1126/science.1091903
Mitchell PS, Parkin RK, Kroh EM, Fritz BR, Wyman SK, Pogosova-Agadjanyan EL, Peterson A, Noteboom J, O’Briant KC, Allen A, Lin DW, Urban N, Drescher CW, Knudsen BS, Stirewalt DL, Gentleman R, Vessella RL, Nelson PS, Martin DB, Tewari M (2008) Circulating microRNAs as stable blood-based markers for cancer detection. Proc Natl Acad Sci U S A 105:10513–10518. doi:10.1073/pnas.0804549105
Lawrie CH (2013) MicroRNAs in medicine. John Wiley & Sons, Inc., Hoboken, NJ. doi:10.1002/9781118300312
Challagundla KB, Fanini F, Vannini I, Wise P, Murtadha M, Malinconico L, Cimmino A, Fabbri M (2014) microRNAs in the tumor microenvironment: solving the riddle for a better diagnostics. Expert Rev Mol Diagn 14:565–574. doi:10.1586/14737159.2014.922879
Palmero EI, de Campos SG, Campos M, de Souza NC, Guerreiro ID, Carvalho AL, Marques MM (2011) Mechanisms and role of microRNA deregulation in cancer onset and progression. Genet Mol Biol 34:363–370. doi:10.1590/S1415-47572011000300001
Mishra PJ, Merlino G (2009) MicroRNA reexpression as differentiation therapy in cancer. J Clin Invest 119:2119–2123. doi:10.1172/JCI40107
Garzon R, Fabbri M, Cimmino A, Calin GA, Croce CM (2006) MicroRNA expression and function in cancer. Trends Mol Med 12:580–587. doi:10.1016/j.molmed.2006.10.006
Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E, Aldler H, Rattan S, Keating M, Rai K, Rassenti L, Kipps T, Negrini M, Bullrich F, Croce CM (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99:15524–15529. doi:10.1073/pnas.242606799
Iorio MV, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M, Campiglio M, Ménard S, Palazzo JP, Rosenberg A, Musiani P, Volinia S, Nenci I, Calin GA, Querzoli P, Negrini M, Croce CM (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65:7065–7070. doi:10.1158/0008-5472.CAN-05-1783
Calin GA, Liu CG, Sevignani C, Ferracin M, Felli N, Dumitru CD, Shimizu M, Cimmino A, Zupo S, Dono M, Dell’Aquila ML, Alder H, Rassenti L, Kipps TJ, Bullrich F, Negrini M, Croce CM (2004) MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias. Proc Natl Acad Sci U S A 101:11755–11760. doi:10.1073/pnas.0404432101
Calin GA, Ferracin M, Cimmino A, Di Leva G, Shimizu M, Wojcik SE, Iorio MV, Visone R, Sever NI, Fabbri M, Iuliano R, Palumbo T, Pichiorri F, Roldo C, Garzon R, Sevignani C, Rassenti L, Alder H, Volinia S, Liu CG, Kipps TJ, Negrini M, Croce CM (2005) A microRNA signature associated with prognosis and progression in chronic lymphocytic leukemia. N Engl J Med 352:1667–1676. doi:10.1056/NEJMMoa050995
Yanaihara N, Caplen N, Bowman E, Seike M, Kumamoto K, Yi M, Stephens RM, Okamoto A, Yokota J, Tanaka T, Calin GA, Liu CG, Croce CM, Harris CC (2006) Unique microRNA molecular profiles in lung cancer diagnosis and prognosis. Cancer Cell 9:189–198. doi:10.1016/j.ccr2006.01.025
Murakami Y, Yasuda T, Saigo K, Urashima T, Toyoda H, Okanoue T, Shimotohno K (2006) Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues. Oncogene 25:2537–2545. doi:10.1038/sj.onc.1209283
Qi J, Wang J, Katayama H, Sen S, Liu SM (2013) Circulating microRNAs (cmiRNAs) as novel potential biomarkers for hepatocellular carcinoma. Neoplasma 60:135–142. doi:10.4149/neo_2013_018
Iorio MV, Visone R, Di Leva G, Donati V, Petrocca F, Casalini P, Taccioli C, Volinia S, Liu CG, Alder H, Calin GA, Menard S, Croce CM (2007) MicroRNA signatures in human ovarian cancer. Cancer Res 67:8699–8707. doi:10.1158/0008-5472.CAN-07-1936
Roldo C, Missiaglia E, Hagan JP, Falconi M, Capelli P, Bersani S, Calin GA, Volinia S, Liu CG, Scarpa A, Croce CM (2006) MicroRNA expression abnormalities in pancreatic endocrine and acinar tumors are associated with distinctive pathological features and clinical behavior. J Clin Oncol 24:4677–4684. doi:10.1200/JCO.2005.05.5194
Wang J, Sen S (2011) MicroRNA functional network in pancreatic cancer: from biology to biomarkers of disease. J Biosci 36:481–491. doi:10.1007/s12038-011-9083-4
He H, Jazdzewski K, Li W, Liyanarachchi S, Nagy R, Volinia S, Calin GA, Liu CG, Franssila K, Suster S, Kloos RT, Croce CM, de la Chapelle A (2005) The role of microRNA genes in papillary thyroid carcinoma. Proc Natl Acad Sci U S A 102:19075–19080. doi:10.1073/pnas.0509603102
Pallante P, Visone R, Ferracin M, Ferraro A, Berlingieri MT, Troncone G, Chiappetta G, Liu CG, Santoro M, Negrini M, Croce CM, Fusco A (2006) MicroRNA deregulation in human thyroid papillary carcinomas. Endocr Relat Cancer 13:497–508. doi:10.1677/erc.1.01209
Ciafrè SA, Galardi S, Mangiola A, Ferracin M, Liu CG, Sabatino G, Negrini M, Maira G, Croce CM, Farace MG (2005) Extensive modulation of a set of microRNAs in primary glioblastoma. Biochem Biophys Res Commun 334:1351–1358. doi:10.1016/j.bbrc.2005.07.030
Porkka KP, Pfeiffer MJ, Waltering KK, Vessella RL, Tammela TLJ, Visakorpi T (2007) MicroRNA expression profiling in prostate cancer. Cancer Res 67:6130–6135. doi:10.1158/0008-5472.CAN-07-0533
Lu J, Getz G, Miska EA, Alvarez-Saavedra E, Lamb J, Peck D, Sweet-Cordero A, Ebert BL, Mak RH, Ferrando AA, Downing JR, Jacks T, Horvitz HR, Golub TR (2005) MicroRNA expression profiles classify human cancers. Nat Cell Biol 435:834–838. doi:10.1038/nature03702
Rosenfeld N, Aharonov R, Meiri E, Rosenwald S, Spector Y, Zepeniuk M, Benjamin H, Shabes N, Tabak S, Levy A, Lebanony D, Goren Y, Silberschein E, Targan N, Ben-Ari A, Gilad S, Sion-Vardy N, Tobar A, Feinmesser M, Kharenko O, Nativ O, Nass D, Perelman M, Yosepovich A, Shalmon B, Polak-Charcon S, Fridman E, Avniel A, Bentwich I, Bentwich Z, Cohen D, Chajut A, Barshack I (2008) MicroRNAs accurately identify cancer tissue origin. Nat Biotechnol 26:462–469. doi:10.1038/nbt1392
Wandt H, Haferlach T, Thiede C, Ehninger G (2010) WHO classification of myeloid neoplasms and leukemia. Blood 115:748–749. doi:10.1182/blood-2009-10-249664
Kumar MS, Lu J, Mercer KL, Golub TR, Jacks T (2007) Impaired microRNA processing enhances cellular transformation and tumorigenesis. Nat Genet 39:673–677. doi:10.1038/ng2003
Esteller M (2011) Noncoding RNAs in human disease. Nat Rev Genet 12:861–874. doi:10.1038/nrg3074
Huang JT, Wang J, Srivastava V, Sen S, Liu SM (2014) MicroRNA machinery genes as novel biomarkers for cancer. Front Oncol 4:113. doi:10.3389/fonc.2014.00113
Shenouda SK, Alahari SK (2009) MicroRNA function in cancer: oncogene or a tumor suppressor? Cancer Metastasis Rev 28:369–378. doi:10.1007/s10555-009-9188-5
Lawrie CH, Soneji S, Marafioti T, Cooper CDO, Palazzo S, Paterson JC, Cattan H, Enver T, Mager R, Boultwood J, Wainscoat JS, Hatton CSR (2007) MicroRNA expression distinguishes between germinal center B cell-like and activated B cell-like subtypes of diffuse large B cell lymphoma. Int J Cancer 121:1156–1161. doi:10.1002/ijc.22800
Etheridge A, Lee I, Hood L, Galas D, Wang K (2011) Extracellular microRNA: a new source of biomarkers. Mutat Res 717:85–90. doi:10.1016/j.mrfmmm.2011.03.004
Hanke M, Hoefig K, Merz H, Feller AC, Kausch I, Jocham D, Warnecke JM, Sczakiel G (2010) A robust methodology to study urine microRNA as tumor marker: microRNA-126 and microRNA-182 are related to urinary bladder cancer. Urol Oncol 28:655–661. doi:10.1016/j.urolonc.2009.01.027
Park NJ, Zhou H, Elashoff D, Henson BS, Kastratovic DA, Abemayor E, Wong DT (2009) Salivary microRNA: discovery, characterization, and clinical utility for oral cancer detection. Clin Cancer Res 15:5473–5477. doi:10.1158/1078-0432.CCR-09-0736
Nielsen LB, Wang C, Sorensen K, Bang-Berthelsen CH, Hansen L, Andersen ML, Hougaard P, Juul A, Zhang CY, Pociot F, Mortensen HB (2012) Circulating levels of microRNA from children with newly diagnosed type 1 diabetes and healthy controls: evidence that miR-25 associates to residual beta-cell function and glycaemic control during disease progression. Exp Diabetes Res 2012:896362. doi:10.1155/2012/896362
Liu Y, Gao G, Yang C, Zhou K, Shen B, Liang H, Jiang X (2014) The role of circulating microRNA-126 (miR-126): a novel biomarker for screening prediabetes and newly diagnosed type 2 diabetes mellitus. Int J Mol Sci 15:10567–10577. doi:10.3390/ijms150610567
Yang Z, Chen H, Si H, Li X, Ding X, Sheng Q, Chen P, Zhang H (2014) Serum miR-23a, a potential biomarker for diagnosis of pre-diabetes and type 2 diabetes. Acta Diabetol 51:823–831. doi:10.1007/s00592-014-0617-8
Zhao C, Dong J, Jiang T, Shi Z, Yu B, Zhu Y, Chen D, Xu J, Huo R, Dai J, Xia Y, Pan S, Hu Z, Sha J (2011) Early second-trimester serum miRNA profiling predicts gestational diabetes mellitus. PLoS One 6:e23925. doi:10.1371/journal.pone.0023925
Skalsky RL, Cullen BR (2010) Viruses, microRNAs, and host interactions. Annu Rev Microbiol 64:123–141. doi:10.1146/annurev.micro.112408.134243
Zhang GL, Li YX, Zheng SQ, Liu M, Li X, Tang H (2010) Suppression of hepatitis B virus replication by microRNA-199a-3p and microRNA-210. Antivir Res 88:169–175. doi:10.1016/j.antiviral.2010.08.008
Murakami Y, Aly HH, Tajima A, Inoue I, Shimotohno K (2009) Regulation of the hepatitis C virus genome replication by miR-199a. J Hepatol 50:453–460. doi:10.1016/j.jhep.2008.06.010
Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber C, Saib A, Voinnet O (2005) A cellular microRNA mediates antiviral defense in human cells. Science 308:557–560. doi:10.1126/science.1108784
Chen AK, Sengupta P, Waki K, Van Engelenburg SB, Ochiya T, Ablan SD, Freed EO, Lippincott-Schwartz J (2014) MicroRNA binding to the HIV-1 Gag protein inhibits Gag assembly and virus production. Proc Natl Acad Sci U S A 111:E2676–E2683. doi:10.1073/pnas.1408037111
Anadol E, Schierwagen R, Elfimova N, Tack K, Schwarze-Zander C, Eischeid H, Noetel A, Boesecke C, Jansen C, Dold L, Wasmuth JC, Strassburg CP, Spengler U, Rockstroh JK, Odenthal M, Trebicka J (2015) Circulating microRNAs as a marker for liver injury in human immunodeficiency virus patients. Hepatology 61:46–55. doi:10.1002/hep.27369
Romaine SP, Tomaszewski M, Condorelli G, Samani NJ (2015) MicroRNAs in cardiovascular disease: an introduction for clinicians. Heart 101:921–928. doi:10.1136/heartjnl-2013-305402
Ai J, Zhang R, Li Y, Pu JL, Lu YJ, Jiao JD, Li K, Yu B, Li ZQ, Wang RR, Wang LH, Li Q, Wang N, Shan HL, Li ZY, Yang BF (2010) Circulating microRNA as a potential novel biomarker for acute myocardial infarction. Biochem Biophys Res Commun 391:73–77. doi:10.1016/j.bbrc.2009.11.005
Zampetaki A, Willeit P, Tilling L, Drozdov I, Prokopi M, Renard JM, Mayr A, Weger S, Schett G, Shah A, Boulanger CM, Willeit J, Chowienczyk PJ, Kiechl S, Mayr M (2012) Prospective study on circulating microRNAs and risk of myocardial infarction. J Am Coll Cardiol 60:290–299. doi:10.1016/j.jacc.2012.03.056
Wang GK, Zhu JQ, Zhang JT, Li Q, Li Y, He J, Qin YW, Jing Q (2010) Circulating microRNA: a novel potential biomarker for early diagnosis of acute myocardial infarction in humans. Eur Heart J 31:659–666. doi:10.1093/eurheartj/ehq013
Devaux Y, Vausort M, McCann GP, Kelly D, Collignon O, Ng LL, Wagner DR, Squire IB (2013) A panel of 4 microRNAs facilitates the prediction of left ventricular contractility after acute myocardial infarction. PLoS One 8:e70644. doi:10.1371/journal.pone.0070644
Fineberg SK, Kosik KS, Davidson BL (2009) MicroRNAs potentiate neural development. Neuron 64:303–309. doi:10.1016/j.neuron.2009.10.020
Williams AH, Valdez G, Moresi V, Qi X, McAnally J, Elliott JL, Bassel-Duby R, Sanes JR, Olson EN (2009) MicroRNA-206 delays ALS progression and promotes regeneration of neuromuscular synapses in mice. Science 326:1549–1554. doi:10.1126/science.1181046
Wang WX, Rajeev BW, Stromberg AJ, Ren N, Tang GL, Huang QW, Rigoutsos I, Nelson PT (2008) The expression of microRNA miR-107 decreases early in Alzheimer’s disease and may accelerate disease progression through regulation of beta-site amyloid precursor protein-cleaving enzyme. J Neurosci 28:1213–1223. doi:10.1523/JNEUROSCI.5065-07.2008
Wang G, van der Walt JM, Mayhew G, Li YJ, Züchner S, Scott WK, Martin ER, Vance JM (2008) Variation in the miRNA-433 binding site of FGF20 confers risk for Parkinson disease by overexpression of alpha-synuclein. Am J Hum Genet 82:283–289. doi:10.1016/j.ajhg.2007.09.021
Margis R, Margis R, Rieder CR (2011) Identification of blood microRNAs associated to Parkinsonis disease. J Biotechnol 152:96–101. doi:10.1016/j.jbiotec.2011.01.023
Zhao Z, Zhao Q, Warrick J, Lockwood CM, Woodworth A, Moley KH, Gronowski AM (2012) Circulating microRNA miR-323-3p as a biomarker of ectopic pregnancy. Clin Chem 58:896–905. doi:10.1373/clinchem.2011.179283
Stanczyk J, Pedrioli DM, Brentano F, Sanchez-Pernaute O, Kolling C, Gay RE, Detmar M, Gay S, Kyburz D (2008) Altered expression of MicroRNA in synovial fibroblasts and synovial tissue in rheumatoid arthritis. Arthritis Rheum 58:1001–1009. doi:10.1002/art.23386
Paraskevi A, Theodoropoulos G, Papaconstantinou I, Mantzaris G, Nikiteas N, Gazouli M (2012) Circulating MicroRNA in inflammatory bowel disease. J Crohns Colitis 6:900–904. doi:10.1016/j.crohns.2012.02.006
Zhang Y, Jia Y, Zheng RY, Guo YJ, Wang Y, Guo H, Fei MY, Sun SH (2010b) Plasma microRNA-122 as a biomarker for viral-, alcohol-, and chemical-related hepatic diseases. Clin Chem 56:1830–1838. doi:10.1373/clinichem.2010.147850
Cermelli S, Ruggieri A, Marrero JA, Ioannou GN, Beretta L (2011) Circulating microRNAs in patients with chronic hepatitis C and non-alcoholic fatty liver disease. PLoS One 6:e23937. doi:10.1371/journal.pone.0023937
Ben-Dov IZ, Tan YC, Morozov P, Wilson PD, Rennert H, Blumenfeld JD, Tuschl T (2014) Urine microRNA as potential biomarkers of autosomal dominant polycystic kidney disease progression: description of miRNA profiles at baseline. PLoS One 9:e86856. doi:10.1371/journal.pone.0086856
Lorenzen JM, Kielstein JT, Hafer C, Gupta SK, Kümpers P, Faulhaber-Walter R, Haller H, Fliser D, Thum T (2011) Circulating miR-210 predicts survival in critically ill patients with acute kidney injury. Clin J Am Soc Nephrol 6:1540–1546. doi:10.2215/CJN.00430111
Aigner A (2008) Cellular delivery in vivo of siRNA-based therapeutics. Curr Pharm Des 14:3603–3619. doi:10.2174/138161208786898815
Yang N (2015) An overview of viral and nonviral delivery systems for microRNA. Int J Pharm Investig 5:179–181. doi:10.4103/2230-973X.167646
Drug labeling, drugs@FDA. https://www.accessdata.fda.gov/scripts/cder/drugsatfda/
Chugh P, Dittmer DP (2012) Potential pitfalls in microRNA profiling. Wiley Interdiscip Rev RNA 3:601–616. doi:10.1002/wrna.1120
Wang Y, Zheng D, Tan Q, Wang MX, Gu LQ (2011) Nanopore-based detection of circulating microRNAs in lung cancer patients. Nat Nanotechnol 6:668–674. doi:10.1038/nnano.2011.147
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Huang, W. (2017). MicroRNAs: Biomarkers, Diagnostics, and Therapeutics. In: Huang, J., et al. Bioinformatics in MicroRNA Research. Methods in Molecular Biology, vol 1617. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7046-9_4
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