Review Article

Updates on the Current Technologies for microRNA Profiling

Author(s): Rebecca Mathew, Valentina Mattei, Muna Al Hashmi and Sara Tomei*

Volume 9, Issue 1, 2020

Page: [17 - 24] Pages: 8

DOI: 10.2174/2211536608666190628112722

Abstract

MicroRNAs are RNA molecules of ~22 nt length that regulate gene expression posttranscriptionally. The role of miRNAs has been reported in many cellular processes including apoptosis, cell differentiation, development and proliferation. The dysregulated expression of miRNAs has been proposed as a biomarker for the diagnosis, onset and prognosis of human diseases. The utility of miRNA profiles to identify and discriminate patients from healthy individuals is highly dependent on the sensitivity and specificity of the technologies used for their detection and the quantity and quality of starting material. In this review, we present an update of the current technologies for the extraction, QC assessment and detection of miRNAs with special focus to the most recent methods, discussing their advantages as well as their shortcomings.

Keywords: Microarray, miRNA, PCR, quality control, sequencing, miRNA extraction.

Graphical Abstract

[1]
Ha M, Kim VN. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 2014; 15(8): 509-24.
[http://dx.doi.org/10.1038/nrm3838] [PMID: 25027649]
[2]
Jonas S, Izaurralde E. Towards a molecular understanding of microRNA-mediated gene silencing. Nat Rev Genet 2015; 16(7): 421-33.
[http://dx.doi.org/10.1038/nrg3965] [PMID: 26077373]
[3]
Gulyaeva LF, Kushlinskiy NE. Regulatory mechanisms of microRNA expression. J Transl Med 2016; 14(1): 143.
[http://dx.doi.org/10.1186/s12967-016-0893-x] [PMID: 27197967]
[4]
Vishnoi A, Rani S. MiRNA biogenesis and regulation of diseases: an overview. Methods Mol Biol 2017; 1509: 1-10.
[http://dx.doi.org/10.1007/978-1-4939-6524-3_1] [PMID: 27826912]
[5]
Kosaka N, Iguchi H, Ochiya T. Circulating microRNA in body fluid: A new potential biomarker for cancer diagnosis and prognosis. Cancer Sci 2010; 101(10): 2087-92.
[http://dx.doi.org/10.1111/j.1349-7006.2010.01650.x] [PMID: 20624164]
[6]
Finnegan EF, Pasquinelli AE. MicroRNA biogenesis: regulating the regulators. Crit Rev Biochem Mol Biol 2013; 48(1): 51-68.
[http://dx.doi.org/10.3109/10409238.2012.738643] [PMID: 23163351]
[7]
Carthew RW, Sontheimer EJ. Origins and mechanisms of miRNAs and siRNAs. Cell 2009; 136(4): 642-55.
[http://dx.doi.org/10.1016/j.cell.2009.01.035] [PMID: 19239886]
[8]
Winter J, Jung S, Keller S, Gregory RI, Diederichs S. Many roads to maturity: microRNA biogenesis pathways and their regulation. Nat Cell Biol 2009; 11(3): 228-34.
[http://dx.doi.org/10.1038/ncb0309-228] [PMID: 19255566]
[9]
Jinek M, Doudna JA. A three-dimensional view of the molecular machinery of RNA interference. Nature 2009; 457(7228): 405-12.
[http://dx.doi.org/10.1038/nature07755] [PMID: 19158786]
[10]
Brown RAM, Epis MR, Horsham JL, Kabir TD, Richardson KL, Leedman PJ. Total RNA extraction from tissues for microRNA and target gene expression analysis: not all kits are created equal. BMC Biotechnol 2018; 18(1): 16.
[http://dx.doi.org/10.1186/s12896-018-0421-6] [PMID: 29548320]
[11]
El-Khoury V, Pierson S, Kaoma T, Bernardin F, Berchem G. Assessing cellular and circulating miRNA recovery: the impact of the RNA isolation method and the quantity of input material. Sci Rep 2016; 6: 19529.
[http://dx.doi.org/10.1038/srep19529] [PMID: 26787294]
[12]
Eldh M, Lötvall J, Malmhäll C, Ekström K. Importance of RNA isolation methods for analysis of exosomal RNA: evaluation of different methods. Mol Immunol 2012; 50(4): 278-86.
[http://dx.doi.org/10.1016/j.molimm.2012.02.001] [PMID: 22424315]
[13]
Lu TX, Rothenberg ME. MicroRNA. J Allergy Clin Immunol 2018; 141(4): 1202-7.
[http://dx.doi.org/10.1016/j.jaci.2017.08.034] [PMID: 29074454]
[14]
Weber JA, Baxter DH, Zhang S, et al. The microRNA spectrum in 12 body fluids. Clin Chem 2010; 56(11): 1733-41.
[http://dx.doi.org/10.1373/clinchem.2010.147405] [PMID: 20847327]
[15]
Moldovan L, Batte KE, Trgovcich J, Wisler J, Marsh CB, Piper M. Methodological challenges in utilizing miRNAs as circulating biomarkers. J Cell Mol Med 2014; 18(3): 371-90.
[http://dx.doi.org/10.1111/jcmm.12236] [PMID: 24533657]
[16]
Kim YK, Yeo J, Kim B, Ha M, Kim VN. Short structured RNAs with low GC content are selectively lost during extraction from a small number of cells. Mol Cell 2012; 46(6): 893-5.
[http://dx.doi.org/10.1016/j.molcel.2012.05.036] [PMID: 22749402]
[17]
Fleige S, Pfaffl MW. RNA integrity and the effect on the real-time qRT-PCR performance. Mol Aspects Med 2006; 27(2-3): 126-39.
[http://dx.doi.org/10.1016/j.mam.2005.12.003] [PMID: 16469371]
[18]
Jones LJ, Yue ST, Cheung CY, Singer VL. RNA quantitation by fluorescence-based solution assay: riboGreen reagent characterization. Anal Biochem 1998; 265(2): 368-74.
[http://dx.doi.org/10.1006/abio.1998.2914] [PMID: 9882416]
[19]
Le Pecq JB, Paoletti C. A new fluorometric method for RNA and DNA determination. Anal Biochem 1966; 17(1): 100-7.
[http://dx.doi.org/10.1016/0003-2697(66)90012-1] [PMID: 6008008]
[20]
Mueller O, Hahnenberger K, Dittmann M, et al. A microfluidic system for high-speed reproducible DNA sizing and quantitation. Electrophoresis 2000; 21(1): 128-34.
[http://dx.doi.org/10.1002/(SICI)1522-2683(20000101)21:1<128:AID-ELPS128>3.0.CO;2-M] [PMID: 10634479]
[21]
Schroeder A, Mueller O, Stocker S, et al. The RIN: an RNA integrity number for assigning integrity values to RNA measurements. BMC Mol Biol 2006; 7: 3.
[http://dx.doi.org/10.1186/1471-2199-7-3] [PMID: 16448564]
[22]
Becker C, Hammerle-Fickinger A, Riedmaier I, Pfaffl MW. mRNA and microRNA quality control for RT-qPCR analysis. Methods 2010; 50(4): 237-43.
[http://dx.doi.org/10.1016/j.ymeth.2010.01.010] [PMID: 20079844]
[23]
Pritchard CC, Cheng HH, Tewari M. MicroRNA profiling: approaches and considerations. Nat Rev Genet 2012; 13(5): 358-69.
[http://dx.doi.org/10.1038/nrg3198] [PMID: 22510765]
[24]
Koshiol J, Wang E, Zhao Y, Marincola F, Landi MT. Strengths and limitations of laboratory procedures for microRNA detection. Cancer Epidemiol Biomarkers Prev 2010; 19(4): 907-11.
[http://dx.doi.org/10.1158/1055-9965.EPI-10-0071] [PMID: 20332265]
[25]
Redshaw N, Wilkes T, Whale A, Cowen S, Huggett J, Foy CA. A comparison of miRNA isolation and RT-qPCR technologies and their effects on quantification accuracy and repeatability. Biotechniques 2013; 54(3): 155-64.
[http://dx.doi.org/10.2144/000114002] [PMID: 23477383]
[26]
Wark AW, Lee HJ, Corn RM. Multiplexed detection methods for profiling microRNA expression in biological samples. Angew Chem Int Ed Engl 2008; 47(4): 644-52.
[http://dx.doi.org/10.1002/anie.200702450] [PMID: 17994653]
[27]
Bartel DP. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 2004; 116(2): 281-97.
[http://dx.doi.org/10.1016/S0092-8674(04)00045-5] [PMID: 14744438]
[28]
Válóczi A, Hornyik C, Varga N, Burgyán J, Kauppinen S, Havelda Z. Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res 2004; 32(22)e175
[http://dx.doi.org/10.1093/nar/gnh171] [PMID: 15598818]
[29]
Hunt EA, Broyles D, Head T, Deo SK. MicroRNA detection: current technology and research strategies. Annu Rev Anal Chem (Palo Alto, Calif) 2015; 8: 217-37.
[http://dx.doi.org/10.1146/annurev-anchem-071114-040343] [PMID: 25973944]
[30]
Kim SW, Li Z, Moore PS, et al. A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res 2010; 38(7)e98
[http://dx.doi.org/10.1093/nar/gkp1235] [PMID: 20081203]
[31]
Pall GS, Codony-Servat C, Byrne J, Ritchie L, Hamilton A. Carbodiimide-mediated cross-linking of RNA to nylon membranes improves the detection of siRNA, miRNA and piRNA by northern blot. Nucleic Acids Res 2007; 35(8)e60
[http://dx.doi.org/10.1093/nar/gkm112] [PMID: 17405769]
[32]
Chen C, Ridzon DA, Broomer AJ, et al. Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 2005; 33(20)e179
[http://dx.doi.org/10.1093/nar/gni178] [PMID: 16314309]
[33]
Shi R, Chiang VL. Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 2005; 39(4): 519-25.
[http://dx.doi.org/10.2144/000112010] [PMID: 16235564]
[34]
Chugh P, Dittmer DP. Potential pitfalls in microRNA profiling. Wiley Interdiscip Rev RNA 2012; 3(5): 601-16.
[http://dx.doi.org/10.1002/wrna.1120] [PMID: 22566380]
[35]
Peltier HJ, Latham GJ. Normalization of microRNA expression levels in quantitative RT-PCR assays: identification of suitable reference RNA targets in normal and cancerous human solid tissues. RNA 2008; 14(5): 844-52.
[http://dx.doi.org/10.1261/rna.939908] [PMID: 18375788]
[36]
Meyer SU, Kaiser S, Wagner C, Thirion C, Pfaffl MW. Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs--a comparative study. PLoS One 2012; 7(6)e38946
[http://dx.doi.org/10.1371/journal.pone.0038946] [PMID: 22723911]
[37]
Popov A, Szabo A, Mandys V. Small nucleolar RNA U91 is a new internal control for accurate microRNAs quantification in pancreatic cancer. BMC Cancer 2015; 15: 774.
[http://dx.doi.org/10.1186/s12885-015-1785-9] [PMID: 26499892]
[38]
Balcells I, Cirera S, Busk PK. Specific and sensitive quantitative RT-PCR of miRNAs with DNA primers. BMC Biotechnol 2011; 11: 70.
[http://dx.doi.org/10.1186/1472-6750-11-70] [PMID: 21702990]
[39]
Dong H, Lei J, Ding L, Wen Y, Ju H, Zhang X. MicroRNA: function, detection, and bioanalysis. Chem Rev 2013; 113(8): 6207-33.
[http://dx.doi.org/10.1021/cr300362f] [PMID: 23697835]
[40]
Tam S, de Borja R, Tsao MS, McPherson JD. Robust global microRNA expression profiling using next-generation sequencing technologies. Lab Invest 2014; 94(3): 350-8.
[http://dx.doi.org/10.1038/labinvest.2013.157] [PMID: 24445778]
[41]
Geiss GK, Bumgarner RE, Birditt B, et al. Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol 2008; 26(3): 317-25.
[http://dx.doi.org/10.1038/nbt1385] [PMID: 18278033]
[42]
Wyman SK, Knouf EC, Parkin RK, et al. Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. Genome Res 2011; 21(9): 1450-61.
[http://dx.doi.org/10.1101/gr.118059.110] [PMID: 21813625]
[43]
Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet 2010; 11(1): 31-46.
[http://dx.doi.org/10.1038/nrg2626] [PMID: 19997069]
[44]
van Rooij E. The art of microRNA research. Circ Res 2011; 108(2): 219-34.
[http://dx.doi.org/10.1161/CIRCRESAHA.110.227496] [PMID: 21252150]
[45]
Peterson SM, Thompson JA, Ufkin ML, Sathyanarayana P, Liaw L, Congdon CB. Common features of microRNA target prediction tools. Front Genet 2014; 5: 23.
[http://dx.doi.org/10.3389/fgene.2014.00023] [PMID: 24600468]
[46]
Ritchie W, Rasko JE, Flamant S. MicroRNA target prediction and validation. Adv Exp Med Biol 2013; 774: 39-53.
[http://dx.doi.org/10.1007/978-94-007-5590-1_3] [PMID: 23377967]
[47]
Tarang S, Weston MD. Macros in microRNA target identification: a comparative analysis of in silico, in vitro, and in vivo approaches to microRNA target identification. RNA Biol 2014; 11(4): 324-33.
[http://dx.doi.org/10.4161/rna.28649] [PMID: 24717361]
[48]
Vlachos IS, Hatzigeorgiou AG. Online resources for miRNA analysis. Clin Biochem 2013; 46(10-11): 879-900.
[http://dx.doi.org/10.1016/j.clinbiochem.2013.03.006] [PMID: 23518312]
[49]
Bedognetti D, Balwit JM, Wang E, et al. SITC/iSBTc cancer immunotherapy biomarkers resource document: online resources and useful tools - a compass in the land of biomarker discovery. J Transl Med 2011; 9: 155.
[http://dx.doi.org/10.1186/1479-5876-9-155] [PMID: 21929757]
[50]
Reczko M, Maragkakis M, Alexiou P, Grosse I, Hatzigeorgiou AG. Functional microRNA targets in protein coding sequences. Bioinformatics 2012; 28(6): 771-6.
[http://dx.doi.org/10.1093/bioinformatics/bts043] [PMID: 22285563]
[51]
Betel D, Koppal A, Agius P, Sander C, Leslie C. Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol 2010; 11(8): R90.
[http://dx.doi.org/10.1186/gb-2010-11-8-r90] [PMID: 20799968]
[52]
Garcia DM, Baek D, Shin C, Bell GW, Grimson A, Bartel DP. Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs. Nat Struct Mol Biol 2011; 18(10): 1139-46.
[http://dx.doi.org/10.1038/nsmb.2115] [PMID: 21909094]
[53]
Vergoulis T, Vlachos IS, Alexiou P, et al. TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support. Nucleic Acids Res 2012; 40(Database issue): D222-9.
[http://dx.doi.org/10.1093/nar/gkr1161] [PMID: 22135297]
[54]
Xiao F, Zuo Z, Cai G, Kang S, Gao X, Li T. miRecords: an integrated resource for microRNA-target interactions. Nucleic Acids Res 2009; 37(Database issue): D105-10.
[http://dx.doi.org/10.1093/nar/gkn851] [PMID: 18996891]
[55]
Qavi AJ, Kindt JT, Bailey RC. Sizing up the future of microRNA analysis. Anal Bioanal Chem 2010; 398(6): 2535-49.
[http://dx.doi.org/10.1007/s00216-010-4018-8] [PMID: 20680616]
[56]
Zhang Y, Shuai Z, Zhou H, et al. Single-molecule analysis of microRNA and logic operations using a smart plasmonic nanobiosensor. J Am Chem Soc 2018; 140(11): 3988-93.
[http://dx.doi.org/10.1021/jacs.7b12772] [PMID: 29504757]
[57]
Cissell KA, Rahimi Y, Shrestha S, Hunt EA, Deo SK. Bioluminescence-based detection of microRNA, miR21 in breast cancer cells. Anal Chem 2008; 80(7): 2319-25.
[http://dx.doi.org/10.1021/ac702577a] [PMID: 18302417]
[58]
Huh YS, Chung AJ, Cordovez B, Erickson D. Enhanced on-chip SERS based biomolecular detection using electrokinetically active microwells. Lab Chip 2009; 9(3): 433-9.
[http://dx.doi.org/10.1039/B809702J] [PMID: 19156293]
[59]
Li P, Shan JX, Chen XH, et al. Epigenetic silencing of microRNA-149 in cancer-associated fibroblasts mediates prostaglandin E2/interleukin-6 signaling in the tumor microenvironment. Cell Res 2015; 25(5): 588-603.
[http://dx.doi.org/10.1038/cr.2015.51] [PMID: 25916550]
[60]
Panebianco F, Mazzanti C, Tomei S, et al. The combination of four molecular markers improves thyroid cancer cytologic diagnosis and patient management. BMC Cancer 2015; 15: 918.
[http://dx.doi.org/10.1186/s12885-015-1917-2] [PMID: 26581891]
[61]
Kleivi Sahlberg K, Bottai G, Naume B, et al. A serum microRNA signature predicts tumor relapse and survival in triple-negative breast cancer patients. Clin Cancer Res 2015; 21(5): 1207-14.
[http://dx.doi.org/10.1158/1078-0432.CCR-14-2011] [PMID: 25547678]
[62]
Skinner HD, Lee JH, Bhutani MS, et al. A validated miRNA profile predicts response to therapy in esophageal adenocarcinoma. Cancer 2014; 120(23): 3635-41.
[http://dx.doi.org/10.1002/cncr.28911] [PMID: 25091571]
[63]
Tang S, Wu WK, Li X, et al. Stratification of digestive cancers with different pathological features and survival outcomes by microRNA expression. Sci Rep 2016; 6: 24466.
[http://dx.doi.org/10.1038/srep24466] [PMID: 27080237]

© 2024 Bentham Science Publishers | Privacy Policy