Quantification of tRNA fragments by electrochemical direct detection in small volume biofluid samples.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
05 05 2020
05 05 2020
Historique:
received:
03
02
2020
accepted:
06
04
2020
entrez:
7
5
2020
pubmed:
7
5
2020
medline:
7
1
2021
Statut:
epublish
Résumé
Elevated levels of transfer RNA (tRNA) fragments were recently identified in plasma samples from people with epilepsy in advance of a seizure, indicting a potential novel class of circulating biomarker. Current methods for detection and quantitation of tRNA fragments (tRFs) include northern blotting, RNA sequencing or custom Taqman-based PCR assays. The development of a simple, at home or clinic-based test, would benefit from a simple and reliable method to detect the tRFs using small volumes of biofluids. Here we describe an electrochemical direct detection method based on electrocatalytic platinum nanoparticles to detect 3 specific tRFs: 5'AlaTGC, 5'GlyGCC, and 5'GluCTC. Using synthetic tRF mimics we showed this system was linear over 9 orders of magnitude with sub-attomolar limits of detection. Specificity was tested using naturally occurring mismatched tRF mimics. Finally, we quantified tRF levels in patient plasma and showed that our detection system recapitulates results obtained by qPCR. We have designed a tRF detection system with high sensitivity and specificity capable of quantifying tRFs in low volumes of plasma using benchtop apparatus. This is an important step in the development of a point-of-care device for quantifying tRFs in whole blood.
Identifiants
pubmed: 32371908
doi: 10.1038/s41598-020-64485-4
pii: 10.1038/s41598-020-64485-4
pmc: PMC7200677
doi:
Substances chimiques
Biomarkers
0
Platinum
49DFR088MY
RNA, Transfer
9014-25-9
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
7516Références
Kuhlmann, L., Lehnertz, K., Richardson, M. P., Schelter, B. & Zaveri, H. P. Seizure prediction - ready for a new era. Nat. Rev. Neurol. 14(10), 618–630 (2018).
doi: 10.1038/s41582-018-0055-2
Cook, M. J. et al. Prediction of seizure likelihood with a long-term, implanted seizure advisory system in patients with drug-resistant epilepsy: a first-in-man study. Lancet Neurol. 12(6), 563–71 (2013).
doi: 10.1016/S1474-4422(13)70075-9
Henshall, D. C. et al. MicroRNAs in epilepsy: pathophysiology and clinical utility. Lancet Neurol. 15(13), 1368–1376 (2016).
doi: 10.1016/S1474-4422(16)30246-0
Hogg, M. C. et al. Elevation in plasma tRNA fragments precede seizures in human epilepsy. J. Clin. Invest. 129(7), 2946–2951 (2019).
doi: 10.1172/JCI126346
Palazzo, A. F. & Lee, E. S. Non-coding RNA: what is functional and what is junk? Front. Genet. 6, 2 (2015).
doi: 10.3389/fgene.2015.00002
Li, S., Z. Xu, and J. Sheng, tRNA-Derived Small RNA: A Novel Regulatory Small Non-Coding RNA. Genes (Basel), 2018. 9(5).
Lee, S. R. & Collins, K. Starvation-induced cleavage of the tRNA anticodon loop in Tetrahymena thermophila. J. Biol. Chem. 280(52), 42744–9 (2005).
doi: 10.1074/jbc.M510356200
Spain, E. et al. Direct, non-amplified detection of microRNA-134 in plasma from epilepsy patients. RSC Adv. 5(109), 90071–90078 (2015).
doi: 10.1039/C5RA16352H
McArdle, H. et al. “TORNADO” - Theranostic One-Step RNA Detector; microfluidic disc for the direct detection of microRNA-134 in plasma and cerebrospinal fluid. Sci. Rep. 7(1), 1750 (2017).
doi: 10.1038/s41598-017-01947-2
Kenny, A. et al. Elevated Plasma microRNA-206 Levels Predict Cognitive Decline and Progression to Dementia from Mild Cognitive Impairment. Biomolecules, 2019. 9(11).
Spain, E., Brennan, E., McArdle, H., Keyes, T. E. & Forster, R. J. High sensitivity DNA detection based on regioselectively decorated electrocatalytic nanoparticles. Anal. Chem. 84(15), 6471–6 (2012).
doi: 10.1021/ac300458x
Spain, E., Brennan, E., Keyes, T. E. & Forster, R. J. Dual function metal nanoparticles: Electrocatalysis and DNA capture. Electrochim. Acta 128, 61–66 (2014).
doi: 10.1016/j.electacta.2013.10.025
Shabaninejad, Z. et al. Electrochemical-based biosensors for microRNA detection: Nanotechnology comes into view. Anal. Biochem. 581, 113349 (2019).
doi: 10.1016/j.ab.2019.113349
Azimzadeh, M., Rahaie, M., Nasirizadeh, N., Ashtari, K. & Naderi-Manesh, H. An electrochemical nanobiosensor for plasma miRNA-155, based on graphene oxide and gold nanorod, for early detection of breast cancer. Biosens. Bioelectron. 77, 99–106 (2016).
doi: 10.1016/j.bios.2015.09.020
Guo, J. et al. An electrochemical biosensor for microRNA-196a detection based on cyclic enzymatic signal amplification and template-free DNA extension reaction with the adsorption of methylene blue. Biosens. Bioelectron. 105, 103–108 (2018).
doi: 10.1016/j.bios.2018.01.036
Sowmya, K., Sudheendra, U., Khan, S., Nagpal, N. & Prathamesh, S. Assessment of morphological changes and DNA quantification: An in vitro study on acid-immersed teeth. J. Forensic Dent. Sci. 5(1), 42–6 (2013).
doi: 10.4103/0975-1475.114560
Spain, E., McArdle, H., Keyes, T. E. & Forster, R. J. Detection of sub-femtomolar DNA based on double potential electrodeposition of electrocatalytic platinum nanoparticles. Analyst 138(15), 4340–4 (2013).
doi: 10.1039/c3an00500c
Azimzadeh, M., Rahaie, M., Nasirizadeh, N., Daneshpour, M. & Naderi-Manesh, H. Electrochemical miRNA Biosensors: The Benefits of nanotechnology. Nanomed. Res. J. 2(1), 36–48 (2017).
Khan, S. et al. Circadian rhythm and epilepsy. Lancet Neurol. 17(12), 1098–1108 (2018).
doi: 10.1016/S1474-4422(18)30335-1
Tao, E. W., Cheng, W. Y., Li, W. L., Yu, J. & Gao, Q. Y. tiRNAs: A novel class of small noncoding RNAs that helps cells respond to stressors and plays roles in cancer progression. J. Cell Physiol. 235(2), 683–690 (2020).
doi: 10.1002/jcp.29057
Emara, M. M. et al. Angiogenin-induced tRNA-derived stress-induced RNAs promote stress-induced stress granule assembly. J. Biol. Chem. 285(14), 10959–68 (2010).
doi: 10.1074/jbc.M109.077560
Ivanov, P., Emara, M. M., Villen, J., Gygi, S. P. & Anderson, P. Angiogenin-induced tRNA fragments inhibit translation initiation. Mol. Cell 43(4), 613–23 (2011).
doi: 10.1016/j.molcel.2011.06.022
Saikia, M. et al. Angiogenin-cleaved tRNA halves interact with cytochrome c, protecting cells from apoptosis during osmotic stress. Mol. Cell Biol. 34(13), 2450–63 (2014).
doi: 10.1128/MCB.00136-14
Kim, H. K. et al. A transfer-RNA-derived small RNA regulates ribosome biogenesis. Nature 552(7683), 57–62 (2017).
doi: 10.1038/nature25005
Chen, Q. et al. Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science 351(6271), 397–400 (2016).
doi: 10.1126/science.aad7977
Sharma, U. et al. Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 351(6271), 391–396 (2016).
doi: 10.1126/science.aad6780
Honda, S. et al. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc. Natl Acad. Sci. USA 112(29), E3816–25 (2015).
doi: 10.1073/pnas.1510077112
Goodarzi, H. et al. Endogenous tRNA-Derived Fragments Suppress Breast Cancer Progression via YBX1 Displacement. Cell 161(4), 790–802 (2015).
doi: 10.1016/j.cell.2015.02.053
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25(4), 402–8 (2001).
doi: 10.1006/meth.2001.1262
Kim, S. W. et al. A sensitive non-radioactive northern blot method to detect small RNAs. Nucleic Acids Res. 38(7), e98 (2010).
doi: 10.1093/nar/gkp1235