基于核酸酶辅助信号放大的2’-O-甲基修饰分子信标用于高灵敏和特异性外泌体肿瘤microRNA分析
2’-O-Methyl-Modified Molecular Beacons for Highly Sensitive and Specific Exosomal Tumor microRNA Analysis Based on Nuclease-Assisted Signal Amplification
摘要: 外泌体是新兴的重要癌症生物标志物。有效检测外泌体和外泌体内容物,特别是microRNA (miRNA),对于癌症的诊断和治疗是迫切且具有挑战性的。基于双链特异性核酸酶(Duplex specific nuclease, DSN)的特异性识别和消化能力,我们设计了一个2’-O-甲基修饰的分子信标(2’-O-methyl-modified molecular beacon, omMB),并开发了一个高灵敏度和特异性分析外泌体miRNA的信号放大检测平台。该方法以A375细胞分泌的外泌体为模型,以microRNA-21 (miR-21)为模型miRNA分子,可以检测到低至37.9 pM的miRNA和2 μg/mL的裂解外泌体。同时,与许多已开发的DSN辅助信号放大方法相比,新方法具有较高的特异性,可以区分错配miRNA。总之,这项工作为医学分析、临床应用和疾病诊断中的外泌体检测提供了一种有效的分析策略。
Abstract: Exosomes are emerging important cancer biomarkers. Effective detection of exosome and exosomal contents, especially microRNA (miRNA), is urgent and challenging for cancer diagnosis and treatment. Based on specific recognition and digestion capacity of duplex specific nuclease (DSN), we designed a 2’-O-methyl-modified molecular beacon (omMB) and proposed an amplified detection platform for highly sensitive and specific analysis of exosomal miRNA. Taking A375 cell secreted exosomes as model targets and microRNA-21 (miR-21) as model miRNA molecules, the proposed method can detect miRNA down to 37.9 pM and 2 μg/mL lysed exosomes. Meanwhile, compared with many developed DSN-assisted amplified methods, the new method has high specificity which can distinguish mismatch miRNA. Overall, this work provides an effective analytical strategy for exosome detection in medical analysis, clinic applications and disease diagnosis.
文章引用:吕天鹏, 柯声锋, 王书皓, 崔亮. 基于核酸酶辅助信号放大的2’-O-甲基修饰分子信标用于高灵敏和特异性外泌体肿瘤microRNA分析[J]. 分析化学进展, 2024, 14(2): 95-105. https://doi.org/10.12677/aac.2024.142012

参考文献

[1] Kalluri, R. and LeBleu, V.S. (2020) The Biology, Function, and Biomedical Applications of Exosomes. Science, 367, eaau6977. [Google Scholar] [CrossRef] [PubMed]
[2] Selmaj, I., Cichalewska, M., Namiecinska, M., Galazka, G., Horzelski, W., Selmaj, K.W. and Mycko, M.P. (2017) Global Exosome Transcriptome Profiling Reveals Biomarkers for Multiple Sclerosis. Annals of Neurology, 81, 703-717. [Google Scholar] [CrossRef] [PubMed]
[3] Barile, L. and Vassalli, G. (2017) Exosomes: Therapy Delivery Tools and Biomarkers of Diseases. Pharmacology & Therapeutics, 174, 63-78. [Google Scholar] [CrossRef] [PubMed]
[4] Cheng, N., Du, D., Wang, X., Liu, D., Xu, W., Luo, Y. and Lin, Y. (2019) Recent Advances in Biosensors for Detecting Cancer-Derived Exosomes. Trends in Biotechnology, 37, 1236-1254. [Google Scholar] [CrossRef] [PubMed]
[5] Stobiecka, M., Ratajczak, K. and Jakiela, S. (2019) Toward Early Cancer Detection: Focus on Biosensing Systems and Biosensors for an Anti-Apoptotic Protein Survivin and Survivin mRNA. Biosensors and Bioelectronics, 137, 58-71. [Google Scholar] [CrossRef] [PubMed]
[6] Drula, R., Ott, L.F., Berindan-Neagoe, I., Pantel, K. and Calin, G.A. (2020) MicroRNAs from Liquid Biopsy Derived Extracellular Vesicles: Recent Advances in Detection and Characterization Methods. Cancers, 12, Article 2009. [Google Scholar] [CrossRef] [PubMed]
[7] Cui, L., Peng, R.X., Zeng, C.F., Zhang, J.L., Lu, Y.Z., Zhu, L., Huang, M.J., Tian, Q.H., Song, Y.L. and Yang, C.Y. (2022) A General Strategy for Detection of Tumor-Derived Extracellular Vesicle MicroRNAs Using Aptamer-Mediated Vesicle Fusion. Nano Today, 46, Article 101599. [Google Scholar] [CrossRef
[8] Niu, Q., Gao, J., Zhao, K., Chen, X., Lin, X., Huang, C., An, Y., Xiao, X., Wu, Q., Cui, L., Zhang, P., Wu, L. and Yang, C. (2022) Fluid Nanoporous Microinterface Enables Multiscale-Enhanced Affinity Interaction for Tumor-Derived Extracellular Vesicle Detection. Proceedings of the National Academy of Sciences of the United States of America, 119, e2213236119. [Google Scholar] [CrossRef] [PubMed]
[9] Jet, T., Gines, G., Rondelez, Y. and Taly, V. (2021) Advances in Multiplexed Techniques for the Detection and Quantification of MicroRNAs. Chemical Society Reviews, 50, 4141-4161. [Google Scholar] [CrossRef
[10] Wu, Y., Zhang, Y., Zhang, X., Luo, S., Yan, X., Qiu, Y., Zheng, L. and Li, L. (2021) Research Advances for Exosomal miRNAs Detection in Biosensing: From the Massive Study to the Individual Study. Biosensors and Bioelectronics, 177, Article 112962. [Google Scholar] [CrossRef] [PubMed]
[11] Ouyang, T., Liu, Z., Han, Z. and Ge, Q. (2019) MicroRNA Detection Specificity: Recent Advances and Future Perspective. Analytical Chemistry, 91, 3179-3186. [Google Scholar] [CrossRef] [PubMed]
[12] Cheng, Y., Dong, L., Zhang, J., Zhao, Y. and Li, Z. (2018) Recent Advances in MicroRNA Detection. Analyst, 143, 1758-1774. [Google Scholar] [CrossRef
[13] Zhou, S., Sun, H., Dong, J., Lu, P., Deng, L., Liu, Y., Yang, M., Huo, D. and Hou, C. (2023) Highly Sensitive and Facile MicroRNA Detection Based on Target Triggered Exponential Rolling-Circle Amplification Coupling with CRISPR/ Cas12a. Analytica Chimica Acta, 1265, Article 341278. [Google Scholar] [CrossRef] [PubMed]
[14] Cui, L., Lin, X., Lin, N., Song, Y., Zhu, Z., Chen, X. and Yang, C.J. (2012) Graphene Oxide-Protected DNA Probes for Multiplex MicroRNA Analysis in Complex Biological Samples Based on a Cyclic Enzymatic Amplification Method. Chemical Communications, 48, 194-196. [Google Scholar] [CrossRef
[15] Jin, D., Yang, F., Zhang, Y., Liu, L., Zhou, Y., Wang, F. and Zhang, G.J. (2018) ExoAPP: Exosome-Oriented, Aptamer Nanoprobe-Enabled Surface Proteins Profiling and Detection. Analytical Chemistry, 90, 14402-14411. [Google Scholar] [CrossRef] [PubMed]
[16] Wang, H., Chen, H., Huang, Z., Li, T., Deng, A. and Kong, J. (2018) DNase I Enzyme-Aided Fluorescence Signal Amplification Based on Graphene Oxide-DNA Aptamer Interactions for Colorectal Cancer Exosome Detection. Talanta, 184, 219-226. [Google Scholar] [CrossRef] [PubMed]
[17] Wu, Y., Cui, S., Li, Q., Zhang, R., Song, Z., Gao, Y., Chen, W. and Xing, D. (2020) Recent Advances in Duplex-Specific Nuclease-Based Signal Amplification Strategies for MicroRNA Detection. Biosensors and Bioelectronics, 165, Article 112449. [Google Scholar] [CrossRef] [PubMed]
[18] Lin, X.Y., Zhang, C., Huang, Y.S., Zhu, Z., Chen, X. and Yang, C.J. (2013) Backbone-Modified Molecular Beacons for Highly Sensitive and Selective Detection of MicroRNAs Based on Duplex Specific Nuclease Signal Amplification. Chemical Communications, 49, 7243-7245. [Google Scholar] [CrossRef] [PubMed]
[19] Li, Y., Zhang, J., Zhao, J., Zhao, L., Cheng, Y. and Li, Z. (2016) A Simple Molecular Beacon with Duplex-Specific Nuclease Amplification for Detection of MicroRNA. Analyst, 141, 1071-1076. [Google Scholar] [CrossRef
[20] Gao, J.F., Li, Y., Li, W.Q., Zeng, C.F., Xi, F.N., Huang, J.H. and Cui, L. (2020) 2’-O-Methyl Molecular Beacon: A Promising Molecular Tool That Permits Elimination of Sticky-End Pairing and Improvement of Detection Sensitivity. RSC Advances, 10, 41618-41624. [Google Scholar] [CrossRef
[21] Zheng, H.Y., Lin, Q.Y., Zhu, J.C., Rao, Y.M., Cui, L., Bao, Y.Y. and Ji, T.H. (2021) DNase I-Assisted 2’-O-Methyl Molecular Beacon for Amplified Detection of Tumor Exosomal MicroRNA-21. Talanta, 235, Article 122727. [Google Scholar] [CrossRef] [PubMed]
[22] Sun, X., Ying, N., Ju, C., Li, Z., Xu, N., Qu, G., Liu, W. and Wan, J. (2018) Modified Beacon Probe Assisted Dual Signal Amplification for Visual Detection of MicroRNA. Analytical Biochemistry, 550, 68-71. [Google Scholar] [CrossRef] [PubMed]
[23] Yin, B.C., Liu, Y.Q. and Ye, B.C. (2012) One-Step, Multiplexed Fluorescence Detection of MicroRNAs Based on Duplex-Specific Nuclease Signal Amplification. Journal of the American Chemical Society, 134, 5064-5067. [Google Scholar] [CrossRef] [PubMed]
[24] Tsourkas, A., Behlke, M.A. and Bao, G. (2002) Hybridization of 2’-O-Methyl and 2’-Deoxy Molecular Beacons to RNA and DNA Targets. Nucleic Acids Research, 30, 5168-5174. [Google Scholar] [CrossRef] [PubMed]
[25] Wang, Y., Gao, X., Wei, F., Zhang, X., Yu, J., Zhao, H., Sun, Q., Yan, F., Yan, C., Li, H. and Ren, X. (2014) Diagnostic and Prognostic Value of Circulating miR-21 for Cancer: A Systematic Review and Meta-Analysis. Gene, 533, 389-397. [Google Scholar] [CrossRef] [PubMed]
[26] Calin, G.A. and Croce, C.M. (2006) MicroRNA Signatures in Human Cancers. Nature Reviews. Cancer, 6, 857-866. [Google Scholar] [CrossRef] [PubMed]
[27] Wang, Q., Yin, B.C. and Ye, B.C. (2016) A Novel Polydopamine-Based Chemiluminescence Resonance Energy Transfer Method for MicroRNA Detection Coupling Duplex-Specific Nuclease-Aided Target Recycling Strategy. Biosensors and Bioelectronics, 80, 366-372. [Google Scholar] [CrossRef] [PubMed]
[28] Yang, C., Dou, B., Shi, K., Chai, Y., Xiang, Y. and Yuan, R. (2014) Multiplexed and Amplified Electronic Sensor for the Detection of MicroRNAs from Cancer Cells. Analytical Chemistry, 86, 11913-11918. [Google Scholar] [CrossRef] [PubMed]
[29] Yuan, Y.H., Chi, B.Z., Wen, S.H., Liang, R.P., Li, Z.M. and Qiu, J.D. (2018) Ratiometric Electrochemical Assay for Sensitive Detecting MicroRNA Based on Dual-Amplification Mechanism of Duplex-Specific Nuclease and Hybridization Chain Reaction. Biosensors and Bioelectronics, 102, 211-216. [Google Scholar] [CrossRef] [PubMed]
[30] Wang, H., He, D., Wan, K., Sheng, X., Cheng, H., Huang, J., Zhou, X., He, X. and Wang, K. (2020) In situ Multiplex Detection of Serum Exosomal MicroRNAs Using an All-in-One Biosensor for Breast Cancer Diagnosis. Analyst, 145, 3289-3296. [Google Scholar] [CrossRef
[31] Lee, J.H., Kim, J.A., Kwon, M.H., Kang, J.Y. and Rhee, W.J. (2015) In situ Single Step Detection of Exosome MicroRNA Using Molecular Beacon. Biomaterials, 54, 116-125. [Google Scholar] [CrossRef] [PubMed]
[32] Gao, Z., Yuan, H., Mao, Y., Ding, L., Effah, C.Y., He, S., He, L., Liu, L.E., Yu, S., Wang, Y., Wang, J., Tian, Y., Yu, F., Guo, H., Miao, L., Qu, L. and Wu, Y. (2021) In situ Detection of Plasma Exosomal MicroRNA for Lung Cancer Diagnosis Using Duplex-Specific Nuclease and MoS2 Nanosheets. Analyst, 146, 1924-1931. [Google Scholar] [CrossRef
[33] Liu, H., Fan, J.L., Liu, W.P., Tong, C.Y., Xie, Z.H., Deng, R.L. and Long, X.Y. (2018) A Dual Signal Amplification Method for miR-204 Assay by Combining Chimeric Molecular Beacon with Double-Stranded Nuclease. Analytical Methods, 10, 5834-5841. [Google Scholar] [CrossRef
[34] Xie, Y., Lin, X.Y., Huang, Y.S., Pan, R.J., Zhu, Z., Zhou, L.J. and Yang, C.Y.J. (2015) Highly Sensitive and Selective Detection of miRNA: DNase I-Assisted Target Recycling Using DNA Probes Protected by Polydopamine Nanospheres. Chemical Communications, 51, 2156-2158. [Google Scholar] [CrossRef
[35] Tang, Y.F., Liu, M.X., Xu, L.C., Tian, J.N., Yang, X.L., Zhao, Y.C. and Zhao, S.L. (2018) A Simple and Rapid Dual-Cycle Amplification Strategy for MicroRNA Based on Graphene Oxide and Exonuclease III-Assisted Fluorescence Recovery. Analytical Methods, 10, 3777-3782. [Google Scholar] [CrossRef
[36] Liu, M.X., Liang, S.P., Tang, Y.F., Tian, J.N., Zhao, Y.C. and Zhao, S.L. (2018) Rapid and Label-Free Fluorescence Bioassay for MicroRNA Based on Exonuclease III-Assisted Cycle Amplification. RSC Advances, 8, 15967-15972. [Google Scholar] [CrossRef
[37] Wei, K.J., Zhao, J.J., Qin, Y.F., Li, S.T., Huang, Y. and Zhao, S.L. (2018) A Novel Multiplex Signal Amplification Strategy Based on Microchip Electrophoresis Platform for the Improved Separation and Detection of MicroRNAs. Talanta, 189, 437-441. [Google Scholar] [CrossRef] [PubMed]
[38] Bonnet, G., Tyagi, S., Libchaber, A. and Kramer, F.R. (1999) Thermodynamic Basis of the Enhanced Specificity of Structured DNA Probes. Proceedings of the National Academy of Sciences of the United States of America, 96, 6171-6176. [Google Scholar] [CrossRef] [PubMed]
[39] Lu, Y.Y., Wang, L. and Chen, H.Q. (2019) Turn-on Detection of MicroRNA155 Based on Simple UCNPs-DNA-AuNPs Luminescence Energy Transfer Probe and Duplex-Specific Nuclease Signal Amplification. Spectrochimica Acta Part A: Molecular Spectroscopy, 223, Article 117345. [Google Scholar] [CrossRef] [PubMed]
[40] Li, Y.T., Tang, D.H., Zhu, L., Cai, J.T., Chu, C.N., Wang, J., Xia, M., Cao, Z.Z. and Zhu, H. (2019) Label-Free Detection of miRNA Cancer Markers Based on Terminal Deoxynucleotidyl Transferase-Induced Copper Nanoclusters. Analytical Biochemistry, 585, Article 113346. [Google Scholar] [CrossRef] [PubMed]
[41] Liu, Q., Kang, P.J., Chen, Z.P., Shi, C.X., Chen, Y. and Yu, R.Q. (2019) Highly Specific and Sensitive Detection of MicroRNAs by Tandem Signal Amplification Based on Duplex-Specific Nuclease and Strand Displacement. Chemical Communications, 55, 14210-14213. [Google Scholar] [CrossRef
[42] Degliangeli, F., Kshirsagar, P., Brunetti, V., Pompa, P.P. and Fiammengo, R. (2014) Absolute and Direct MicroRNA Quantification Using DNA-Gold Nanoparticle Probes. Journal of the American Chemical Society, 136, 2264-2267. [Google Scholar] [CrossRef] [PubMed]
[43] Tan, L., Xu, L., Liu, J.W., Tang, L.J., Tang, H. and Yu, R.Q. (2019) Duplex-Specific Nuclease-Mediated Target Recycling Amplification for Fluorescence Detection of MicroRNA. Analytical Methods, 11, 200-204. [Google Scholar] [CrossRef
[44] Peng, W.P., Zhao, Q., Piao, J.F., Zhao, M., Huang, Y.W., Zhang, B., Gao, W.C., Zhou, D.M., Shu, G.M., Gong, X.Q. and Chang, J. (2018) Ultra-Sensitive Detection of MicroRNA-21 Based on Duplex-Specific Nuclease-Assisted Target Recycling and Horseradish Peroxidase Cascading Signal Amplification. Sensors and Actuators B: Chemical, 263, 289-297. [Google Scholar] [CrossRef
[45] Xiao, M.S., Chandrasekaran, A.R., Ji, W., Li, F., Man, T.T., Zhu, C.F., Shen, X.Z., Pei, H., Li, Q. and Li, L. (2018) Affinity-Modulated Molecular Beacons on MoS2 Nanosheets for MicroRNA Detection. ACS Applied Materials & Interfaces, 10, 35794-35800. [Google Scholar] [CrossRef] [PubMed]
[46] Wu, Z.F., Zhou, H., He, J., Li, M., Ma, X.M., Xue, J., Li, X. and Fan, X.T. (2019) G-Triplex Based Molecular Beacon with Duplex-Specific Nuclease Amplification for the Specific Detection of MicroRNA. Analyst, 144, 5201-5206. [Google Scholar] [CrossRef