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Ariyeloye S, Kämmerer S, Klapproth E, Wielockx B, El-Armouche A. Intertwined regulators: hypoxia pathway proteins, microRNAs, and phosphodiesterases in the control of steroidogenesis. Pflugers Arch 2024; 476:1383-1398. [PMID: 38355819 PMCID: PMC11310285 DOI: 10.1007/s00424-024-02921-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/25/2024] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
Oxygen sensing is of paramount importance for maintaining cellular and systemic homeostasis. In response to diminished oxygen levels, the hypoxia-inducible factors (HIFs) orchestrate various biological processes. These pivotal transcription factors have been identified as key regulators of several biological events. Notably, extensive research from our group and others has demonstrated that HIF1α exerts an inverse regulatory effect on steroidogenesis, leading to the suppression of crucial steroidogenic enzyme expression and a subsequent decrease in steroid levels. These steroid hormones occupy pivotal roles in governing a myriad of physiological processes. Substantial or prolonged fluctuations in steroid levels carry detrimental consequences across multiple organ systems and underlie various pathological conditions, including metabolic and immune disorders. MicroRNAs serve as potent mediators of multifaceted gene regulatory mechanisms, acting as influential epigenetic regulators that modulate a broad spectrum of gene expressions. Concomitantly, phosphodiesterases (PDEs) play a crucial role in governing signal transduction. PDEs meticulously manage intracellular levels of both cAMP and cGMP, along with their respective signaling pathways and downstream targets. Intriguingly, an intricate interplay seems to exist between hypoxia signaling, microRNAs, and PDEs in the regulation of steroidogenesis. This review highlights recent advances in our understanding of the role of microRNAs during hypoxia-driven processes, including steroidogenesis, as well as the possibilities that exist in the application of HIF prolyl hydroxylase (PHD) inhibitors for the modulation of steroidogenesis.
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Affiliation(s)
- Stephen Ariyeloye
- Institute of Clinical Chemistry and Laboratory Medicine, Dresden, Germany
| | - Susanne Kämmerer
- Department of Pharmacology and Toxicology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Erik Klapproth
- Department of Pharmacology and Toxicology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany
| | - Ben Wielockx
- Institute of Clinical Chemistry and Laboratory Medicine, Dresden, Germany.
| | - Ali El-Armouche
- Department of Pharmacology and Toxicology, Medical Faculty, Technische Universität Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
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2
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Tian Z, Luo J, Zhang C, Li Y, Hu S, Li Y. Photonic crystal-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit for enzyme-free and ultrasensitive analysis of two microRNAs. Talanta 2024; 277:126428. [PMID: 38897009 DOI: 10.1016/j.talanta.2024.126428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 05/18/2024] [Accepted: 06/13/2024] [Indexed: 06/21/2024]
Abstract
The development of sensitive and efficient analytical methods for multiple biomarkers is crucial for cancer screening at early stage. MicroRNAs (miRNAs) are a kind of biomarkers with diagnostic potential for cancer. However, the ultrasensitive and logical analysis of multiple miRNAs with simple operation still faces some challenges. Herein, a photonic crystal (PC)-enhanced fluorescence biosensor with logic gate operation based on one-pot cascade amplification DNA circuit was developed for enzyme-free and ultrasensitive analysis of two cancer-related miRNAs. The fluorescence biosensor was performed by biochemical recognition amplification module (BCRAM) and physical enhancement module (PEM) to achieve logical and sensitive detection. In the BCRAM, one-pot cascade amplification circuit consisted of the upstream parallel entropy-driven circuit (EDC) and the downstream shared catalytic hairpin assembly (CHA). The input of target miRNA would trigger each corresponding EDC, and the parallel EDCs released the same R strand for triggering subsequent CHA; thus, the OR logic gate was obtained with minimization of design and operation. In the PEM, photonic crystal (PC) array was prepared easily for specifically enhancing the fluorescence output from BCRAM by the optical modulation capabilities; meanwhile, the high-throughput signal readout was achieved by microplate analyzer. Benefiting from the integrated advantages of two modules, the proposed biosensor achieved ultrasensitive detection of two miRNAs with easy logic gate operation, obtaining the LODs of 8.6 fM and 6.7 fM under isothermal and enzyme-free conditions. Hence, the biosensor has the advantages of high sensitivity, easy operation, multiplex and high-throughput analysis, showing great potential for cancer screening at early stage.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jie Luo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Chuyan Zhang
- Precision Medicine Center, Medical Equipment Innovation Research Center, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongru Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
| | - Shunming Hu
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
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Qi Y, Sun J, Wang S, Ren W, Liu C. Mix-and-Read Digital MicroRNA Analysis Based on Flow Cytometric Counting of Target-Clicked Nanobead Dimer. Anal Chem 2024; 96:13734-13741. [PMID: 39114879 DOI: 10.1021/acs.analchem.4c03092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
A one-step, enzyme-free, and highly sensitive digital microRNA (miRNA) assay is rationally devised based on flow cytometric counting of target miRNA-clicked nanobead dimers via a facile mix-and-read manner. In this strategy, highly efficient miRNA-sandwiched click chemical ligation of two DNA probes may remarkably stabilize and boost the dimer formation between two kinds of fluorescence-coded nanobeads, and the number of as-produced bead dimers will be target dose-responsive, particularly when the trace number of miRNA is much less than that of employed nanobeads. Finally, each fluorescence-coded bead dimer can be easily identified and digitally counted by a powerful flow cytometer (FCM) and accordingly, the amount of target miRNA can be accurately quantified in a digital way. This new digital miRNA assay can be accomplished with a facile mix-and-read operation just by simply mixing the target miRNA with two kinds of preprepared DNA probe-functionalized nanobeads, which do not require any nucleic acid amplification, purification, and complex operation procedures. In spite of the extremely simple one-step operation, benefiting from the low-background but high target-mediated click ligation efficiency, and the powerfully digital statistical capability of FCM, this strategy achieves high sensitivity with a quite low detection limit of 5.2 fM target miRNA as well as high specificity and good generality for miRNA analysis, pioneering a new direction for fabricating digital bioassays.
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Affiliation(s)
- Yan Qi
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an 710021, Shaanxi Province, P. R. China
- Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an 710021, Shaanxi Province, P. R. China
| | - Junyue Sun
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Shan Wang
- Institute of Basic and Translational Medicine & Shaanxi Key Laboratory of Brain Disorders, Xi'an Medical University, Xi'an 710021, Shaanxi Province, P. R. China
- Engineering Research Center of Brain Diseases Drug Development, Universities of Shaanxi Province, Xi'an Medical University, Xi'an 710021, Shaanxi Province, P. R. China
| | - Wei Ren
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; School of Chemistry & Chemical Engineering, Shaanxi Normal University, Xi'an 710119, Shaanxi Province, P. R. China
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Saadh MJ, Muhammad FA, Singh A, Mustafa MA, Al Zuhairi RAH, Ghildiyal P, Hashim G, Alsaikhan F, Khalilollah S, Akhavan-Sigari R. MicroRNAs Modulating Neuroinflammation in Parkinson's disease. Inflammation 2024:10.1007/s10753-024-02125-z. [PMID: 39162871 DOI: 10.1007/s10753-024-02125-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/20/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024]
Abstract
Parkinson's disease (PD) is one of the most frequent age-associated neurodegenerative disorder. Presence of α-synuclein-containing aggregates in the substantia nigra pars compacta (SNpc) and loss of dopaminergic (DA) neurons are among the characteristic of PD. One of the hallmarks of PD pathophysiology is chronic neuroinflammation. Activation of glial cells and elevated levels of pro-inflammatory factors are confirmed as frequent features of the PD brain. Chronic secretion of pro-inflammatory cytokines by activated astrocytes and microglia exacerbates DA neuron degeneration in the SNpc. MicroRNAs (miRNAs) are among endogenous non-coding small RNA with the ability to perform post-transcriptional regulation in target genes. In that regard, the capability of miRNAs for modulating inflammatory signaling is the center of attention in many investigations. MiRNAs could enhance or limit inflammatory signaling, exacerbating or ameliorating the pathological consequences of extreme neuroinflammation. This review summarizes the importance of inflammation in the pathophysiology of PD. Besides, we discuss the role of miRNAs in promoting or protecting neural cell injury in the PD model by controlling the inflammatory pathway. Modifying the neuroinflammation by miRNAs could be considered a primary therapeutic strategy for PD.
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Affiliation(s)
- Mohamed J Saadh
- Faculty of Pharmacy, Middle East University, Amman, 11831, Jordan
| | | | - Anamika Singh
- Department of Biotechnology and Genetics, Jain (Deemed-to-Be) University, Bengaluru, Karnataka, 560069, India
- Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan, 303012, India
| | - Mohammed Ahmed Mustafa
- School of Pharmacy-Adarsh Vijendra Institute of Pharmaceutical Sciences, Shobhit University, Gangoh, Uttar Pradesh, 247341, India
- Department of Pharmacy, Arka Jain University, Jamshedpur,, Jamshedpur,, India, Jharkhand, 831001
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Ghassan Hashim
- Department of Nursing, Al-Zahrawi University College, Karbala, Iraq
| | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia.
- School of Pharmacy, Ibn Sina National College for Medical Studies, Jeddah, Saudi Arabia.
| | - Shayan Khalilollah
- Department of Neurosurgery, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Reza Akhavan-Sigari
- Department of Neurosurgery, University Medical Center, Tuebingen, Germany
- Department of Health Care Management and Clinical Research, Collegium Humanum Warsaw Management University Warsaw, Warszawa, Poland
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5
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Yu L, Peng Y, Sheng M, Wang Q, Jin Z, Huang J, Yang X. Electrochemical Biosensing Platform Based on Toehold-Mediated Strand Displacement Reaction and DSN Enzyme-Assisted Amplification for Two-Target Detection. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39157906 DOI: 10.1021/acsami.4c08515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Simultaneous detection of multiple targets is of great significance for accurate disease diagnosis. Herein, based on duplex-specific nuclease (DSN) assisted signal amplification and the toehold-mediated strand displacement reaction (TSDR), we constructed an electrochemical biosensor with high sensitivity and high specificity for dual-target detection. MiRNA-141 and miRNA-133a were used as the targets, and ferrocene (Fc) and methylene blue (MB) with significant peak potential differentiation were used as the electrochemical signal probes. The elaborately designed hairpin probe H1, which was fixed on the electrode surface, could be hybridized with the target miRNA-141 to perform signal amplification by the DSN-assisted enzyme cleavage cycle; thus, miRNA-141 could be detected by Fc signal changes at 0.41 V. The hairpin H1 can also combine with the MB-labeled signal probe (SP) output from miRNA-133a-induced TSDR, and the detection of miRNA-133a can be realized according to the response signal generated by MB at -0.26 V. The two sensing lines are independent of each other, and there is no mutual interference in the detection process. Therefore, two independent detection lines could be connected in series, and the simultaneous detection of two targets can be achieved on a single electrode. This novel detection strategy provides a new way to simultaneously detect different biomarkers.
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Affiliation(s)
- Linying Yu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yao Peng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Mengting Sheng
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Qian Wang
- Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Zhiying Jin
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jianshe Huang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
| | - Xiurong Yang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China
- School of Applied Chemistry and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, China
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Ali M, Hasan E, Barman SC, Hedhili MN, Alshareef HN, Alsulaiman D. Peptide nucleic acid-clicked Ti 3C 2T x MXene for ultrasensitive enzyme-free electrochemical detection of microRNA biomarkers. MATERIALS HORIZONS 2024. [PMID: 39102217 DOI: 10.1039/d4mh00714j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
We report the engineering and synthesis of peptide nucleic acid-functionalized Ti3C2Tx MXene nanosheets as a novel transducing material for amplification-free, nanoparticle-free, and isothermal electrochemical detection of microRNA biomarkers. Through bio-orthogonal copper-free click chemistry, azido-modified MXene nanosheets are covalently functionalized with clickable peptide nucleic acid probes targeting prostate cancer biomarker hsa-miR-141. The platform demonstrates a wide dynamic range, single-nucleotide specificity, and 40 aM detection limit outperforming more complex, amplification-based methods. Its versatility, analytical performance, and stability under serum exposure highlight the immense potential of this first example of click-conjugated MXene in the next generation of amplification-free biosensors.
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Affiliation(s)
- Muhsin Ali
- Material Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science & Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Erol Hasan
- Material Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science & Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Sharat Chandra Barman
- Material Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science & Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Mohamed Nejib Hedhili
- Imaging and Characterization Core Lab, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Husam N Alshareef
- Material Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science & Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Dana Alsulaiman
- Material Science and Engineering, Physical Science and Engineering Division, King Abdullah University of Science & Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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7
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Zhang J, Bai D, Xie G, Xie Y, Lin Y, Hou Y, Yu Y, Zhang Y, Zhao R, Wang Z, Wang L, Chen H. A novel entropy-driven dual-output mode integrated with DNAzyme for enhanced microRNA detection. Talanta 2024; 275:126123. [PMID: 38663065 DOI: 10.1016/j.talanta.2024.126123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 05/30/2024]
Abstract
Accurate microRNA (miRNA) detection is pivotal in the diagnosis and monitoring of cancer. Entropy-driven catalysis (EDC) has attracted widespread attention as an enzyme-free, isothermal technique for miRNA detection owing to its inherent simplicity and reliability. However, conventional EDC is a single-output mode, limiting the efficiency of signal amplification. In this study, a novel EDC dual-output mode was employed in conjunction with DNAzyme, resulting in the development of an EDC dual-end DNAzyme (EDC-DED) approach for highly sensitive miRNA detection. In this system, miRNA-21 initiated the EDC reaction, producing a large amount of catalytically active dual-end Mg2+-dependent DNAzyme. The DNAzyme further cleaved the reporter cyclically, generating a notably amplified fluorescence signal. The proposed method achieved a low detection limit of 2 pM. Compared with the traditional EDC single-end DNAzyme (EDC-SED) strategy, the present method exhibited superior amplification efficiency, enhancing detection sensitivity by approximately 46.5-fold. Furthermore, this platform demonstrated ideal specificity, satisfactory reproducibility and acceptable detection capabilities in clinical serum samples. Therefore, the straightforward and convenient strategy is a potential tool for miRNA analysis, which may provide a new perspective for biological analysis and clinical application.
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Affiliation(s)
- Jianhong Zhang
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Dan Bai
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaxing Xie
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Yu Lin
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yulei Hou
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Ying Yu
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China
| | - Yaoyi Zhang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Rong Zhao
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Zhongzhong Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Luojia Wang
- Key Laboratory of Laboratory Medical Diagnostics, Chinese Ministry of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Hui Chen
- Clinical Laboratories, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, PR China.
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8
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Meng X, Pang X, Liu X, Luo S, Zhang X, Dong H. Ultrasensitive Electrochemiluminescence Biosensor Based on DNA-Bio-Bar-Code and Hybridization Chain Reaction Dual Signal Amplification for Exosomes Detection. Anal Chem 2024. [PMID: 39090799 DOI: 10.1021/acs.analchem.4c02917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Exosomes have received considerable attention as potent reference markers for the diagnosis of various neoplasms due to their close and direct relationship with the proliferation, adhesion, and migration of tumor. The ultrasensitive detection of cancer-derived low-abundance exosomes is imperative, but still a great challenge. Herein, we report an electrochemiluminescence (ECL) biosensor based on the DNA-bio-bar-code and hybridization chain reaction (HCR)-mediated dual signal amplification for the ultrasensitive detection of cancer-derived exosomes. In this system, two types of aptamers were modified on the magnetic nanoprobe (MNPs) and gold nanoparticles (AuNPs) with numerous bio-bar-code DNA, respectively, which formed "sandwich" structures in the presence of specific target exosomes. The "sandwich" structures were separated under magnetic field, and the numerous bio-bar-code DNA were released by dissolving AuNPs. The released bio-bar-code DNA triggered the HCR procedure to produce a good deal of long DNA duplex structure for embedding in hemin, which generated strong ECL signal in the presence of coreactors for ultrasensitive detection of exosomes. Under the optimal conditions, it exhibited a good linearly of exosomes ranging from 10 to 104 exosomes particle μL-1 with limit of detection down to 5.01 exosome particle μL-1. Furthermore, the high ratio of ECL signal and minor change of ECL intensity indicated the good specificity, stability, and repeatability of this ECL biosensor. Given the good performance for exosome analysis, this ultrasensitive ECL biosensor has a promising application in the clinical diagnosis of early cancers.
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Affiliation(s)
- Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 10083, P. R. China
| | - Xuejiao Pang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 10083, P. R. China
| | - Xiangyu Liu
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing 100083, People's Republic of China
| | - Shuiyou Luo
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 10083, P. R. China
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong 518060, P. R. China
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9
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Liu H, Dong J, Duan Z, Xia F, Willner I, Huang F. Light-activated CRISPR-Cas12a for amplified imaging of microRNA in cell cycle phases at single-cell levels. SCIENCE ADVANCES 2024; 10:eadp6166. [PMID: 39047109 PMCID: PMC11268419 DOI: 10.1126/sciadv.adp6166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 06/20/2024] [Indexed: 07/27/2024]
Abstract
An ortho-nitrobenzyl phosphate ester-caged nucleic acid hairpin structure coupled to the CRISPR-Cas12a complex is introduced as a functional reaction module for the light-induced activation of the CRISPR-Cas12a (LAC12a) machinery toward the amplified fluorescence detection of microRNA-21 (miRNA-21). The LAC12a machinery is applied for the selective, in vitro sensing of miRNA-21 and for the intracellular imaging of miRNA-21 in different cell lines. The LAC12a system is used to image miRNA-21 in different cell cycle phases of MCF-7 cells. Moreover, the LAC12a machinery integrated in cells enables the two-photon laser confocal microscopy-assisted, light-stimulated spatiotemporal, selective activation of the CRISPR-Cas12a miRNA-21 imaging machinery at the single-cell level and the evaluation of relative expression levels of miRNA-21 at distinct cell cycle phases. The method is implemented to map the distribution of cell cycle phases in an array of single cells.
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Affiliation(s)
- Hong Liu
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Jiantong Dong
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Zhijuan Duan
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
| | - Itamar Willner
- Institute of Chemistry and Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fujian Huang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P.R. China
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10
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Jia Y, Zhao S, Wang A, Huang J, Yang J, Yang L. Target-induced multiregion MNAzyme nanowires for ultrasensitive homogeneous detection of microRNAs. Int J Biol Macromol 2024; 277:134175. [PMID: 39067728 DOI: 10.1016/j.ijbiomac.2024.134175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 07/19/2024] [Accepted: 07/24/2024] [Indexed: 07/30/2024]
Abstract
A target-induced multiregion MNAzyme nanowire system is designed for the ultrasensitive and homogeneous detection of microRNAs (miRNAs). miRNA-21 and miRNA-375 are chosen as analytes, and a miRNA-induced primer exchange reaction (PER) is utilized to construct a long DNA strand with repetitive sequences. This innovative design enables the efficient anchoring of numerous MNAzymes. This unique architecture significantly boosts the effective local concentration of MNAzymes, thereby enhancing the sensitivity and efficiency of miRNA detection. Notably, the limit of detection (LOD) achieved with our target-induced multiregion MNAzyme nanowire approach is over an order of magnitude lower than most other MNAzyme-based methods, while the MNAzyme reaction time is reduced from several hours to 50 min. The method has demonstrated successful applications in quantitatively determining the expression levels of two miRNAs in cell lysates of MCF-7, HeLa and MCF-10 A cells, highlighting its potential for assaying miRNA biomarkers in clinical samples.
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Affiliation(s)
- Yaxue Jia
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Siqi Zhao
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Anping Wang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Jing Huang
- Laboratory Department of The First Hospital of Jilin University, Changchun, P. R. China
| | - Jinlan Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China
| | - Li Yang
- Department of Chemistry, Northeast Normal University, 5268 Renmin Street, Changchun, Jilin Province 130024, China.
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11
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Ma Y, Li M, Zhang Y. Ratiometric electrochemical biosensor based on hybridization chain reaction signal amplification for sensitive microRNA-155 detection. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5032-5037. [PMID: 38980034 DOI: 10.1039/d4ay00868e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
In this work, a sensitive ratiometric electrochemical biosensor for microRNA-155 (miRNA-155) detection is reported based on a hybridization chain reaction amplifying the electrochemical signal. The biosensor was fabricated using Au NPs as a modified material to assemble capture DNA labeled with ferrocene (Fc) molecules, and a DNA probe labeled with methylene blue (MB) was employed for the signal probe. In the presence of target miRNA-155, it can be dual hybridized with capture and signal probe, especially with signal probe to continuously produce long concatemers containing lots of MB molecules. The electrochemical signal of Fc was used for the internal signal, and the signal from MB was used as an indicator signal. As the concentration of miRNA-155 was altered, the internal reference signal of Fc remained constant, and only the indicator signal changed in a sensitive way. The change in the ratio (IMB/IFc) between the indicator signal of MB and internal reference signal of Fc can be used to monitor the concentration of miRNA-155. Under optimal conditions, the prepared ratiometric biosensor could detect miRNA-155 within a wide linear range from 100 fM to 100 nM with low detection limit of 33 fM (at S/N = 3). Moreover, the biosensor was evaluated with human serum samples, and satisfactory recoveries were obtained, indicating that the ratiometric biosensor can be applied to clinical sample analysis.
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Affiliation(s)
- Yan Ma
- College of Chemistry and Materials Science, Anhui Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Normal University, Wuhu 241000, People's Republic of China.
| | - Mengyao Li
- College of Chemistry and Materials Science, Anhui Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Normal University, Wuhu 241000, People's Republic of China.
| | - Yuzhong Zhang
- College of Chemistry and Materials Science, Anhui Key Laboratory of Biomedical Materials and Chemical Measurement, Anhui Normal University, Wuhu 241000, People's Republic of China.
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He X, Deng L, Zhou S, Dong J, Zhu S, Li J, Li X, Huo D, Hou C. CRISPR/Cas12a-coupled multiplexed strand displacement amplification for miRNA155 one-tube detection: via a dual-cavity PCR tube. Mikrochim Acta 2024; 191:470. [PMID: 39023769 DOI: 10.1007/s00604-024-06538-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 06/30/2024] [Indexed: 07/20/2024]
Abstract
A CRISPR/Cas12a-coupled multiplexed strand displacement amplification (CMSDA) for the detection of miR155 has been developed. Non-specific amplification was avoided by designing a single-stranded DNA template with a hairpin structure. The detection target miR155 was used as a primer to initiate a multiple-strand displacement reaction to produce abundant ssDNA. ssDNA was recognized by the Cas12a/CrRNA binary complex, activating the trans-cleaving activity of Cas12a. The multiple-strand displacement reaction is more efficiently detected compared with a single-strand displacement reaction. The detection range is from 250 pM to 1 nM, and the limit of the detection is 6.5 pM. The proposed method showed a good applicability in complex serum environments, indicating that the method has a broad prospect for disease detection and clinical application. In addition, we designed a dual-cavity PCR tube, which realized one-tube detection of miRNA155 and avoided open-cap contamination.
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Affiliation(s)
- Xinyu He
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Liyuan Deng
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Jiangbo Dong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Shuyu Zhu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Jiawei Li
- Chongqing University Three Gorges Hospital, Chongqing, 404000, PR China
| | - Xinyao Li
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China.
- State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing, 210018, PR China.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, 400044, PR China.
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing, 400044, PR China.
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13
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Liu X, Jia Y, Zheng C. Recent progress in Surface-Enhanced Raman Spectroscopy detection of biomarkers in liquid biopsy for breast cancer. Front Oncol 2024; 14:1400498. [PMID: 39040452 PMCID: PMC11260621 DOI: 10.3389/fonc.2024.1400498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/24/2024] [Indexed: 07/24/2024] Open
Abstract
Breast cancer is the most commonly diagnosed cancer in women globally and a leading cause of cancer-related mortality. However, current detection methods, such as X-rays, ultrasound, CT scans, MRI, and mammography, have their limitations. Recently, with the advancements in precision medicine and technologies like artificial intelligence, liquid biopsy, specifically utilizing Surface-Enhanced Raman Spectroscopy (SERS), has emerged as a promising approach to detect breast cancer. Liquid biopsy, as a minimally invasive technique, can provide a temporal reflection of breast cancer occurrence and progression, along with a spatial representation of overall tumor information. SERS has been extensively employed for biomarker detection, owing to its numerous advantages such as high sensitivity, minimal sample requirements, strong multi-detection ability, and controllable background interference. This paper presents a comprehensive review of the latest research on the application of SERS in the detection of breast cancer biomarkers, including exosomes, circulating tumor cells (CTCs), miRNA, proteins and others. The aim of this review is to provide valuable insights into the potential of SERS technology for early breast cancer diagnosis.
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Affiliation(s)
- Xiaobei Liu
- Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yining Jia
- Department of Breast Surgery, The Second Hospital of Shandong University, Jinan, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
| | - Chao Zheng
- Department of Breast Surgery, The Second Hospital of Shandong University, Jinan, China
- Institute of Translational Medicine of Breast Disease Prevention and Treatment, Shandong University, Jinan, China
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14
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Feng X, Bi X, Feng J, Hu S, Wang Y, Zhao S, Zhang L. Proximity-Induced Bipedal DNA Walker for Accurately Visualizing microRNA in Living Cancer Cell. Anal Chem 2024; 96:10669-10676. [PMID: 38913536 DOI: 10.1021/acs.analchem.4c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
DNA walker, a type of dynamic DNA device that is capable of moving progressively along prescribed walking tracks, has emerged as an ideal and powerful tool for biosensing and bioimaging. However, most of the reported three-dimensional (3D) DNA walker were merely designed for the detection of a single target, and they were not capable of achieving universal applicability. Herein, we reported for the first time the development of a proximity-induced 3D bipedal DNA walker for imaging of low abundance biomolecules. As a proof of concept, miRNA-34a, a biomarker of breast cancer, is chosen as the model system to demonstrate this approach. In our design, the 3D bipedal DNA walker can be generated only by the specific recognition of two proximity probes for miRNA-34a. Meanwhile, it stochastically and autonomously traveled on 3D tracks (gold nanoparticles) via catalytic hairpin assembly (CHA), resulting in the amplified fluorescence signal. In comparison with some conventional DNA walkers that were utilized for living cell imaging, the 3D DNA walkers induced by proximity ligation assay can greatly improve and ensure the high selectivity of bioanalysis. By taking advantage of these unique features, the proximity-induced 3D bipedal DNA walker successfully realizes accurate and effective monitoring of target miRNA-34a expression levels in living cells, affording a universal, valuable, and promising platform for low-abundance cancer biomarker detection and accurate identification of cancer.
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Affiliation(s)
- Xiyuan Feng
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Xiaofeng Bi
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Jinyue Feng
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Yumin Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
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Pan W, Niu H, Luo S, Chen L, Wu ZS. Intelligent Reconfiguration-Promoted Cellular Internalization of Core-Shell DNA Nanoprobe Equipped with Successive Dual Stimuli-Responsive Protective Satellites for Amplification Fluorescence Imaging of Tumor Cells. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2311388. [PMID: 38282377 DOI: 10.1002/smll.202311388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Indexed: 01/30/2024]
Abstract
Although DNA probes have attracted increasing interest for precise tumor cell identification by imaging intracellular biomarkers, the requirement of commercial transfection reagents, limited targeting ligands, and/or non-biocompatible inorganic nanostructures has hampered the clinic translation. To circumvent these shortcomings, a reconfigurable ES-NC (Na+-dependent DNAzyme (E)-based substrate (S) cleavage core/shell DNA nanocluster (NC)) entirely from DNA strands is assembled for precise imaging of cancerous cells in a successive dual-stimuli-responsive manner. This nanoprobe is composed of a strung DNA tetrahedral satellites-based protective (DTP) shell, parallelly aligned target-responsive sensing (PTS) interlayer, and hydrophobic cholesterol-packed innermost layer (HCI core). Tetrahedral axial rotation-activated reconfiguration of DTP shell promotes the exposure of interior hydrophobic moieties, enabling cholesterol-mediated cellular internalization without auxiliary elements. Within cells, over-expressed glutathione triggers the disassembly of the DTP protective shell (first stimulus), facilitating target-stimulated signal transduction/amplification process (second stimuli). Target miRNA-21 is detected down to 10.6 fM without interference from coexisting miRNAs. Compared with transfection reagent-mediated counterpart, ES-NC displays a higher imaging ability, resists nuclease degradation, and has no detectable damage to healthy cells. The blind test demonstrates that the ES-NC is suitable for the identification of cancerous cells from healthy cells, indicating a promising tool for early diagnosis and prediction of cancer.
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Affiliation(s)
- Wenhao Pan
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
- Fujian Key Laboratory of Aptamers Technology, The 900th Hospital of Joint Logistics Support Force, Fuzhou, 350025, China
| | - Shasha Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Linhuan Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350108, China
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16
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Jeung JH, Han H, Jang SH, Lee CY, Ahn JK. One-pot, one-step, label-free miRNA detection method based on the structural transition of dumbbell probe. Talanta 2024; 274:125944. [PMID: 38537347 DOI: 10.1016/j.talanta.2024.125944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 02/15/2024] [Accepted: 03/16/2024] [Indexed: 05/04/2024]
Abstract
In this study, we present a one-pot, one-step, label-free miRNA detection method through a structural transition of a specially designed dumbbell-shape probe, initiating a rolling circle transition (RCT). In principle, target miRNA binds to right loop of the dumbbell probe (DP), which allows structural change of the DP to circular form, exposing a sequence complementary to the T7 promoter (T7p) previously hidden within the stem. This exposure allows T7 RNA polymerase to initiate RCT, producing a repetitive Mango aptamer sequence. TO1-biotin, fluorescent dye, binds to the aptamer, inducing a detectable enhancement of fluorescence intensity. Without miR-141, the DP stays closed, RCT is prevented, and the fluorescence intensity remains low. By employing this novel strategy, target miRNA was successfully identified with a detection of 73 pM and a dynamic linear range of 0-10 nM. Additionally, the method developed enables one-pot, one-step, and label-free detection of miRNA, demonstrating potential for point-of-care testing (POCT) applications. Furthermore, the practical application of the designed technique was demonstrated by reliably detecting the target miRNA in the human serum sample. We also believe that the conceived approach could be widely used to detect not only miRNAs but also diverse biomolecules by simply replacing the detection probe.
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Affiliation(s)
- Jae Hoon Jeung
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Biological Engineering, College of Engineering, Konkuk University, Seoul, 05029, Republic of Korea
| | - Hyogu Han
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Chemistry, Gangneung-Wonju National University, Gangneung, 25457, Republic of Korea
| | - Se Hee Jang
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea; Department of Medical Device Engineering and Management, College of Medicine, Yonsei University, Seoul, 03722, Republic of Korea
| | - Chang Yeol Lee
- Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Jun Ki Ahn
- Material & Component Convergence R&D Department, Korea Institute of Industrial Technology (KITECH), Ansan, Republic of Korea.
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17
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Zhang M, Zhang Y, Zhang X, Liu K, Li L, Yu Z, Yuan J, Zhang W. An Enzymatically Activated and Catalytic Hairpin Assembly-Driven Intelligent AND-Gated DNA Network for Tumor Molecular Imaging. Anal Chem 2024; 96:10084-10091. [PMID: 38836421 DOI: 10.1021/acs.analchem.4c02076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Due to the potential off-tumor signal leakage and limited biomarker content, there is an urgent need for stimulus-responsive and amplification-based tumor molecular imaging strategies. Therefore, two tetrahedral framework DNA (tFNA-Hs), tFNA-H1AP, and tFNA-H2, were rationally engineered to form a polymeric tFNA network, termed an intelligent DNA network, in an AND-gated manner. The intelligent DNA network was designed for tumor-specific molecular imaging by leveraging the elevated expression of apurinic/apyrimidinic endonuclease 1 (APE1) in tumor cytoplasm instead of normal cells and the high expression of miRNA-21 in tumor cytoplasm. The activation of tFNA-H1AP can be achieved through specific recognition and cleavage by APE1, targeting the apurinic/apyrimidinic site (AP site) modified within the stem region of hairpin 1 (H1AP). Subsequently, miRNA-21 facilitates the hybridization of activated H1AP on tFNA-H1AP with hairpin 2 (H2) on tFNA-H2, triggering a catalytic hairpin assembly (CHA) reaction that opens the H1AP at the vertices of tFNA-H1AP to bind with H2 at the vertices of tFNA-H2 and generate fluorescence signals. Upon completion of hybridization, miRNA-21 is released, initiating the subsequent cycle of the CHA reaction. The AND-gated intelligent DNA network can achieve specific tumor molecular imaging in vivo and also enables risk stratification of neuroblastoma patients.
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Affiliation(s)
- Mengxin Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Yingyu Zhang
- Henan Key Laboratory of Rare Diseases, Endocrinology and Metabolism Center, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang 471003, China
| | - Xianwei Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Kangbo Liu
- Henan Institute for Drug and Medical Device Inspection (Henan Vaccine Issuance Center), Zhengzhou 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Zhidan Yu
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Jingya Yuan
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
| | - Wancun Zhang
- Health Commission of Henan Province Key Laboratory for Precision Diagnosis and Treatment of Pediatric Tumor, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
- Henan International Joint Laboratory for Prevention and Treatment of Pediatric Disease, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou 450018, China
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18
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Zhu D, Zhao D, Hu Y, Wei T, Su T, Su S, Chao J, Wang L. Programmably engineered stochastic RNA nanowalker for ultrasensitive miRNA detection. Chem Commun (Camb) 2024; 60:6142-6145. [PMID: 38804211 DOI: 10.1039/d4cc01656d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
A programmably engineered stochastic RNA nanowalker powered by duplex-specific nuclease (DSN) is developed. By utilizing poly-adenine-based spherical nucleic acids (polyA-SNA) to accurately regulate the densities of DNA tracks, the nanowalker showcases its capability to identify miRNA-21, miRNA-486, and miRNA-155 with quick kinetics and attomolar sensitivity, positioning it as a promising option for cancer clinical surveillance.
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Affiliation(s)
- Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai 200050, China
| | - Dongxia Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Yang Hu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tianhui Wei
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Tong Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Shao Su
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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19
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Zhu F, Yang X, Ouyang L, Man T, Chao J, Deng S, Zhu D, Wan Y. DNA Framework-Based Programmable Atom-Like Nanoparticles for Non-Coding RNA Recognition and Differentiation of Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400492. [PMID: 38569466 PMCID: PMC11187905 DOI: 10.1002/advs.202400492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/27/2024] [Indexed: 04/05/2024]
Abstract
The cooperative diagnosis of non-coding RNAs (ncRNAs) can accurately reflect the state of cell differentiation and classification, laying the foundation of precision medicine. However, there are still challenges in simultaneous analyses of multiple ncRNAs and the integration of biomarker data for cell typing. In this study, DNA framework-based programmable atom-like nanoparticles (PANs) are designed to develop molecular classifiers for intra-cellular imaging of multiple ncRNAs associated with cell differentiation. The PANs-based molecular classifier facilitates signal amplification through the catalytic hairpin assembly. The interaction between PAN reporters and ncRNAs enables high-fidelity conversion of ncRNAs expression level into binding events, and the assessment of in situ ncRNAs levels via measurement of the fluorescent signal changes of PAN reporters. Compared to non-amplified methods, the detection limits of PANs are reduced by four orders of magnitude. Using human gastric cancer cell lines as a model system, the PANs-based molecular classifier demonstrates its capacity to measure multiple ncRNAs in living cells and assesses the degree of cell differentiation. This approach can serve as a universal strategy for the classification of cancer cells during malignant transformation and tumor progression.
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Affiliation(s)
- Fulin Zhu
- School of Mechanical EngineeringNanjing University of Science and Technology200 Xiaolingwei StreetNanjing210094China
| | - Xinyu Yang
- School of Mechanical EngineeringNanjing University of Science and Technology200 Xiaolingwei StreetNanjing210094China
| | - Lilin Ouyang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for BiosensorsInstitute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)Nanjing University of Posts and Telecommunications9 Wenyuan RoadNanjing210023China
| | - Tiantian Man
- School of Mechanical EngineeringNanjing University of Science and Technology200 Xiaolingwei StreetNanjing210094China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for BiosensorsInstitute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)Nanjing University of Posts and Telecommunications9 Wenyuan RoadNanjing210023China
| | - Shengyuan Deng
- School of Environmental and Biological EngineeringNanjing University of Science and Technology200 Xiaolingwei StreetNanjing210094China
| | - Dan Zhu
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for BiosensorsInstitute of Advanced Materials (IAM)Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM)Nanjing University of Posts and Telecommunications9 Wenyuan RoadNanjing210023China
| | - Ying Wan
- School of Mechanical EngineeringNanjing University of Science and Technology200 Xiaolingwei StreetNanjing210094China
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20
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Slawski J, Jaśkiewicz M, Barton A, Kozioł S, Collawn JF, Bartoszewski R. Regulation of the HIF switch in human endothelial and cancer cells. Eur J Cell Biol 2024; 103:151386. [PMID: 38262137 DOI: 10.1016/j.ejcb.2024.151386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 01/17/2024] [Accepted: 01/17/2024] [Indexed: 01/25/2024] Open
Abstract
Hypoxia-inducible factors (HIFs) are transcription factors that reprogram the transcriptome for cells to survive hypoxic insults and oxidative stress. They are important during embryonic development and reprogram the cells to utilize glycolysis when the oxygen levels are extremely low. This metabolic change facilitates normal cell survival as well as cancer cell survival. The key feature in survival is the transition between acute hypoxia and chronic hypoxia, and this is regulated by the transition between HIF-1 expression and HIF-2/HIF-3 expression. This transition is observed in many human cancers and endothelial cells and referred to as the HIF Switch. Here we discuss the mechanisms involved in the HIF Switch in human endothelial and cancer cells which include mRNA and protein levels of the alpha chains of the HIFs. A major continuing effort in this field is directed towards determining the differences between normal and tumor cell utilization of this important pathway, and how this could lead to potential therapeutic approaches.
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Affiliation(s)
- Jakub Slawski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Maciej Jaśkiewicz
- International Research Agenda 3P, Medicine Laboratory, Medical University of Gdansk, Gdansk, Poland
| | - Anna Barton
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - Sylwia Kozioł
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland
| | - James F Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
| | - Rafał Bartoszewski
- Department of Biophysics, Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland.
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21
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Lei S, Ji Y, Zhang Q, Li G, Zou L, Chai G, Mao J, Zhang J, Ye B. A rapid one-step electrochemical method based on cleat-equipped molecular walking machine. Talanta 2024; 272:125756. [PMID: 38364562 DOI: 10.1016/j.talanta.2024.125756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/29/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
Various nucleic acid molecular machines have emerged in recent years. However, when the nucleic acid tracks are fully depleted, these walkers are highly susceptible to premature release or stalling in regions where the tracks are locally exhausted. In this work, a molecular walking machine with a cleat domain preventing dissociation from the track was explored for ultrasensitive detection of miRNA. It has been verified that the cleat design can enhance the signal amplification efficiency of molecular walking machines for electrochemical miRNA-141 detection. Notably, the single-step electrochemical biosensing platform utilizing the cleat-equipped molecular walking machine (CMWM) is exceptionally straightforward and rapid, concluding the reaction within 90 min and achieving a remarkable low detection limit of 0.26 fM. The proposed molecular walking machine with this specific cleat structure was utilized for the identification of miRNA-141 in cellular lysates, exhibiting remarkable selectivity and consistent reproducibility, showcasing its effective utility in bioanalysis. Therefore, the cleat walker developed in this study introduces an innovative method for constructing a miRNA electrochemical biosensing platform, offering new perspectives for its application in biomolecule detection and clinical disease diagnosis.
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Affiliation(s)
- Sheng Lei
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou, 450001, PR China; College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Yanli Ji
- Key Clinical Laboratory of Henan Province, Department of Clinical Laboratory, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, PR China
| | - Qidong Zhang
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou, 450001, PR China; Flavor Research Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Gaiping Li
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Lina Zou
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Guobi Chai
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou, 450001, PR China; Flavor Research Center, Zhengzhou University, Zhengzhou, 450001, PR China
| | - Jian Mao
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou, 450001, PR China; Beijing Life Science Academy, Beijing, 102299, PR China
| | - Jianxun Zhang
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou, 450001, PR China; Flavor Research Center, Zhengzhou University, Zhengzhou, 450001, PR China.
| | - Baoxian Ye
- College of Chemistry, Zhengzhou University, Zhengzhou, 450001, PR China.
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22
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Wu Y, Jin R, Chang Y, Liu M. A high-fidelity DNAzyme-assisted CRISPR/Cas13a system with single-nucleotide resolved specificity. Chem Sci 2024; 15:6934-6942. [PMID: 38725495 PMCID: PMC11077575 DOI: 10.1039/d4sc01501k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 04/01/2024] [Indexed: 05/12/2024] Open
Abstract
A CRISPR/Cas system represents an innovative tool for developing a new-generation biosensing and diagnostic strategy. However, the off-target issue (i.e., mistaken cleavage of nucleic acid targets and reporters) remains a great challenge for its practical applications. We hypothesize that this issue can be overcome by taking advantage of the site-specific cleavage ability of RNA-cleaving DNAzymes. To test this idea, we propose a DNAzyme Operation Enhances the Specificity of CRISPR/Cas13a strategy (termed DOES-CRISPR) to overcome the problem of relatively poor specificity that is typical of the traditional CRISPR/Cas13a system. The key to the design is that the partial hybridization of the CRISPR RNA (crRNA) with the cleavage fragment of off-target RNA was not able to activate the collateral cleavage activity of Cas13a. We showed that DOES-CRISPR can significantly improve the specificity of traditional CRISPR/Cas13a-based molecular detection by up to ∼43-fold. The broad utility of the strategy is illustrated through engineering three different systems for the detection of microRNAs (miR-17 and let-7e), CYP2C19*17 gene, SARS-Cov-2 variants (Gamma, Delta, and Omicron) and Omicron subtypes (BQ.1 and XBB.1) with single-nucleotide resolved specificity. Finally, clinical evaluation of this assay using 10 patient blood samples demonstrated a clinical sensitivity of 100% and specificity of 100% for genotyping CYP2C19*17, and analyzing 20 throat swab samples provided a diagnostic sensitivity of 95% and specificity of 100% for Omicron detection, and a clinical sensitivity of 92% and specificity of 100% for XBB.1 detection.
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Affiliation(s)
- Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Ruigang Jin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian POCT Laboratory Dalian 116024 China
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23
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Rahmati A, Mafi A, Vakili O, Soleymani F, Alishahi Z, Yahyazadeh S, Gholinezhad Y, Rezaee M, Johnston TP, Sahebkar A. Non-coding RNAs in leukemia drug resistance: new perspectives on molecular mechanisms and signaling pathways. Ann Hematol 2024; 103:1455-1482. [PMID: 37526673 DOI: 10.1007/s00277-023-05383-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 07/22/2023] [Indexed: 08/02/2023]
Abstract
Like almost all cancer types, timely diagnosis is needed for leukemias to be effectively cured. Drug efflux, attenuated drug uptake, altered drug metabolism, and epigenetic alterations are just several of the key mechanisms by which drug resistance develops. All of these mechanisms are orchestrated by up- and downregulators, in which non-coding RNAs (ncRNAs) do not encode specific proteins in most cases; albeit, some of them have been found to exhibit the potential for protein-coding. Notwithstanding, ncRNAs are chiefly known for their contribution to the regulation of physiological processes, as well as the pathological ones, such as cell proliferation, apoptosis, and immune responses. Specifically, in the case of leukemia chemo-resistance, ncRNAs have been recognized to be responsible for modulating the initiation and progression of drug resistance. Herein, we comprehensively reviewed the role of ncRNAs, specifically its effect on molecular mechanisms and signaling pathways, in the development of leukemia drug resistance.
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Affiliation(s)
- Atefe Rahmati
- Department of Hematology and Blood Banking, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Alireza Mafi
- Department of Clinical Biochemistry, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omid Vakili
- Department of Clinical Biochemistry, Autophagy Research Center, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Firooze Soleymani
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Zahra Alishahi
- Department of Basic Sciences, Faculty of Medicine, Neyshabur University of Medical Sciences, Neyshabur, Iran
| | - Sheida Yahyazadeh
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Yasaman Gholinezhad
- Department of Pharmacology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Malihe Rezaee
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Tehran Heart Center, Cardiovascular Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Thomas P Johnston
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO, USA
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
- Department of Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, the, Islamic Republic of Iran.
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24
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Meng X, Pang X, Yang J, Zhang X, Dong H. Recent Advances in Electrochemiluminescence Biosensors for MicroRNA Detection. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307701. [PMID: 38152970 DOI: 10.1002/smll.202307701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/06/2023] [Indexed: 12/29/2023]
Abstract
Electrochemiluminescence (ECL) as an analytical technology with a perfect combination of electrochemistry and spectroscopy has received considerable attention in bioanalysis due to its high sensitivity and broad dynamic range. Given the selectivity of bio-recognition elements and the high sensitivity of the ECL analysis technique, ECL biosensors are powerful platforms for the sensitive detection of biomarkers, achieving the accurate prognosis and diagnosis of diseases. MicroRNAs (miRNAs) are crucial biomarkers involved in a variety of physiological and pathological processes, whose aberrant expression is often related to serious diseases, especially cancers. ECL biosensors can fulfill the highly sensitive and selective requirements for accurate miRNA detection, prompting this review. The ECL mechanisms are initially introduced and subsequently categorize the ECL biosensors for miRNA detection in terms of the quenching agents. Furthermore, the work highlights the signal amplification strategies for enhancing ECL signal to improve the sensitivity of miRNA detection and finally concludes by looking at the challenges and opportunities in ECL biosensors for miRNA detection.
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Affiliation(s)
- Xiangdan Meng
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Xuejiao Pang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
| | - Junyan Yang
- School of Materials Science and Engineering, University of Science and Technology Beijing, Beijing, 100083, P. R. China
| | - Xueji Zhang
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518060, P. R. China
| | - Haifeng Dong
- Beijing Key Laboratory for Bioengineering and Sensing Technology Research Centre for Bioengineering and Sensing Technology School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 10083, P. R. China
- Marshall Laboratory of Biomedical Engineering, Precision Medicine and Health Research Institute, Shenzhen Key Laboratory for Nano-Biosensing Technology, School of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518060, P. R. China
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25
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Fu J, Liu J, Zou X, Deng M, Liu G, Sun B, Guo Y, Liu D, Li Y. Transcriptome analysis of mRNA and miRNA in the development of LeiZhou goat muscles. Sci Rep 2024; 14:9858. [PMID: 38684760 PMCID: PMC11058254 DOI: 10.1038/s41598-024-60521-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/24/2024] [Indexed: 05/02/2024] Open
Abstract
The progression of muscle development is a pivotal aspect of animal ontogenesis, where miRNA and mRNA exert substantial influence as prominent players. It is important to understand the molecular mechanisms involved in skeletal muscle development to enhance the quality and yield of meat produced by Leizhou goats. We employed RNA sequencing (RNA-SEQ) technology to generate miRNA-mRNA profiles in Leizhou goats, capturing their developmental progression at 0, 3, and 6 months of age. A total of 977 mRNAs and 174 miRNAs were found to be differentially expressed based on our analysis. Metabolic pathways, calcium signaling pathways, and amino acid synthesis and metabolism were found to be significantly enriched among the differentially expressed mRNA in the enrichment analysis. Meanwhile, we found that among these differentially expressed mRNA, some may be related to muscle development, such as MYL10, RYR3, and CSRP3. Additionally,, we identified five muscle-specific miRNAs (miR-127-3p, miR-133a-3p, miR-193b-3p, miR-365-3p, and miR-381) that consistently exhibited high expression levels across all three stages. These miRNAs work with their target genes (FHL3, SESN1, PACSIN3, LMCD1) to regulate muscle development. Taken together, our findings suggest that several miRNAs and mRNAs are involved in regulating muscle development and cell growth in goats. By uncovering the molecular mechanisms involved in muscle growth and development, these findings contribute valuable knowledge that can inform breeding strategies aimed at enhancing meat yield and quality in Leizhou goats.
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Affiliation(s)
- Junjie Fu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Jie Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Xian Zou
- State Key Laboratory of Livestock and Poultry Breeding, Guangdong Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China
| | - Ming Deng
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Guangbin Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Baoli Sun
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Yongqing Guo
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Dewu Liu
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China
- National Local Joint Engineering Research Center of Livestock and Poultry, South China Agricultural University, Guangzhou, 510642, China
| | - Yaokun Li
- College of Animal Science, South China Agricultural University, Guangzhou, 510642, China.
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26
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Lei S, Liu Z, Zhang Q, Li Z, Li G, Zou L, Chai G, Mao J, Ye B, Zhang J. Twice-walk strategy based on three-dimensional DNA walking machine driven by duplex-specific nuclease. Chem Commun (Camb) 2024; 60:3778-3781. [PMID: 38494893 DOI: 10.1039/d3cc06058f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
A twice-walk strategy based on a three-dimensional (3D) cleat-equipped DNA walking machine with a high signal amplification efficiency was investigated for ultrasensitive detection of miRNA. Impressively, addition of duplex-specific nuclease (DSN) just once drove the twice-walk strategy, making the strategy simpler. With the advantages of being simple, rapid and ultrasensitive, the biosensor offers potential for use in early clinical diagnosis.
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Affiliation(s)
- Sheng Lei
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, P. R. China
| | - Zi Liu
- Henan Key Laboratory of Biomolecular Recognition and Sensing, Henan Joint International Research Laboratory of Chemo/Biosensing and Early Diagnosis of Major Diseases, College of Chemistry and Chemical Engineering, Shangqiu Normal University, Shangqiu 476000, P. R. China
| | - Qidong Zhang
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
| | - Zezhi Li
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
- School of Light Industry, Beijing Technology and Business University, Beijing 100048, P. R. China
| | - Gaiping Li
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Lina Zou
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Guobi Chai
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
| | - Jian Mao
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
- Beijing Life Science Academy, Beijing, 102299, P. R. China
| | - Baoxian Ye
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Jianxun Zhang
- Zhengzhou Tobacco Research Institute of China National Tobacco Company, Zhengzhou 450001, P. R. China.
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27
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Shi J, Zhou S, Zhao J, Xu D, Huang H, Li M, Tian X, He L, Wu C, Wang Q, Zhao Y, Zeng X. Microarray analysis of microrna expression in peripheral blood mononuclear cells of patients with polymyositis and dermatomyositis. J Transl Int Med 2024; 12:170-176. [PMID: 38779122 PMCID: PMC11107181 DOI: 10.2478/jtim-2022-0055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
Background and Objectives MicroRNAs (miRNAs) represent a new class of biomarkers in the context of connective tissue disorders. The miRNA expression profiles in peripheral blood mononuclear cells (PBMCs) of patients with polymyositis (PM) and dermatomyositis (DM) have not been fully elucidated. The objective is to investigate miRNAs expression profile in PBMCs of patients with PM/DM. Methods Microarray technology was used to identify differentially expressed miRNAs in PBMCs obtained from 6 untreated PM/DM patients and 3 healthy controls (HCs). TaqMan-based stem-loop real-time PCR detection was used for validation in a cohort of 34 PM/DM patients and 20 HCs. Results Microarray analysis revealed 38 differentially expressed miRNAs (24 up-regulated and 14 down-regulated) in PM/DM patients compared to HCs. Four miRNAs (miR-320a, miR-335-3p, miR-34a-5p and miR-454-3p) were chosen for real-time PCR validation. The expression of miR-34a-5p was significantly upregulated in PM/DM group (P < 0.05). In subgroup analysis, miR-34a-5p was significantly upregulated in interstitial lung disease (ILD) group and DM group (P < 0.001). The level of SIRT1, a validated target of miR-34a, was significantly lower in PBMCs of PM/DM patients compared with HCs. Conclusions MiR-34a-5p may potentially participate in the pathogenesis of PM/DM through SIRT1, and may serve as a potential new biomarker for PM/DM-ILD.
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Affiliation(s)
- Jia Shi
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Shuang Zhou
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Jiuliang Zhao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Dong Xu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Hui Huang
- Department of Respiratory Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing100730, China
| | - Mengtao Li
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Xinping Tian
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Linrong He
- China-Japan Friendship Hospital, Yinghua East Road, Chaoyang District, Beijing100029, China
| | - Chanyuan Wu
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Qian Wang
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Yan Zhao
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
| | - Xiaofeng Zeng
- Department of Rheumatology and Clinical Immunology, Chinese Academy of Medical Sciences & Peking Union Medical College; National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Ministry of Science & Technology; State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital (PUMCH); Key Laboratory of Rheumatology and Clinical Immunology, Ministry of Education, Beijing100730, China
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Cai R, Chen X, Khan S, Li H, Tan J, Tian Y, Zhao S, Yin Z, Jin D, Guo J. Aspongopus chinensis Dallas induces pro-apoptotic and cell cycle arresting effects in hepatocellular carcinoma cells by modulating miRNA and mRNA expression. Heliyon 2024; 10:e27525. [PMID: 38500987 PMCID: PMC10945178 DOI: 10.1016/j.heliyon.2024.e27525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/20/2024] Open
Abstract
Aspongopus chinensis Dallas is a traditional Chinese medicinal insect with several anticancer properties can inhibit cancer cell growth, by inhibiting cell division, autophagy and cell cycle. However, the precise therapeutics effects and mechanisms of this insect on liver cancer are still unknown. This study examined the inhibitory influence of A. chinensis on the proliferation of hepatocellular carcinoma (HCC) cells and explore the underlying mechanism using high-throughput sequencing. The results showed that A. chinensis substantially reduced the viability of Hep G2 cells. A total of 33 miRNAs were found to be upregulated, while 43 miRNAs were downregulated. Additionally, 754 mRNAs were upregulated and 863 mRNAs were downregulated. Significant enrichment of differentially expressed genes was observed in signaling pathways related to tumor cell growth, cell cycle regulation, and apoptosis. Differentially expressed miRNAs exhibited a targeting relationship with various target genes, including ARC, HSPA6, C11orf86, and others. Hence, cell cycle and apoptosis were identified by flow cytometry. These findings indicate that A. chinensis impeded cell cycle advancement, halted the cell cycle in the G0/G1 and S stages, and stimulated apoptosis. Finally, mouse experiments confirmed that A. chinensis significantly inhibits tumor growth in vivo. Therefore, our findings indicate that A. chinensis has a notable suppressive impact on the proliferation of HCC cells. The potential mechanism of action could involve the regulation of mRNA expression via miRNA, ultimately leading to cell cycle arrest and apoptosis. The results offer a scientific foundation for the advancement and application of A. chinensis in the management of HCC.
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Affiliation(s)
- Renlian Cai
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Xumei Chen
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Samiullah Khan
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Haiyin Li
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Jun Tan
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Ying Tian
- Department of Histology and Embryology, Zunyi Medical University, Zunyi, Guizhou, 563000, China
| | - Shuai Zhao
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Zhiyong Yin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Daochao Jin
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Jianjun Guo
- Provincial Key Laboratory for Agricultural Pest Management of Mountainous Region, Institute of Entomology, Guizhou University, Guiyang, Guizhou, 550025, China
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29
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Tian Z, Zhang C, Wu M, Luo J, Zhou H, Duan Y, Li Y. Flexible-Arranged Biomimetic Array Integrated with Parallel Entropy-Driven Circuits for Ultrasensitive, Multiple, and Reliable Detection of Cancer-Related MicroRNAs. ACS Sens 2024; 9:1290-1300. [PMID: 38478991 DOI: 10.1021/acssensors.3c02183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
With the emergence of microRNA (miRNA) as a promising biomarker in cancer diagnosis, it is significant to develop multiple analyses of miRNAs. However, it still faces difficulties in ensuring the sensitivity and accuracy during multiplex detection owing to the low abundance and experimental deviation of miRNAs. In this work, a flexible-arranged biomimetic array integrated with parallel entropy-driven circuits (EDCs) was developed for ultrasensitive, multiplex, reliable, and high-throughput detection of miRNAs. The biomimetic array was fabricated by arrangement of various photonic crystals (PCs) for adjustable photonic band gaps (PBGs) and specific fluorescence enhancement. Meanwhile, two cancer-related miRNAs and one reference miRNA were introduced as multiple analytes as a proof-of-concept. The parallel EDCs with negligible crosstalk were designed based on the modular property. Because of the one-to-one match between the emitted fluorescence of parallel EDCs and the PBGs of the flexible-arranged biomimetic array, the generated fluorescence signal triggered by target miRNAs can be enhanced on the corresponding domain of the array. Furthermore, the amplified signal of the array was detected with high-throughput scanning, which could reveal specific information on cancer-related miRNAs as well as reference miRNA, enhancing the abundance and reliability of the analysis. The proposed array has the merits of a modular design, flexible deployment, simple operation (nonenzymatic and isothermal), improved accuracy, high sensitivity, and multiplex analysis, showing potential in disease diagnosis.
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Affiliation(s)
- Ziyi Tian
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Chuyan Zhang
- Precision Medicine Center, Medical Equipment Innovation Research Center, Med-X Center for Manufacturing, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Mengfan Wu
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Jie Luo
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Huiling Zhou
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, School of Mechanical Engineering, Sichuan University, Chengdu, Sichuan 610065, P. R. China
| | - Yongxin Li
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
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Li Y, Jiang L, Yu Z, Jiang C, Zhang F, Jin S. SPRi/SERS dual-mode biosensor based on ployA-DNA/ miRNA/AuNPs-enhanced probe sandwich structure for the detection of multiple miRNA biomarkers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 308:123664. [PMID: 38029598 DOI: 10.1016/j.saa.2023.123664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
MicroRNA (miRNA) has broad application prospects in the early detection of various cancers. In this work, a SPRi/SERS dual-mode biosensor was developed on the same gold chip by AuNPs as the reinforcing medium. High throughput and sensitivity detection of three typical cervical cancer markers miRNA21, miRNA124 and miRNA143 were achieved based on the sandwich structure of polyA blocks-DNA capture probe/target miRNA/AuNPs-assistant probe or SERS nanoprobes. AuNPs greatly improved the SPR response due to mass increase and more sensitive refractive index changes. Meanwhile, due to the LSPR effect of AuNPs, the signal of SERS nanoprobe can be amplified. The miRNAs were detected in serum to verify its practicality. SPRi achieved detection of three miRNAs simultaneously. LODs were 6.3 fM, 5.3 fM and 4.6 fM, respectively, and wide dynamic response range of 500 pM-10 nM. While SERS assay ensured high sensitivity with LODs as low as 1 fM, 0.8 fM and 1.2 fM, respectively, and with the recoveries in the range of 90.0 %-100.2 %. The redundant detection signals of the two modes can provide more reliable data to prevent false positive or false negative detection, and have great application prospects in detection of cancer-related nucleic acids in early stage of disease.
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Affiliation(s)
- Yifan Li
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China
| | - Li Jiang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China.
| | - Zizhen Yu
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China
| | - Cailing Jiang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China
| | - Fei Zhang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China
| | - Shangzhong Jin
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China.
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Wang SH, Zhao Y, Wang CC, Chu F, Miao LY, Zhang L, Zhuo L, Chen X. RFEM: A framework for essential microRNA identification in mice based on rotation forest and multiple feature fusion. Comput Biol Med 2024; 171:108177. [PMID: 38422957 DOI: 10.1016/j.compbiomed.2024.108177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/21/2024] [Accepted: 02/18/2024] [Indexed: 03/02/2024]
Abstract
With the increasing number of microRNAs (miRNAs), identifying essential miRNAs has become an important task that needs to be solved urgently. However, there are few computational methods for essential miRNA identification. Here, we proposed a novel framework called Rotation Forest for Essential MicroRNA identification (RFEM) to predict the essentiality of miRNAs in mice. We first constructed 1,264 miRNA features of all miRNA samples by fusing 38 miRNA features obtained from the PESM paper and 1,226 miRNA functional features calculated based on miRNA-target gene interactions. Then, we employed 182 training samples with 1,264 features to train the rotation forest model, which was applied to compute the essentiality scores of the candidate samples. The main innovations of RFEM were as follows: 1) miRNA functional features were introduced to enrich the diversity of miRNA features; 2) the rotation forest model used decision tree as the base classifier and could increase the difference among base classifiers through feature transformation to achieve better ensemble results. Experimental results show that RFEM significantly outperformed two previous models with the AUC (AUPR) of 0.942 (0.944) in three comparison experiments under 5-fold cross validation, which proved the model's reliable performance. Moreover, ablation study was further conducted to demonstrate the effectiveness of the novel miRNA functional features. Additionally, in the case studies of assessing the essentiality of unlabeled miRNAs, experimental literature confirmed that 7 of the top 10 predicted miRNAs have crucial biological functions in mice. Therefore, RFEM would be a reliable tool for identifying essential miRNAs.
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Affiliation(s)
- Shu-Hao Wang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China; Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
| | - Yan Zhao
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Chun-Chun Wang
- School of Science, Jiangnan University, Wuxi, 214122, China
| | - Fei Chu
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China; Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
| | - Lian-Ying Miao
- School of Mathematics, China University of Mining and Technology, Xuzhou, 221116, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Linlin Zhuo
- School of Data Science and Artificial Intelligence, Wenzhou University of Technology, Wenzhou, 325000, China.
| | - Xing Chen
- School of Science, Jiangnan University, Wuxi, 214122, China.
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Watanabe Y, Yajima S, Koda M, Kinjou A, Koto A, Takamura E, Sakamoto H, Suye SI. Selective miR-21 detection technology based on photocrosslinkable artificial nucleic acid-modified magnetic particles and hybridization chain reaction. Biosens Bioelectron 2024; 247:115920. [PMID: 38091896 DOI: 10.1016/j.bios.2023.115920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/02/2024]
Abstract
Recently, microRNA (miRNA) detection in blood has attracted attention as a new early detection technology for cancer. The extraction of target miRNA is a necessary preliminary step for detection; however, currently, most extraction methods extract all RNA from the blood, which limits the detection selectivity. Therefore, a method for the selective extraction and detection of target miRNA from blood is very important. In this study, we utilized photocrosslinkable artificial nucleic acids and the hybridization chain reaction (HCR) in an attempt to improve upon the current standard method RT-qPCR, which is hampered by problems with primer design and enzymatic amplification. By introducing photocrosslinkable artificial nucleic acids to oligonucleotide probes modified with magnetic particles with a sequence complementary to that of the target miRNA and irradiating them with light, covalent bonds were formed between the target miRNA and the oligonucleotide probes. These tight covalent bonds enabled the capture of miRNA in blood, and intensive washing ensured that only the target miRNA were extracted. After extraction, two types of DNA (H1 and H2) modified with fluorescent dyes were added and the fluorescence signals were amplified by the HCR in the presence of the target miRNA bound to the photocrosslinkable artificial nucleic acids, allowing for isothermal and enzyme-free miRNA detection. The novel method is suitable for selective miRNA detection in real blood samples. Because the reaction proceeds isothermally and no specialized equipment is used for washing, this detection technology is simple and selective and suitable for application to point-of-care technology using microfluidic devices.
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Affiliation(s)
- Yui Watanabe
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Shuto Yajima
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Maho Koda
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Ayumu Kinjou
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | | | - Eiichiro Takamura
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
| | - Hiroaki Sakamoto
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan.
| | - Shin-Ichiro Suye
- University of Fukui, Faculty of Engineering, Graduate School of Engineering, Fukui, Japan
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Xue Y, Wang K, Jiang Y, Dai Y, Liu X, Pei B, Li H, Xu H, Zhao G. An ultrasensitive and multiplexed miRNA one-step real time RT-qPCR detection system and its application in esophageal cancer serum. Biosens Bioelectron 2024; 247:115927. [PMID: 38113694 DOI: 10.1016/j.bios.2023.115927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 11/30/2023] [Accepted: 12/10/2023] [Indexed: 12/21/2023]
Abstract
MicroRNAs (miRNAs) are increasingly recognized as promising biomarkers for early disease diagnosis and prognosis. Therefore, the need for rapid, robust methods for multiplex miRNA detection in biological research and clinical diagnosis is crucial. This study introduces a novel multiplex miRNA detection method, SMOS-qPCR (Sensitive and Multiplexed One-Step RT-qPCR). The method integrates multiplexed reverse transcription and TaqMan-based qPCR into a single tube, employing a one-step operation on a real-time PCR system. We investigated the effect of 3' end phosphorylation of the Linker, Linker concentration and probe concentration on the SMOS-qPCR, resulted in a wide linear range from 1 fM to 0.1 zM (R2 ≥ 0.99 for each miRNA), surpassing the capabilities of stem-loop RT-qPCR and SYBR Green One-step RT-qPCR. The method showed excellent performance in distinguishing mature miRNA from miRNA precursor, and successfully detected four miRNAs in a single tube without cross-interference. Its high specificity enables precise differentiation of less than 1% nonspecific signal. Finally, we demonstrated the effectiveness of the SMOS-qPCR system in detecting circulating miRNAs in serum samples, distinguishing between esophageal cancers and health individuals with high AUC values (>0.940). In conclusion, the proposed SMOS-qPCR system offers a straightforward and promising approach for miRNA profiling in future clinical applications.
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Affiliation(s)
- Ying Xue
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Suzhou Jiangsu 215000, China.
| | - Kai Wang
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Yunli Jiang
- Department of Gastroenterology, The First People's Hospital of Xuzhou, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, The Affiliated Hospital of China University of Mining and Technology, Xuzhou, Jiangsu, 221002, China
| | - Yanmiao Dai
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan Jiangsu, 215300, China
| | - Xiaoyu Liu
- Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China
| | - Bing Pei
- Department of Clinical Laboratory, The Affiliated Suqian First People's Hospital of Nanjing Medical University, Suqian, Jiangsu, 223800, China
| | - Hui Li
- Department of Gastroenterology, The First People's Hospital of Xuzhou, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, The Affiliated Hospital of China University of Mining and Technology, Xuzhou, Jiangsu, 221002, China
| | - Hongwei Xu
- Department of Spleen and Stomach Diseases, Kunshan Hospital of Traditional Chinese Medicine, Kunshan Jiangsu, 215300, China.
| | - Guodong Zhao
- Zhejiang University of Technology, Zhejiang, Hangzhou 310014, China; Suzhou VersaBio Technologies Co. Ltd., Kunshan, Jiangsu 215300, China; ZJUT Yinhu Research Institute of Innovation and Entrepreneurship, Zhejiang, Hangzhou 311400, China.
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Zhang M, Han Y. MicroRNAs in chronic pediatric diseases (Review). Exp Ther Med 2024; 27:100. [PMID: 38356668 PMCID: PMC10865459 DOI: 10.3892/etm.2024.12388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/15/2023] [Indexed: 02/16/2024] Open
Abstract
MicroRNAs are small non-coding RNAs with a length of 20-24 nucleotides. They bind to the 3'-untranslated region of target genes to induce the degradation of target mRNAs or inhibit their translation. Therefore, they are involved in the regulation of development, apoptosis, proliferation, differentiation and other biological processes (including hormone secretion, signaling and viral infections). Chronic diseases in children may be difficult to treat and are often associated with malnutrition resulting from a poor diet. Consequently, further complications, disease aggravation and increased treatment costs impose a burden on patients and their families. Existing evidence suggests that microRNAs are involved in various chronic non-neoplastic diseases in children. The present review discusses the roles of microRNAs in five major chronic diseases in children, namely, diabetes mellitus, congenital heart diseases, liver diseases, bronchial asthma and epilepsy, providing a theoretical basis for them to become therapeutic biomarkers in chronic pediatric diseases.
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Affiliation(s)
- Mingyao Zhang
- Department of Pediatrics, The Third Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, Jilin 130117, P.R. China
| | - Yanhua Han
- Department of Pediatrics, Affiliated Hospital to Changchun University of Chinese Medicine, Changchun, Jilin 130021, P.R. China
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Wang H, Yang S, Chen L, Li Y, He P, Wang G, Dong H, Ma P, Ding G. Tumor diagnosis using carbon-based quantum dots: Detection based on the hallmarks of cancer. Bioact Mater 2024; 33:174-222. [PMID: 38034499 PMCID: PMC10684566 DOI: 10.1016/j.bioactmat.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/15/2023] [Accepted: 10/05/2023] [Indexed: 12/02/2023] Open
Abstract
Carbon-based quantum dots (CQDs) have been shown to have promising application value in tumor diagnosis. Their use, however, is severely hindered by the complicated nature of the nanostructures in the CQDs. Furthermore, it seems impossible to formulate the mechanisms involved using the inadequate theoretical frameworks that are currently available for CQDs. In this review, we re-consider the structure-property relationships of CQDs and summarize the current state of development of CQDs-based tumor diagnosis based on biological theories that are fully developed. The advantages and deficiencies of recent research on CQDs-based tumor diagnosis are thus explained in terms of the manifestation of nine essential changes in cell physiology. This review makes significant progress in addressing related problems encountered with other nanomaterials.
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Affiliation(s)
- Hang Wang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Siwei Yang
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Liangfeng Chen
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Yongqiang Li
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peng He
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Gang Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and Technology, Ningbo University, Ningbo, 315211, PR China
| | - Hui Dong
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- CAS Center for Excellence in Superconducting Electronics (CENSE), Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
| | - Peixiang Ma
- Shanghai Key Laboratory of Orthopedic Implants, Department of Orthopedic Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, PR China
| | - Guqiao Ding
- National Key Laboratory of Materials for Integrated Circuit, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, PR China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, PR China
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Wang W, Liu L, Zhu J, Xing Y, Jiao S, Wu Z. AI-Enhanced Visual-Spectral Synergy for Fast and Ultrasensitive Biodetection of Breast Cancer-Related miRNAs. ACS NANO 2024; 18:6266-6275. [PMID: 38252138 DOI: 10.1021/acsnano.3c10543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
In biomedical testing, artificial intelligence (AI)-enhanced analysis has gradually been applied to the diagnosis of certain diseases. This research employs AI algorithms to refine the precision of integrative detection, encompassing both visual results and fluorescence spectra from lateral flow assays (LFAs), which signal the presence of cancer-linked miRNAs. Specifically, the color shift of gold nanoparticles (GNPs) is paired with the red fluorescence from nitrogen vacancy color centers (NV-centers) in fluorescent nanodiamonds (FNDs) and is integrated into LFA strips. While GNPs amplify the fluorescence of FNDs, in turn, FNDs enhance the color intensity of GNPs. This reciprocal intensification of fluorescence and color can be synergistically augmented with AI algorithms, thereby improving the detection sensitivity for early diagnosis. Supported by the detection platform based on this strategy, the fastest detection results with a limit of detection (LOD) at the fM level and the R2 value of ∼0.9916 for miRNA can be obtained within 5 min. Meanwhile, by labeling the capture probes for miRNA-21 and miRNA-96 (both of which are early indicators of breast cancer) on separate T-lines, simultaneous detection of them can be achieved. The miRNA detection methods employed in this study may potentially be applied in the future for the early detection of breast cancer.
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Affiliation(s)
- Wei Wang
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Lei Liu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Jianxiong Zhu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Youqiang Xing
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Songlong Jiao
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
| | - Ze Wu
- School of Mechanical Engineering, Southeast University, Nanjing 211189, People's Republic of China
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Mu Y, Huang X, Yang Y, Huang Z, Chen J, Li S, Dong Y, Chen F, Zhang R, Chen J, Feng H, Zhou Q. Study of serum exosome miRNA as a biomarker for early onset adult ouclar myastthenia gravis. Gene 2024; 896:148034. [PMID: 38013129 DOI: 10.1016/j.gene.2023.148034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/13/2023] [Accepted: 11/24/2023] [Indexed: 11/29/2023]
Abstract
BACKGROUND By extracting and sequencing miRNAs from serum exosomes of patients with early-onset ocular myasthenia gravis (OMG), generalized myasthenia gravis (GMG) and healthy controls, we screened differentially expressed miRNAs and explored the possibility as potential biomarkers for early-onset OMG. METHODS Peripheral blood samples were collected from patients with early-onset OMG, early-onset GMG, and age-matched healthy subjects, with 6 samples in each group. All these patients were diagnosed as MG for the first time and did not undergo any treatment. Exosomes miRNAs were extracted from the serum and performed deep sequencing; the differentially expressed miRNAs were compared and analyzed between OMG, GMG, and healthy control groups using edgeR. The differential expression standard was set to | log2FC |>1, p < 0.05. Target prediction of mRNAs were performed using miRTarBase, TargetScan, and miRDB databases, and a protein-protein interaction (PPI) network was constructed subsequently. The miRNAs with a significant difference were validated using RT-qPCR (10 early-onset OMG patients, 10 early-onset GMG patients and 10 age-sex-matched healthy subjects), and the value of the area under the ROC curve (AUC) was used to assess the diagnostic accuracy and evaluate clinical prognostic value. RESULTS In total, one upregulated (miR-130a-3p) miRNA was obtained through the upregulated intersection between control vs OMG and OMG vs GMG; four downregulated (miR-4712-3p; miR-6752-5p; miR-320d; miR-3614-3p) miRNAs were obtained through the downregulated intersection between control vs OMG and OMG vs GMG. A total of 408 target genes were predicted for the five differentially expressed miRNAs. The mTOR signaling pathway and Rap1 signaling pathway were significantly enriched based on the enrichment results. RT-qPCR findings revealed that for the OMG, the expression of miR-320d, miR-4712-3p and miR-3614-3p was markedly up-/down-regulated as compared to GMG and healthy control group. The AUC for the three miRNAs between OMG and healthy control groups were 0.78, 0.79 and 0.79 respectively; the AUC between OMG and GMG was 0.84. CONCLUSIONS The present study identified three novel miRNAs as candidate biomarkers for early-onset OMG patients and it was expected to provide a possibility and a new orientation for serum exosomal miRNAs as OMG diagnostic biomarkers.
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Affiliation(s)
- Yajun Mu
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Xin Huang
- Department of Neurology, The First Affiliated Hospital of Sun Yat sen University, Guangzhou, China
| | - Yuanting Yang
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Ziqing Huang
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jiaxin Chen
- Department of Neurology, The First Affiliated Hospital of Sun Yat sen University, Guangzhou, China
| | - Shiyin Li
- Department of Neurology, The First Affiliated Hospital of Sun Yat sen University, Guangzhou, China
| | - Yuying Dong
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Fangyuan Chen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Rijia Zhang
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jian Chen
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Huiyu Feng
- Department of Neurology, The First Affiliated Hospital of Sun Yat sen University, Guangzhou, China.
| | - Qing Zhou
- Department of Ophthalmology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
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Guo H, Chen J, Feng Y, Dai Z. A Simple and Robust Exponential Amplification Reaction (EXPAR)-Based Hairpin Template (exp-Hairpin) for Highly Specific, Sensitive, and Universal MicroRNA Detection. Anal Chem 2024; 96:2643-2650. [PMID: 38295438 DOI: 10.1021/acs.analchem.3c05323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2024]
Abstract
Specific and sensitive detection of microRNAs continues to encounter significant challenges, especially in the development of rapid and efficient isothermal amplification strategies for point-of-care settings. The exponential amplification reaction (EXPAR) has garnered significant attention owing to its simplicity and rapid amplification of signals within a short period. However, a substantial loss of amplification efficiency, difficulty in distinguishing closely related homologous sequences, and adapting the designed templates to other targets seriously hamper the practical application of the EXPAR. In this work, a hairpin template tailored for the EXPAR system (exp-Hairpin) was constructed by adding identical trigger sequences and enzyme cleavage sites on two arms of the hairpin, achieving theoretically more than 2n amplification efficiency and minimal background amplification of EXPAR. Modulating the stability of the exp-Hairpin template by increasing the stem length, the specificity of detecting target miRNA in highly homologous sequences could be significantly improved. Using miRNA let-7a as a target model, the exp-Hairpin with 8 bp stem length for EXPAR amplification curves could effectively distinguish target let-7a and nontarget let-7b/7c/7f/7g/7i homologous sequences. This strategy enabled the sensitive and accurate analysis of let-7a in diluted human serum with satisfactory recoveries. By simply replacing the loop recognition sequence of exp-Hairpin, the specific detection of miR-200b was also achieved, demonstrating the universality of this strategy. The exp-Hairpin EXPAR accelerates simple and rapid molecular diagnostic applications for short nucleic acids.
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Affiliation(s)
- Haijing Guo
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Jun Chen
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, PR China
| | - Yaqiang Feng
- College of Chemistry and Materials Science, Northwest University, Xi'an 710127, PR China
| | - Zong Dai
- Key Laboratory of Sensing Technology and Biomedical Instrument of Guangdong Province, School of Biomedical Engineering, Sun Yat-Sen University, Guangzhou 510006, PR China
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Ma Y, Guo X, He Q, Liu L, Li Z, Zhao X, Gu W, Zhong Q, Li N, Yao G, Ma X. Integrated analysis of microRNA and messenger RNA expression profiles reveals functional microRNA in infectious bovine rhinotracheitis virus-induced mitochondrial damage in Madin-Darby bovine kidney cells. BMC Genomics 2024; 25:158. [PMID: 38331736 PMCID: PMC10851472 DOI: 10.1186/s12864-024-10042-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Accepted: 01/22/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Studies have confirmed that Infectious bovine rhinotracheitis virus (IBRV) infection induces mitochondrial damage. MicroRNAs (miRNAs) are a class of noncoding RNA molecules, which are involved in various biological processes and pathological changes associated with mitochondrial damage. It is currently unclear whether miRNAs participate in IBRV-induced mitochondrial damage in Madin-Darby bovine kidney (MDBK) cells. RESULTS In the present study, we used high-throughput sequencing technology, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis to screen for mitochondria-related miRNAs and messenger RNAs (mRNAs). In total, 279 differentially expressed miRNAs and 832 differentially expressed mRNAs were identified in 6 hours (IBRV1) versus 24 hours (IBRV2) after IBRV infection in MDBK cells. GO and KEGG enrichment analysis revealed that 42 differentially expressed mRNAs and 348 target genes of differentially expressed miRNAs were correlated with mitochondrial damage, and the miRNA-mitochondria-related target genes regulatory network was constructed to elucidate their potential regulatory relationships. Among the 10 differentially expressed miRNAs, 8 showed expression patterns consistent with the high-throughput sequencing results. Functional validation results showed that overexpression of miR-10a and miR-182 aggravated mitochondrial damage, while inhibition of miR-10a and miR-182 alleviated mitochondrial damage. CONCLUSIONS This study not only revealed the expression changes of miRNAs and mRNAs in IBRV-infected MDBK cells, but also revealed possible biological regulatory relationship between them. MiR-10a and miR-182 may have the potential to be developed as biomarkers for the diagnosis and treatment of IBRV. Together, Together, these data and analyses provide additional insights into the roles of miRNA and mRNA in IBRV-induced mitochondria damage.
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Affiliation(s)
- Yingcai Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xueping Guo
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Qin He
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Lu Liu
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Zelong Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Xiaomin Zhao
- College of Veterinary Medicine, Northwest A & F University, Yangling, 712100, China
| | - Wenxi Gu
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Qi Zhong
- Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, 830011, China
| | - Na Li
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China
| | - Gang Yao
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China.
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China.
| | - Xuelian Ma
- College of Veterinary Medicine, Xinjiang Agricultural University, Urumqi, 830052, China.
- Xinjiang key Laboratory of New Drug Study and Creation for Herbivorous Animal (XJ-KLNDSCHA), Xinjiang Agricultural University, Urumqi, 830052, China.
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Hu C, Wang L, Liu S, Sheng X, Yin L. Recent Development of Implantable Chemical Sensors Utilizing Flexible and Biodegradable Materials for Biomedical Applications. ACS NANO 2024; 18:3969-3995. [PMID: 38271679 DOI: 10.1021/acsnano.3c11832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Implantable chemical sensors built with flexible and biodegradable materials exhibit immense potential for seamless integration with biological systems by matching the mechanical properties of soft tissues and eliminating device retraction procedures. Compared with conventional hospital-based blood tests, implantable chemical sensors have the capability to achieve real-time monitoring with high accuracy of important biomarkers such as metabolites, neurotransmitters, and proteins, offering valuable insights for clinical applications. These innovative sensors could provide essential information for preventive diagnosis and effective intervention. To date, despite extensive research on flexible and bioresorbable materials for implantable electronics, the development of chemical sensors has faced several challenges related to materials and device design, resulting in only a limited number of successful accomplishments. This review highlights recent advancements in implantable chemical sensors based on flexible and biodegradable materials, encompassing their sensing strategies, materials strategies, and geometric configurations. The following discussions focus on demonstrated detection of various objects including ions, small molecules, and a few examples of macromolecules using flexible and/or bioresorbable implantable chemical sensors. Finally, we will present current challenges and explore potential future directions.
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Affiliation(s)
- Chen Hu
- School of Materials Science and Engineering, The Key Laboratory of Advanced Materials of Ministry of Education, State Key Laboratory of New Ceramics and Fine Processing, Laboratory of Flexible Electronics Technology, Tsinghua University, Beijing 100084, P. R. China
| | - Liu Wang
- Key Laboratory of Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, Beihang University, Beijing 100083, P. R. China
| | - Shangbin Liu
- School of Materials Science and Engineering, The Key Laboratory of Advanced Materials of Ministry of Education, State Key Laboratory of New Ceramics and Fine Processing, Laboratory of Flexible Electronics Technology, Tsinghua University, Beijing 100084, P. R. China
| | - Xing Sheng
- Department of Electronic Engineering, Beijing National Research Center for Information Science and Technology, Institute for Precision Medicine, Laboratory of Flexible Electronics Technology, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, P. R. China
| | - Lan Yin
- School of Materials Science and Engineering, The Key Laboratory of Advanced Materials of Ministry of Education, State Key Laboratory of New Ceramics and Fine Processing, Laboratory of Flexible Electronics Technology, Tsinghua University, Beijing 100084, P. R. China
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Kong D, Zhang S, Guo M, Li S, Wang Q, Gou J, Wu Y, Chen Y, Yang Y, Dai C, Tian Z, Wee ATS, Liu Y, Wei D. Ultra-Fast Single-Nucleotide-Variation Detection Enabled by Argonaute-Mediated Transistor Platform. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307366. [PMID: 37805919 DOI: 10.1002/adma.202307366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 10/03/2023] [Indexed: 10/09/2023]
Abstract
"Test-and-go" single-nucleotide variation (SNV) detection within several minutes remains challenging, especially in low-abundance samples, since existing methods face a trade-off between sensitivity and testing speed. Sensitive detection usually relies on complex and time-consuming nucleic acid amplification or sequencing. Here, a graphene field-effect transistor (GFET) platform mediated by Argonaute protein that enables rapid, sensitive, and specific SNV detection is developed. The Argonaute protein provides a nanoscale binding channel to preorganize the DNA probe, accelerating target binding and rapidly recognizing SNVs with single-nucleotide resolution in unamplified tumor-associated microRNA, circulating tumor DNA, virus RNA, and reverse transcribed cDNA when a mismatch occurs in the seed region. An integrated microchip simultaneously detects multiple SNVs in agreement with sequencing results within 5 min, achieving the fastest SNV detection in a "test-and-go" manner without the requirement of nucleic acid extraction, reverse transcription, and amplification.
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Affiliation(s)
- Derong Kong
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Shen Zhang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Mingquan Guo
- Department of Laboratory Medicine, Shanghai Public Health Clinical Center, Fudan University, Shanghai, 200433, P. R. China
| | - Shenwei Li
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Qiang Wang
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Jian Gou
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yungen Wu
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yiheng Chen
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Yuetong Yang
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
| | - Changhao Dai
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
| | - Zhengan Tian
- Shanghai International Travel Healthcare Center, Shanghai, 200335, P. R. China
| | - Andrew Thye Shen Wee
- Department of Physics, National University of Singapore, Singapore, 117542, Singapore
| | - Yunqi Liu
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
- Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Dacheng Wei
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200433, P. R. China
- Laboratory of Molecular Materials and Devices, Fudan University, Shanghai, 200433, P. R. China
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Wang T, Jiang K, Wang Y, Xu L, Liu Y, Zhang S, Xiong W, Wang Y, Zheng F, Zhu JJ. Prolonged near-infrared fluorescence imaging of microRNAs and proteases in vivo by aggregation-enhanced emission from DNA-AuNC nanomachines. Chem Sci 2024; 15:1829-1839. [PMID: 38303939 PMCID: PMC10829036 DOI: 10.1039/d3sc05887e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/20/2023] [Indexed: 02/03/2024] Open
Abstract
Developing a comprehensive strategy for imaging various biomarkers (i.e., microRNAs and proteases) in vivo is an exceptionally formidable task. Herein, we have designed a deoxyribonucleic acid-gold nanocluster (DNA-AuNC) nanomachine for detecting tumor-related TK1 mRNA and cathepsin B in living cells and in vivo. The DNA-AuNC nanomachine is constructed using AuNCs and DNA modules that incorporate a three component DNA hybrid (TD) and a single-stranded fuel DNA (FD). Upon being internalized into tumor cells, the TK1 mRNA initiates the DNA-AuNC nanomachine through DNA strand displacement cascades, leading to the amplified self-assembly and the aggregation-enhanced emission of AuNCs for in situ imaging. Furthermore, with the aid of a protease nanomediator consisting of a mediator DNA/peptide complex and AuNCs (DpAuNCs), the DNA-AuNC nanomachine can be triggered by the protease-activated disassembly of the DNA/peptide complex on the nanomediator, resulting in the aggregation of AuNCs for in vivo protease amplified detection. It is worth noting that our study demonstrates the impressive tumor permeability and accumulation capabilities of the DNA-AuNC nanomachines via in situ amplified self-assembly, thereby facilitating prolonged imaging of TK1 mRNA and cathepsin B both in vitro and in vivo. This strategy presents a versatile and biomarker-specific paradigm for disease diagnosis.
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Affiliation(s)
- Ting Wang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Kai Jiang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Yifan Wang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Limei Xu
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Yingqi Liu
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Shiling Zhang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Weiwei Xiong
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Yemei Wang
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Fenfen Zheng
- School of Environmental & Chemical Engineering, Jiangsu University of Science and Technology Changhui Rd. 666 Zhenjiang Jiangsu 212003 China
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical for Life Science, School of Chemistry and Chemical Engineering, Nanjing University Xianlin Ave 163 Nanjing Jiangsu 210023 China
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Zhang Y, Sun M, Xie J, Chen J, Huang T, Duan WJ, Chen JX, Chen J, Dai Z, Li M. Dual-Signal Amplification Strategy Based on Catalytic Hairpin Assembly and APE1-Assisted Amplification for High-Contrast miRNA Imaging in Living Cells. Anal Chem 2024; 96:910-916. [PMID: 38171356 DOI: 10.1021/acs.analchem.3c05013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Early tumor diagnosis is crucial to successful treatment. Earlier studies have shown that microRNA is a biomarker for early tumor diagnosis. The development of highly sensitive miRNA detection methods, especially in living cells, plays an indispensable role for early diagnosis and treatment of tumor. Although the catalytic hairpin assembly (CHA)-based miRNA analysis strategy is commonly used for disease diagnosis, further application of CHA is hindered due to its low amplification efficiency and low tumor recognition contrast. To address these limitations, we propose a dual-signal amplification strategy based on CHA and APE1-assisted amplification, enabling highly sensitive and high-contrast miRNA imaging. The miR-221 was selected as a target model. This dual-signal amplification strategy has exhibited high amplification efficiency, which could analyze miRNA as low as 21 fM. This strategy also exhibited high specificity, which could distinguish target miRNA and nontarget with single-base differences. Moreover, this method showed significant potential for practical application, as it could successfully distinguish the expression difference of miR-221 in the plasma samples of normal people and patients. Most importantly, the expression level of the APE1 enzyme in tumor cells is higher than that in normal cells, allowing this strategy to sensitively and specifically image miRNA within tumor cells. This proposed method has also been successfully used to indicate fluctuations of intracellular miRNA and to distinguish miRNA expression between normal cells and cancer cells with high contrast. We anticipate that this method will provide fresh insights and can be a powerful tool for tumor diagnosis and treatment based on miRNA analysis.
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Affiliation(s)
- Ya Zhang
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Mengxu Sun
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Juan Xie
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Jing Chen
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
| | - Ting Huang
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Wen-Jun Duan
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jin-Xiang Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
| | - Jun Chen
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P.R. China
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Qingdao University of Science and Technology, Qingdao 266042, P.R. China
| | - Zong Dai
- Guangdong Provincial Key Laboratory of Sensing Technology and Biomedical Instrument, School of Biomedical Engineering, Sun Yat-Sen University, Shenzhen 518107, P.R. China
| | - Minmin Li
- Center of Clinical Laboratory, The First Affiliated Hospital of Jinan University, Guangzhou 510632, P.R. China
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Feng Y, Liu S, Yao Y, Chen M, Liu Q, Chen X. Endogenous mRNA-Powered and Spatial Confinement-Derived DNA Nanomachines for Ultrarapid and Sensitive Imaging of Let-7a. Anal Chem 2024; 96:564-571. [PMID: 38112715 DOI: 10.1021/acs.analchem.3c04837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
DNA nanostructure-based signal amplifiers offer new tools for imaging intracellular miRNA. However, the inadequate kinetics and susceptibility to enzymatic hydrolysis of these amplifiers, combined with a deficient cofactor concentration within the intracellular environment, significantly undermine their operational efficiency. In this study, we address these challenges by encapsulating a localized target strand displacement assembly (L-SD) and a toehold-exchange endogenous-powered component (R-mRNA) within a framework nucleic acid (FNA) structure─20 bp cubic DNA nanocage (termed RL-cube). This design enables the construction of an endogenous-powered and spatial-confinement DNA nanomachine for ratiometric fluorescence imaging of intracellular miRNA Let-7a. The R-mRNA is designed to be specifically triggered by glyceraldehyde 3-phosphate dehydrogenase (GAPDH), an abundant cellular enzyme, and concurrently releases a component that can recycle the target Let-7a. Meanwhile, L-SD reacts with Let-7a to release a stem-loop beacon, generating a FRET signal. The spatial confinement provided by the framework, combined with the ample intracellular supply of GAPDH, imparts remarkable sensitivity (7.57 pM), selectivity, stability, biocompatibility, and attractive dynamic performance (2240-fold local concentration, approximately four times reaction rate, and a response time of approximately 7 min) to the nanomachine-based biosensor. Consequently, this study introduces a potent sensing approach for detecting nucleic acid biomarkers with significant potential for application in clinical diagnostics and therapeutics.
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Affiliation(s)
- Yinghui Feng
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Shenghong Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Yao Yao
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Miao Chen
- College of Life Science, Central South University, Changsha 410083, Hunan, China
| | - Qi Liu
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
| | - Xiaoqing Chen
- College of Chemistry and Chemical Engineering, the Hunan Provincial Key Laboratory of Water Environment and Agriculture Product Safety, Central South University, Changsha 410083, Hunan, China
- Xiangjiang Laboratory, Changsha 410205, Hunan, China
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Zhang XW, Du L, Liu MX, Wang JH, Chen S, Yu YL. All-in-one nanoflare biosensor combined with catalyzed hairpin assembly amplification for in situ and sensitive exosomal miRNA detection and cancer classification. Talanta 2024; 266:125145. [PMID: 37660618 DOI: 10.1016/j.talanta.2023.125145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/12/2023] [Accepted: 08/30/2023] [Indexed: 09/05/2023]
Abstract
Exosomal miRNAs can reflect tumor progression and metastasis, and are effective biomarkers for cancer diagnosis. However, the accuracy of exosomal miRNA-based cancer diagnosis is limited by the low sensitivity and complicated RNA extraction of traditional approaches. Herein, a novel biosensor is developed for in situ, extraction-free, and highly sensitive analysis of exosomal miRNAs via nanoflare combined with catalyzed hairpin assembly (CHA) amplification. Without cumbersome and costly miRNA extraction or transfection agents, nanoflare can directly enter the exosomes to bind target miRNAs and generate a fluorescence signal that can be amplified by the CHA reaction to achieve the in situ and highly sensitive detection of exosomal miRNAs. Under the optimal conditions, the detection limit of 5 aM is obtained for three exosomal miRNAs, which is an order of magnitude lower than quantitative real time polymerase chain reaction (qRT-PCR). In combination with the linear discriminant analysis algorithm, five exosomes are distinguished with 100% accuracy. Importantly, five cancers including breast, lung, liver, cervical, and colon cancer from 64 patients are distinguished with 99% accuracy by testing exosomal miRNAs in clinical plasma. This simple, accurate, and sensitive biosensor holds the potential to be expanded into clinical non-invasive cancer diagnostic tests.
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Affiliation(s)
- Xue-Wei Zhang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Li Du
- Department of Pharmacy, Shanxi Provincial Cancer Hospital, Taiyuan, 110819, China
| | - Meng-Xian Liu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Jian-Hua Wang
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China
| | - Shuai Chen
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
| | - Yong-Liang Yu
- Research Center for Analytical Sciences, Department of Chemistry, College of Sciences, Northeastern University, Shenyang, 110819, China.
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Wang WT, Yang Y, Zhang Y, Le YN, Wu YL, Liu YY, Tu YJ. EBV-microRNAs as Potential Biomarkers in EBV-related Fever: A Narrative Review. Curr Mol Med 2024; 24:2-13. [PMID: 36411555 PMCID: PMC10825793 DOI: 10.2174/1566524023666221118122005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/31/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022]
Abstract
At present, timely and accurate diagnosis and effective treatment of Epstein- Barr Virus (EBV) infection-associated fever remain a difficult challenge. EBV encodes 44 mature microRNAs (miRNAs) that inhibit viral lysis, adjust inflammatory response, regulate cellular apoptosis, promote tumor genesis and metastasis, and regulate tumor cell metabolism. Herein, we have collected the specific expression data of EBV-miRNAs in EBV-related fevers, including infectious mononucleosis (IM), EBVassociated hemophagocytic lymphohistiocytosis (EBV-HLH), chronic active EBV infection (CAEBV), and EBV-related tumors, and proposed the potential value of EBVmiRNAs as biomarkers to assist in the identification, diagnosis, and prognosis of EBVrelated fever, as well as therapeutic targets for drug development.
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Affiliation(s)
- Wei-ting Wang
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai (201203), China
| | - Yun Yang
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai (201203), China
| | - Yang Zhang
- Information Center of Science and Technology, Shanghai Innovation Center of TCM Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai (201203), China
| | - Yi-ning Le
- National Key Laboratory of Medical Immunology & Institute of Immunology, Second Military Medical University, Shanghai (200433), China
| | - Yu-lin Wu
- School of Acupuncture-moxibustion and Tuina, Shanghai University of Traditional Chinese Medicine, Shanghai (201203), China
| | - Yi-yi Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai (200032), China
| | - Yan-jie Tu
- Department of Febrile Disease, Basic Medical College, Shanghai University of Traditional Chinese Medicine, Shanghai (201203), China
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Meng F, Wang Y, Lv X, Feng F, Yang G. Electrochemiluminescent bioassay based on Ru@Zr-BTC-MOFs nanoparticles for determination of let-7a miRNA using the hybridization chain reaction. Mikrochim Acta 2023; 191:23. [PMID: 38091146 DOI: 10.1007/s00604-023-06107-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023]
Abstract
Carboxyl-rich tris(4,4'-dicarboxylic acid-2,2'-bipyridyl) ruthenium(II) ([Ru(dcbpy)3]2+) and 1,3,5-phenyl tricarboxylic acid (H3BTC) were used as the organic ligand to synthesize the metal-organic frameworks by a simple one-pot hydrothermal method with ZrCl4 as metal ion source. Subsequently, the excellent electrochemiluminescence (ECL) luminophore (denoted as Ru@Zr-BTC-MOFs) was obtained. The Ru@Zr-BTC-MOFs displayed outstanding ECL properties, and a sensitive ECL bioassay based on Ru@Zr-BTC-MOFs was designed for the detection of let-7a microRNA (miRNA) using hybrid chain reaction (HCR). Under the optimal experimental conditions, the proposed bioassay exhibited a good linear relationship in the range from 50.0 fM to 5.00 × 102 pM with a detection limit of 3.71 fM. Besides, the proposed sensor exhibited satisfactory performance in real samples. The recovery was 91 ~ 108%, and the relative standard deviation was less than 5.6%. It might have potential clinical applications for detecting miRNA in biomedical research and clinical diagnosis. The schematic diagram of the preparation of Ru@Zr-BTC-MOFs (a) and ECL sensor for detecting let -7a (b).
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Affiliation(s)
- Fei Meng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Yisi Wang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Xinxin Lv
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China
| | - Fang Feng
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Gongjun Yang
- Key Laboratory of Drug Quality Control and Pharmacovigilance (China Pharmaceutical University), Ministry of Education, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
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Wang C, Xie Y, Song X, Chao Z, Wu K, Fang Y, Zhao H, Ju H, Liu Y. A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer. Angew Chem Int Ed Engl 2023; 62:e202312665. [PMID: 37903741 DOI: 10.1002/anie.202312665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/28/2023] [Accepted: 10/30/2023] [Indexed: 11/01/2023]
Abstract
Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid "false positive" signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.
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Affiliation(s)
- Caixia Wang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yuxin Xie
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Xuefang Song
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Zhicong Chao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Kun Wu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Yanyun Fang
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Hongxia Zhao
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ying Liu
- State Key Laboratory of Analytical Chemistry for Life Science Department, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
- Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing, 210023, China
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Guan L, Peng J, Liu T, Huang S, Yang Y, Wang X, Hao X. Ultrasensitive miRNA Detection Based on Magnetic Upconversion Nanoparticle Enhancement and CRISPR/Cas13a-Driven Signal Amplification. Anal Chem 2023; 95:17708-17715. [PMID: 38000080 DOI: 10.1021/acs.analchem.3c03554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2023]
Abstract
MicroRNAs (miRNAs), a class of small molecules with important regulatory functions, have been widely used in the field of biosensing as biomarkers for the early diagnosis of various diseases. Therefore, it is crucial to develop an miRNA detection platform with high sensitivity and specificity. Here, we have designed a CRISPR/Cas13-based enzymatic cyclic amplification system and regarded the magnetic upconversion nanoparticles (MUCNPs) as a biosensor of outputting the detection signal for the highly sensitive and high-fidelity detection of miRNAs. MUCNPs were composed of UCNPs (fluorescence donors) and Fe3O4@AuNPs (fluorescence acceptors) through double-stranded DNA hybrid coupling. The target miRNA acted as an activator, which could activate the trans-cleavage activity of Cas13a to the well-designed Trigger containing two uracil ribonucleotides (rU) in its loop and trigger a strand displacement reaction to generate a large amount of single-stranded DNA, resulting in the release of the UCNPs from MUCNPs. Benefiting from the high fidelity and high selectivity of CRISPR/Cas13a, the great effect of triggered enzymatic cycle amplification, and the high-intensity luminescent signal of MUCNPs, this method possessed miRNA detection capability with high sensitivity and specificity even in the complex environment with 10% fetal bovine serum (FBS) and a serum sample. Meanwhile, the detection limit could be as low as 83.2 fM. In addition, this method effectively reduced the effect of photobleaching and maintained high stability, which was expected to achieve efficient and sensitive miRNA detection.
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Affiliation(s)
- Liwen Guan
- School of Public Health, Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Jiawei Peng
- School of Public Health, Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Ting Liu
- School of Public Health, Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Shuangyi Huang
- Nanchang University Queen Mary School, Nanchang, Jiangxi 330031 , P.R. China
| | - Yifei Yang
- School of Public Health, Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Xiaolei Wang
- The National Engineering Research Center for Bioengineering Drugs and the Technologies, Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi 330031 , P.R. China
- School of Chemistry and Chemical Engineering, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
| | - Xian Hao
- School of Public Health, Jiangxi Provincial Key Laboratory of Preventive Medicine, Nanchang University, Nanchang, Jiangxi 330031, P.R. China
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Chen Y, Liang J, Tan X, Shan L, Zhang L, Li L, Ge S, Cui K, Yu J. Constructing DNAzyme-driven three-dimensional DNA nanomachine-mediated paper-based photoelectrochemical device for ultrasensitive detection of miR-486-5p. Biosens Bioelectron 2023; 241:115671. [PMID: 37714060 DOI: 10.1016/j.bios.2023.115671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 09/17/2023]
Abstract
As a unique class of dynamic nanostructures, biomimetic DNA walking machines that exhibit geometrical complexity and nanometre precision have gained great success in photoelectrochemical (PEC) bioanalysis. Despite certain achievements, the slow reaction kinetics and low processivity severely restrict the amplification efficiency of the DNA walker-mediated biosensors. Herein, by taking advantage of efficient DNA rolling machines, a three-dimensional (3D) DNA nanomachine-mediated paper-based PEC device for speedy ultrasensitive detection of miR-486-5p was successfully constructed. To achieve it, a novel In2S3/SnS2 sensitized heterojunction was firstly in-situ grown on the Au-modified paper fibers and implemented as the photoanode with effective separation of photogenerated carriers to achieve an enhanced initial photocurrent. Subsequently, the copper hexacyanoferrate(II)-modified CuO nanosphere was introduced as a multifunctional signal regulator via the competitive capture of electron donors and photon energy with the photoelectric layer for efficiently quenching the PEC signal. With the introduction of targets, the DNAzyme-driven DNA nanomachine with editable motion modes was gradually activated and it could continuously cleave the tracks DNA labeled quenching probes, finally achieving the recovery of PEC signal. As a proof of concept, the elaborated paper-based PEC device presented a wide linear range from 0.1 fM to 100 pM and a detection limit of 35 aM for miR-486-5p bioassay. This work provides an innovative insight to the exploitation of DNA nanobiotechnology and nucleic acid signal amplification strategy.
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Affiliation(s)
- Yuanyuan Chen
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Jiaxin Liang
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Xiaoran Tan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Li Shan
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Lina Zhang
- Shandong Provincial Key Laboratory of Preparation and Measurement of Building Materials, University of Jinan, Jinan, Shandong, 250022, PR China
| | - Li Li
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China.
| | - Shenguang Ge
- Institute for Advanced Interdisciplinary Research, University of Jinan, Jinan, 250022, PR China
| | - Kang Cui
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China.
| | - Jinghua Yu
- School of Chemistry and Chemical Engineering, University of Jinan, Jinan, Shandong, 250022, PR China
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