1
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Guo C, Wang X, Ren H. Databases and computational methods for the identification of piRNA-related molecules: A survey. Comput Struct Biotechnol J 2024; 23:813-833. [PMID: 38328006 PMCID: PMC10847878 DOI: 10.1016/j.csbj.2024.01.011] [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: 09/11/2023] [Revised: 12/31/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Abstract
Piwi-interacting RNAs (piRNAs) are a class of small non-coding RNAs (ncRNAs) that plays important roles in many biological processes and major cancer diagnosis and treatment, thus becoming a hot research topic. This study aims to provide an in-depth review of computational piRNA-related research, including databases and computational models. Herein, we perform literature analysis and use comparative evaluation methods to summarize and analyze three aspects of computational piRNA-related research: (i) computational models for piRNA-related molecular identification tasks, (ii) computational models for piRNA-disease association prediction tasks, and (iii) computational resources and evaluation metrics for these tasks. This study shows that computational piRNA-related research has significantly progressed, exhibiting promising performance in recent years, whereas they also suffer from the emerging challenges of inconsistent naming systems and the lack of data. Different from other reviews on piRNA-related identification tasks that focus on the organization of datasets and computational methods, we pay more attention to the analysis of computational models, algorithms, and performances that aim to provide valuable references for computational piRNA-related identification tasks. This study will benefit the theoretical development and practical application of piRNAs by better understanding computational models and resources to investigate the biological functions and clinical implications of piRNA.
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Affiliation(s)
- Chang Guo
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
| | - Xiaoli Wang
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Han Ren
- Laboratory of Language Engineering and Computing, Guangdong University of Foreign Studies, Guangzhou 510420, China
- Laboratory of Language and Artificial Intelligence, Guangdong University of Foreign Studies, Guangzhou 510420, China
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2
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Mo L, Mo M, Yang C, Lin W. Enhancing RNA detection and breast cancer subtyping with a universal 3D-hybridization chain reaction system. Talanta 2024; 277:126387. [PMID: 38876028 DOI: 10.1016/j.talanta.2024.126387] [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: 02/21/2024] [Revised: 05/16/2024] [Accepted: 06/05/2024] [Indexed: 06/16/2024]
Abstract
Breast cancer, a globally prevalent malignancy, is characterized by pronounced heterogeneity. Accurate subtyping requires the simultaneous detection of different biomarkers, which is crucial for personalized treatment strategies. However, existing methodologies are hindered by limited versatility and sensing performance. To overcome these hurdles, this study presents a universal 3D-Hybridization Chain Reaction (3D-HCR) system for RNA detection and subtype-specific diagnosis of breast cancer. The system integrated a universal trigger for HCR, thereby circumventing the need for complex sequence design and enabling the analysis of various RNA targets. Leveraging the spatial-confinement effect offered by DNA nanocarriers, this system exhibited superior amplification efficiency, achieving detection limits of 3.83 pM and 4.96 pM for PD-L1 mRNA and miR-21, respectively. Importantly, the system could differentiate between triple-negative breast cancer and estrogen receptor-positive breast cancer in both living cells and clinical tissues. These findings underscore the potential of the universal 3D-HCR system as a promising tool in clinical diagnostics. With its proven proficiency in breast cancer diagnostics and versatility in RNA analysis, this system holds the promise of broadening the horizons of precision medicine.
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Affiliation(s)
- Liuting Mo
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Mingxiu Mo
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Chan Yang
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China
| | - Weiying Lin
- Institute of Optical Materials and Chemical Biology, Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, College of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, PR China.
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3
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Yuan H, Hu J, Ge QQ, Liu WJ, Ma F, Zhang CY. Construction of a Spatial-Confined Self-Stacking Catalytic Circuit for Rapid and Sensitive Imaging of Piwi-Interacting RNA in Living Cells. NANO LETTERS 2024; 24:8732-8740. [PMID: 38958407 DOI: 10.1021/acs.nanolett.4c02230] [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: 07/04/2024]
Abstract
Piwi-interacting RNAs (piRNAs) are small noncoding RNAs that repress transposable elements to maintain genome integrity. The canonical catalytic hairpin assembly (CHA) circuit relies on random collisions of free-diffused reactant probes, which substantially slow down reaction efficiency and kinetics. Herein, we demonstrate the construction of a spatial-confined self-stacking catalytic circuit for rapid and sensitive imaging of piRNA in living cells based on intramolecular and intermolecular hybridization-accelerated CHA. We rationally design a 3WJ probe that not only accelerates the reaction kinetics by increasing the local concentration of reactant probes but also eliminates background signal leakage caused by cross-entanglement of preassembled probes. This strategy achieves high sensitivity and good specificity with shortened assay time. It can quantify intracellular piRNA expression at a single-cell level, discriminate piRNA expression in tissues of breast cancer patients and healthy persons, and in situ image piRNA in living cells, offering a new approach for early diagnosis and postoperative monitoring.
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Affiliation(s)
- Huimin Yuan
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Qi-Qin Ge
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Wen-Jing Liu
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Fei Ma
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Digital Medical Engineering, Southeast University, Nanjing 211189, China
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4
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Bai Y, Xu P, Li S, Wang D, Zhang K, Zheng D, Yue D, Zhang G, He S, Li Y, Zou H, Deng Y. Signal amplification strategy of DNA self-assembled biosensor and typical applications in pathogenic microorganism detection. Talanta 2024; 272:125759. [PMID: 38350248 DOI: 10.1016/j.talanta.2024.125759] [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: 11/05/2023] [Revised: 01/17/2024] [Accepted: 02/06/2024] [Indexed: 02/15/2024]
Abstract
Biosensors have emerged as ideal analytical devices for various bio-applications owing to their low cost, convenience, and portability, which offer great potential for improving global healthcare. DNA self-assembly techniques have been enriched with the development of innovative amplification strategies, such as dispersion-to-localization of catalytic hairpin assembly, and dumbbell hybridization chain reaction, which hold great significance for building biosensors capable of realizing sensitive, rapid and multiplexed detection of pathogenic microorganisms. Here, focusing primarily on the signal amplification strategies based on DNA self-assembly, we concisely summarized the strengths and weaknesses of diverse isothermal nucleic acid amplification techniques. Subsequently, both single-layer and cascade amplification strategies based on traditional catalytic hairpin assembly and hybridization chain reaction were critically explored. Furthermore, a comprehensive overview of the recent advances in DNA self-assembled biosensors for the detection of pathogenic microorganisms is presented to summarize methods for biorecognition and signal amplification. Finally, a brief discussion is provided about the current challenges and future directions of DNA self-assembled biosensors.
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Affiliation(s)
- Yuxin Bai
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Pingyao Xu
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shi Li
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongsheng Wang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Kaijiong Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Dongming Zheng
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Daifan Yue
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China
| | - Guiji Zhang
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Shuya He
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China
| | - Yan Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, 610075, Chengdu, China.
| | - Haimin Zou
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
| | - Yao Deng
- Department of Clinical Laboratory, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, 610041, Chengdu, China.
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5
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Chen J, Zhang J, Xie Q, Chu Z, Lu Y, Zhang F, Wang Q. Isothermal strand displacement polymerase reaction (ISDPR)-assisted microchip electrophoresis for highly sensitive detection of cancer associated microRNAs. Anal Chim Acta 2024; 1300:342469. [PMID: 38521570 DOI: 10.1016/j.aca.2024.342469] [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: 01/24/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
More and more studies have found that microRNAs (miRNAs) are markers of cancer, and detection of miRNAs is beneficial for early diagnosis and prognosis of cancer. In this paper, the isothermal strand displacement polymerase reaction (ISDPR), which is an enzyme-assisted nucleic acid amplification method, was studied to combine with microchip electrophoresis (MCE) for a simultaneously detection of two cancer related miRNAs named microRNA-21 (miR-21) and microRNA-221 (miR-221). In the ISDPR amplification, two different DNA hairpins (HPs) were specifically designed, so that miR-21 and miR-221 could respectively bind to HPs and started ISDPR amplification to generate two different products which were ultimately detected by MCE. The optimal conditions of ISDPR were carefully investigated, and the limits of detection (LOD) of miR-21 and miR-221 were as low as 0.35 fM and 0.25 fM (S/N = 3) respectively under these conditions. The human lung tumor cells and serum samples were analyzed by this ISDPR-MCE method and satisfactory results were obtained, which means that this method is of high sensitivity, high efficiency, low reagent consumption and simple operation in miRNAs detection.
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Affiliation(s)
- Jingyi Chen
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Jingzi Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Qihui Xie
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Zhaohui Chu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Yuqi Lu
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China
| | - Fan Zhang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China.
| | - Qingjiang Wang
- School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, PR China.
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6
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Zhang Q, Wang H, Liu Q, Zeng N, Fu G, Qiu Y, Yang Y, Yuan H, Wang W, Li B. Exosomes as Powerful Biomarkers in Cancer: Recent Advances in Isolation and Detection Techniques. Int J Nanomedicine 2024; 19:1923-1949. [PMID: 38435755 PMCID: PMC10906735 DOI: 10.2147/ijn.s453545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
Exosomes, small extracellular vesicles derived from cells, are known to carry important bioactive molecules such as proteins, nucleic acids, and lipids. These bioactive components play crucial roles in cell signaling, immune response, and tumor metastasis, making exosomes potential diagnostic biomarkers for various diseases. However, current methods for detecting tumor exosomes face scientific challenges including low sensitivity, poor specificity, complicated procedures, and high costs. It is essential to surmount these obstacles to enhance the precision and dependability of diagnostics that rely on exosomes. Merging DNA signal amplification techniques with the signal boosting capabilities of nanomaterials presents an encouraging strategy to overcome these constraints and improve exosome detection. This article highlights the use of DNA signal amplification technology and nanomaterials' signal enhancement effect to improve the detection of exosomes. This review seeks to offer valuable perspectives for the enhancement of amplification methods applied in practical cancer diagnosis and prognosis by providing an overview of how these novel technologies are utilized in exosome-based diagnostic procedures.
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Affiliation(s)
- Qiongdan Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Qingyi Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Ni Zeng
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Gang Fu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Hanwen Yuan
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha, People’s Republic of China
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7
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Ge QQ, Han Q, Han Y, Ma F, Li CZ, Zhang CY. A multi-cycle signal amplification-mediated single quantum dot nanosensor for PIWI-interacting RNA detection. Chem Commun (Camb) 2024; 60:408-411. [PMID: 38084051 DOI: 10.1039/d3cc05639b] [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
We construct a single quantum dot-based nanosensor for piRNA detection based on ligation-mediated multi-cycle signal amplification. This nanosensor is homogenous, selective, and sensitive with a detection limit of 0.104 fM. Moreover, it can detect the endogenous piRNA level in different cell lines, and discriminate cancer tissues from normal tissues.
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Affiliation(s)
- Qi-Qin Ge
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Yun Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Fei Ma
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| | - Chen-Zhong Li
- Biomedical Engineering, School of Medicine, The Chinese University of Hong Kong, Shenzhen, 518172, China.
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
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8
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Li W, Wang W, Luo S, Chen S, Ji T, Li N, Pan W, Zhang X, Wang X, Li K, Zhang Y, Yan X. A sensitive and rapid electrochemical biosensor for sEV-miRNA detection based on domino-type localized catalytic hairpin assembly. J Nanobiotechnology 2023; 21:328. [PMID: 37689652 PMCID: PMC10492399 DOI: 10.1186/s12951-023-02092-x] [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: 07/26/2023] [Accepted: 08/31/2023] [Indexed: 09/11/2023] Open
Abstract
Small extracellular-vesicule-associated microRNA (sEV-miRNA) is an important biomarker for cancer diagnosis. However, rapid and sensitive detection of low-abundance sEV-miRNA in clinical samples is challenging. Herein, a simple electrochemical biosensor that uses a DNA nanowire to localize catalytic hairpin assembly (CHA), also called domino-type localized catalytic hairpin assembly (DT-LCHA), has been proposed for sEV-miRNA1246 detection. The DT-LCHA offers triple amplification, (i). CHA system was localized in DNA nanowire, which shorten the distance between hairpin substrate, inducing the high collision efficiency of H1 and H2 and domino effect. Then, larger numbers of CHAs were triggered, capture probe bind DT-LCHA by exposed c sites. (ii) The DNA nanowire can load large number of electroactive substance RuHex as amplified electrochemical signal tags. (iii) multiple DT-LCHA was carried by the DNA nanowire, only one CHA was triggered, the DNA nanowire was trapped by the capture probe, which greatly improve the detection sensitivity, especially when the target concentration is extremely low. Owing to the triple signal amplification in this strategy, sEV-miRNA at a concentration of as low as 24.55 aM can be detected in 20 min with good specificity. The accuracy of the measurements was also confirmed using reverse transcription quantitative polymerase chain reaction. Furthermore, the platform showed good performance in discriminating healthy donors from patients with early gastric cancer (area under the curve [AUC]: 0.96) and was equally able to discriminate between benign gastric tumors and early cancers (AUC: 0.77). Thus, the platform has substantial potential in biosensing and clinical diagnosis.
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Affiliation(s)
- Wenbin Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Wen Wang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Medical Laboratory of the Third Affiliated Hospital of Shenzhen University, Shenzhen, 518001, People's Republic of China
| | - Shihua Luo
- Center for Clinical Laboratory Diagnosis and Research, The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, People's Republic of China
| | - Siting Chen
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Tingting Ji
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ningcen Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Weilun Pan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Xiaohe Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Xiaojing Wang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ke Li
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China
| | - Ye Zhang
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China.
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China.
| | - Xiaohui Yan
- Laboratory Medicine Center, Department of Laboratory Medicine, Nanfang Hospital, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, People's Republic of China.
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, People's Republic of China.
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9
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Ma X, Liu H, Tao S. A simple, sensitive and label-free method for miRNA analysis in gastric cancer via catalytic hairpin assembly assisted programming of split-G-quadruplexes. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4236-4242. [PMID: 37584656 DOI: 10.1039/d3ay00989k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Accurate analysis of miRNA is valuable for the diagnosis of various diseases. Herein, a sensitive and accurate fluorescence method was developed for miRNA detection based on catalytic hairpin assembly (CHA) and split-G-quadruplex (split-G4) based signal reactions. The presence of target miRNA activated the CHA process through unfolding the H1 probe, which could continuously induce the proximity of split-G4. The formed intact G4 can be specifically recognized by the commercial fluorescent dye ThT (thioflavin T), allowing for the highly sensitive, label-free detection of miRNAs. By utilizing split-G4 to generate a signal, the method exhibited a low background signal and a high reliability. In addition, the method is demonstrated to be applied for clinical sample detection, implying its promising prospect for disease diagnosis.
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Affiliation(s)
- Xiaoli Ma
- Gastroenterology Department, People's Hospital of Chong Qing Liang Jiang New Area, No. 199 Renxing Road, Renhe Street, Yubei District, Chongqing, 401120, China.
| | - Hongmei Liu
- Gastroenterology Department, People's Hospital of Chong Qing Liang Jiang New Area, No. 199 Renxing Road, Renhe Street, Yubei District, Chongqing, 401120, China.
| | - Siyu Tao
- Gastroenterology Department, People's Hospital of Chong Qing Liang Jiang New Area, No. 199 Renxing Road, Renhe Street, Yubei District, Chongqing, 401120, China.
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10
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Limanówka P, Ochman B, Świętochowska E. PiRNA Obtained through Liquid Biopsy as a Possible Cancer Biomarker. Diagnostics (Basel) 2023; 13:diagnostics13111895. [PMID: 37296747 DOI: 10.3390/diagnostics13111895] [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: 04/20/2023] [Revised: 05/21/2023] [Accepted: 05/27/2023] [Indexed: 06/12/2023] Open
Abstract
In recent years PIWI-interacting RNAs (piRNAs) have gained the interest of scientists, mainly because of their possible implications in cancer. Many kinds of research showed how their expression can be linked to malignant diseases. However, most of them evaluated the expression of piRNAs in tumor tissues. It was shown how these non-coding RNAs can interfere with many signaling pathways involved in the regulation of proliferation or apoptosis. A comparison of piRNA expression in tumor tissue and adjacent healthy tissues has demonstrated they can be used as biomarkers. However, this way of obtaining samples has a significant drawback, which is the invasiveness of such a procedure. Liquid biopsy is an alternative for acquiring biological material with little to no harm to a patient. Several different piRNAs in various types of cancer were shown to be expressed in bodily fluids such as blood or urine. Furthermore, their expression significantly differed between cancer patients and healthy individuals. Hence, this review aimed to assess the possible use of liquid biopsy for cancer diagnosis with piRNAs as biomarkers.
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Affiliation(s)
- Piotr Limanówka
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Błażej Ochman
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
| | - Elżbieta Świętochowska
- Department of Medical and Molecular Biology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, 19 Jordana, 41-800 Zabrze, Poland
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11
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Tong Y, Guan B, Sun Z, Dong X, Chen Y, Li Y, Jiang Y, Li J. Ratiometric fluorescent detection of exosomal piRNA-823 based on Au NCs/UiO-66-NH 2 and target-triggered rolling circle amplification. Talanta 2023; 257:124307. [PMID: 36764170 DOI: 10.1016/j.talanta.2023.124307] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 02/05/2023]
Abstract
piR-823 is a newly discovered colorectal cancer marker with high diagnostic efficacy. However, the current quantification methods have complicated operations and high cost, which restrict its clinical application. Herein, a metal-organic framework (MOF) with a UiO-66 prototype structure which supports gold nanoclusters (Au NCs), Au NCs/UiO-66-NH2, were prepared as a model nanobiosensing platform for ratiometric detection of exosomal piR-823. The rolling circle amplification process provides high sensitivity and the ratiometric detection process ensures good accuracy of the sensor. Such biosensor showed a wide linear range of 0.04-4 pM, and a low detection limit of 10.2 fM towards piR-823. In addition, piR-823 can be used as an effective supplement to carcinoembryonic antigen (CEA) in clinical diagnosis of colorectal cancer. This study not only provides a potentially valuable ratio fluorescence platform involving enzyme catalytic reaction, but also offers a design blueprint for further expansion of nanotechnology in the diverse biological analysis.
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Affiliation(s)
- Yao Tong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Bingxin Guan
- Department of Pathology, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Zhiwei Sun
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China
| | - Xiangjun Dong
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yuqing Chen
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanru Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China
| | - Yanyan Jiang
- Key Laboratory for Liquid-Solid Structural Evolution and Processing of Materials, Ministry of Education, Shandong University, Jinan, Shandong, China.
| | - Juan Li
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, Shandong, China.
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12
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Mo L, He W, Li Z, Liang D, Qin R, Mo M, Yang C, Lin W. Recent progress in the development of DNA-based biosensors integrated with hybridization chain reaction or catalytic hairpin assembly. Front Chem 2023; 11:1134863. [PMID: 36874074 PMCID: PMC9978474 DOI: 10.3389/fchem.2023.1134863] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
As isothermal, enzyme-free signal amplification strategies, hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) possess the advantages such as high amplification efficiency, excellent biocompatibility, mild reactions, and easy operation. Therefore, they have been widely applied in DNA-based biosensors for detecting small molecules, nucleic acids, and proteins. In this review, we summarize the recent progress of DNA-based sensors employing typical and advanced HCR and CHA strategies, including branched HCR or CHA, localized HCR or CHA, and cascaded reactions. In addition, the bottlenecks of implementing HCR and CHA in biosensing applications are discussed, such as high background signals, lower amplification efficiency than enzyme-assisted techniques, slow kinetics, poor stability, and internalization of DNA probes in cellular applications.
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Affiliation(s)
- Liuting Mo
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Wanqi He
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Ziyi Li
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Danlian Liang
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Runhong Qin
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Mingxiu Mo
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Chan Yang
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
| | - Weiying Lin
- Guangxi Key Laboratory of Guangxi Key Laboratory of Electrochemical Energy Materials, School of Chemistry and Chemical Engineering, Institute of Optical Materials and Chemical Biology, Guangxi University, Nanning, China
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13
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Akimniyazova AN, Niyazova TK, Yurikova OY, Pyrkova AY, Zhanuzakov MA, Ivashchenko AT. piRNAs may regulate expression of candidate genes of esophageal adenocarcinoma. Front Genet 2022; 13:1069637. [PMID: 36531220 PMCID: PMC9747755 DOI: 10.3389/fgene.2022.1069637] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 07/29/2023] Open
Abstract
Elucidation of ways to regulate the expression of candidate cancer genes will contribute to the development of methods for cancer diagnosis and therapy. The aim of the present study was to show the role of piRNAs as efficient regulators of mRNA translation of esophageal adenocarcinoma (EAC) candidate genes. We used bioinformatic methods to study the interaction characteristics of up to 200 thousand piRNAs with mRNAs of 38 candidate EAC genes. The piRNAs capable of binding to mRNA of AR, BTG3, CD55, ERBB3, FKBP5, FOXP1, LEP, SEPP1, SMAD4, and TP53 genes with high free energy by the formation of hydrogen bonds between canonical (G-C, A-U) and noncanonical (G-U, A-C) piRNA and mRNA nucleotide pairs were revealed. The organization of piRNA binding sites (BSs) in the mRNA of candidate genes was found to overlap nucleotide sequences to form clusters. Clusters of piRNA BSs were detected in the 5'-untranslated region, coding domain sequence, and 3'-untranslated region of mRNA. Due to the formation of piRNA binding site clusters, compaction of BSs occurs and competition between piRNAs for binding to mRNA of candidate EAC genes occurs. Associations of piRNA and candidate genes were selected for use as markers for the diagnosis of EAC.
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Affiliation(s)
- A. N. Akimniyazova
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - T. K. Niyazova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - O. Yu. Yurikova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - A. Yu. Pyrkova
- Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
- Center for Bioinformatics and Nanomedicine, Almaty, Kazakhstan
| | - M. A. Zhanuzakov
- Higher School of Medicine, Faculty of Medicine and Healthcare, Al-Farabi Kazakh National University, Almaty, Kazakhstan
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14
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Zhang LM, Gao QX, Xie BP, Chen J, Duan WJ. Highly accelerated isothermal nucleic acid amplifications by butanol dehydration: simple, more efficient, and ultrasensitive. Chem Commun (Camb) 2022; 58:5793-5796. [PMID: 35466974 DOI: 10.1039/d2cc01589g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzyme-free isothermal amplification reactions for nucleic acid analysis usually take several hours to obtain sufficient detection sensitivity, which limits their practical applications. Herein, we report a butanol dehydration-based method to greatly improve both the efficiency and the sensitivity of nucleic acid detections by three types of enzyme-free isothermal amplification reactions. The reaction time has been shortened from 3 h to 5-20 min with higher sensitivities. Especially in the DNAzyme-based amplification, the detection limit can be lowered over 16 000-fold to 3 × 10-17 mol L-1 in 2 h compared to the normal 3 h-reaction. We demonstrate that the high amplification efficiencies are attributed to the greatly accelerated reaction rates in the extremely concentrated reaction solutions caused by the butanol dehydration. This approach enhances the potential of applications of isothermal amplification reactions in clinical rapid tests, nanostructure synthesis, etc. and is promising to expand to other types of chemical reactions.
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Affiliation(s)
- Li-Min Zhang
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Qing-Xin Gao
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Bao-Ping Xie
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Jun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Wen-Jun Duan
- Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China.
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15
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Catalytic hairpin assembly as cascade nucleic acid circuits for fluorescent biosensor: design, evolution and application. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116582] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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