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Liu J, Lu Y, Hu Y, Zhang Q, Wang S, Guo Z, Qing Z. Portable Detection of Lysine Acetyltransferase Activity in Lung Cancer Cells Based on a Miniature Electrochemical Sensor. Anal Chem 2024; 96:5546-5553. [PMID: 38551480 DOI: 10.1021/acs.analchem.3c05908] [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: 04/10/2024]
Abstract
The detection of lysine acetyltransferases is crucial for diagnosing and treating lung cancer, highlighting the necessity for highly efficient detection methods. We developed a portable, highly accurate, and sensitive technique using fast-scan cyclic voltammetry (FSCV) to determine the activity of the lysine acetyltransferase TIP60, employing a novel miniature electrochemical sensor. This approach involves a compact electrochemical cell, merely 3 mm in diameter, that holds solutions up to 50 μL, equipped with a conductive indium tin oxide working electrode. Uniquely, this system operates on a two-electrode model compatible with the FSCV, obviating the traditional requirement for a reference electrode. The system detects TIP60 activity through the continuous generation of CoA molecules that engage in reactions with Cu(II), thereby significantly improving the accuracy of the acetylation analysis. Remarkably, the detection limit achieved for TIP60 is notably low at 3.3 pg/mL (S/N = 3). The results show that the reversible dynamic acetylation can be effectively regulated by inhibitor incubation and glucose stimulation. This cutting-edge strategy enhances the analysis of a broad spectrum of biomarkers by modifying the responsive unit, and its miniaturization and portability significantly amplify its applicability in biomedical research, promising it to be a versatile tool for early diagnostic and therapeutic interventions in lung cancer.
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Affiliation(s)
- Jiayue Liu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Yanmei Lu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Yufang Hu
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
| | - Qingqing Zhang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Sui Wang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhiyong Guo
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, School of Materials Science & Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha 410114, China
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Shi L, Ying K, Sha L, Zhang Y, Sun L, Li G. DNA-Peptide Interaction-Modulated Charge Reversal in Biomimetic Nanochannels for Simple and Efficient Detection of Histone Deacetylases. Anal Chem 2024; 96:4817-4824. [PMID: 38482584 DOI: 10.1021/acs.analchem.3c04819] [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: 03/27/2024]
Abstract
Protein acetylation, a fundamental post-translational modification, plays a critical role in the regulation of gene expression and cellular processes. Monitoring histone deacetylases (HDACs) is important for understanding epigenetic dynamics and advancing the early diagnosis of malignancies. Here, we leverage the dynamic characteristics of DNA-peptide interactions in biomimetic nanochannels to develop a HDAC detection method. In specific, the catalysis of peptide deacetylation by HDACs triggers alterations in the charge states of the nanochannel surface to accommodate DNA molecules. Then, the interaction between DNA and peptides shifts the nanochannel surface charge from positive to negative, leading to a reversal of the ion current rectification (ICR). By calculation of the ICR ratio, quantitative detection of HDACs can be efficiently achieved using the nanochannel-based method in an enzyme-free and label-free manner. Our experimental results demonstrate that HDACs can be detected by using this method within a concentration range of 0.5-500 nM. The innate simplicity and efficiency of this strategy may render it a valuable tool for advancing both fundamental research and clinical applications in the realm of epigenetics and personalized medicine.
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Affiliation(s)
- Liu Shi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
| | - Keqin Ying
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Lingjun Sha
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
| | - Yuanyuan Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Life Sciences, Nanjing University, Nanjing 210023, P. R. China
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai 200444, P. R. China
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Gao L, Zhou Y, Cao L, Cao Y, Zhang H, Zhang M, Yin H, Ai S. Photoelectrochemical sensor for histone deacetylase Sirt1 detection based on Z-scheme heterojunction of CuS-BiVO 4 photoactive material and the cyclic etching of MnO 2 by NADH. Talanta 2024; 268:125307. [PMID: 37866306 DOI: 10.1016/j.talanta.2023.125307] [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: 09/18/2023] [Revised: 10/09/2023] [Accepted: 10/12/2023] [Indexed: 10/24/2023]
Abstract
A novel photoelectrochemical (PEC) biosensor was constructed for histone deacetylase Sirt1 detection based on the Z-Scheme heterojunction of CuS-BiVO4 and reduced nicotinamide adenine dinucleotide (NADH) induced cyclic etching of MnO2 triggered by Sirt1 enzyme catalytic histone deacetylation event. Based on the Z-Scheme heterojunction, the photoactivity of the CuS-BiVO4 was improved greatly due to the highly effective separation of the photogenerated electron-hole pairs. In the presence of MnO2 nanosheets on the CuS-BiVO4/ITO electrode surface, the photocurrent decreased due to the inhibition effect of MnO2. However, this inhibition effect was eliminated by the incubation of MnO2/CuS-BiVO4/ITO with NADH, where NADH was produced in the deacetylation process of acetylated peptide catalyzed by Sirt1 with NAD+. The formed NADH etched MnO2, resulting in an increased photocurrent. In this process, NADH was oxidized to produce NAD+, which further involved the deacetylation process. Based on this cycle, the photocurrent of the biosensor was improved greatly and the sensitive and selective detection of Sirt1 was achieved. The biosensor presented a wide linear range from 0.005 to 10 nM with the low detection limit of 3.38 pM (S/N = 3). In addition, the applicability of the developed method was evaluated by investigating the effect of sodium butyrate and perfluorohexane sulfonate on Sirt1 activity.
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Affiliation(s)
- Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China.
| | - Lulu Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Yaoyuan Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Haowei Zhang
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Miao Zhang
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
| | - Shiyun Ai
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, 271018, Taian, Shandong, China
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Liu Z, Duan X, Yun Y, Li S, Feng Z, Zhan J, Liu R, Li Y, Zhang J. Photoactivatable Aptamer-CRISPR Nanodevice Enables Precise Profiling of Interferon-Gamma Release in Humanized Mice. ACS NANO 2024; 18:3826-3838. [PMID: 38241471 DOI: 10.1021/acsnano.3c12499] [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: 01/21/2024]
Abstract
Real-time dynamic imaging of immunoactivation-related cytokines is crucial for evaluating the efficacy of immune checkpoint blockade therapy and optimizing the treatment regimen. We introduce herein a spatiotemporally controlled nanodevice that allows in situ photoactivated imaging of interferon-gamma (IFN-γ) secretion from T cells in vitro and in vivo. The nanodevice is constructed by rational engineering of an aptamer-embedded, UV-cleavable PC-DNA probe and further integration with upconversion nanoparticles- and CRISPR-Cas12a-enhanced fluorescence systems. Using human peripheral blood mononuclear cells (PBMC)-engrafted mouse models, this nanodevice allows for the quantitative imaging of endogenous IFN-γ and its intratumoral dynamics responding to antiprogrammed cell death receptor 1 (anti-PD-1) therapy. This study thus provides a toolbox for boosting the sensitivity and precision of cytokine imaging during immune checkpoint blockade therapy, enlightening research toward imaging-guided tumor therapy.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Xiang Duan
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Yangfang Yun
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Siqi Li
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Zhiyuan Feng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Jiayin Zhan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ran Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Yan Li
- State Key Laboratory of Pharmaceutical Biotechnology, National Resource Center for Mutant Mice, MOE Key Laboratory of Model Animals for Disease Study, MOE Engineering Research Center of Protein and Peptide Medicine, Chemistry and Biomedicine Innovation Center, Jiangsu Key Laboratory of Molecular Medicine, Model Animal Research Center, Medical School of Nanjing University, Nanjing 210061, China
| | - Jingjing Zhang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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Wang W, Geng L, Zhang Y, Shen W, Bi M, Gong T, Hu Z, Guo C, Wang T, Sun T. Development of antibody-aptamer sandwich-like immunosensor based on RCA and Nicked-PAM CRISPR/Cas12a system for the ultra-sensitive detection of a biomarker. Anal Chim Acta 2023; 1283:341849. [PMID: 37977804 DOI: 10.1016/j.aca.2023.341849] [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: 09/12/2023] [Revised: 09/22/2023] [Accepted: 09/24/2023] [Indexed: 11/19/2023]
Abstract
Biomarkers are the most sensitive reactants and early indicators of many kinds of diseases. The development of highly sensitive and simple techniques to quantify them is challenging. In this study, based on rolling cycle amplification (RCA) and the Nicked PAM/CRISPR-Cas12a system (RNPC) as a signal reporter, a sandwich-type method was developed using antibody@magnetic beads and aptamer for the high-sensitive detection of the C-reactive protein (CRP). The antibody-antigen (target)-aptamer sandwich-like reaction was coupled to RCA, which can produce hundreds of similar binding sites and are discriminated by CRISPR/Cas12a for signal amplification. The ultrasensitivity is achieved based on the dual-signal enhancing strategy, which involves the special recognition of aptamers, RCA, and trans-cleavage of CRISPR/Cas12a. By incorporating the CRISPR/Cas12a system with cleaved PAM, the nonspecific amplification of the RCA reaction alone was greatly reduced, and the dual signal output of RCA and Cas12a improved the detection sensitivity. Our assay can be performed only in two steps. The first step takes only 20 min of target capture, followed by a one-pot reaction, where the target concentration can be obtained by fluorescence values as long as there are 37 °C reaction conditions. Under optimal conditions, this system detected CRP with high sensitivity. The fabricated biosensor showed detection limits of 0.40 pg/mL in phosphate-buffered saline and 0.73 pg/mL in diluted human serum and a broad linear dynamic range of 1.28 pg/mL to 100 ng/mL within a total readout time of 90 min. The method could be used to perform multi-step signal amplification, which can help in the ultrasensitive detection of other proteins. Overall, the proposed biosensor might be used as an immunosensor biosensor platform.
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Affiliation(s)
- Wen Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China; School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China
| | - Lu Geng
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Yiyang Zhang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Weili Shen
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Meng Bi
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Tingting Gong
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China
| | - Zhiyong Hu
- School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China
| | - Changjiang Guo
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China; School of Public Health and Management, Binzhou Medical College, Shandong, 264003, PR China.
| | - Tianhui Wang
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China.
| | - Tieqiang Sun
- Tianjin Key Laboratory of Risk Assessment and Control Technology for Environment and Food Safety, Tianjin Institute of Environmental and Operational Medicine, Tianjin, 300050, PR China.
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Deng L, Zhou S, Dong J, Liu Y, Huang Z, Sun H, Jin L, Huo D, Hou C. CRISPR/Cas12a and primer-assisted rolling circle amplification integrated ultra-sensitive dual-signal sensing platform for EGFR 19 detection. Anal Chim Acta 2023; 1279:341755. [PMID: 37827629 DOI: 10.1016/j.aca.2023.341755] [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: 05/05/2023] [Revised: 07/13/2023] [Accepted: 08/23/2023] [Indexed: 10/14/2023]
Abstract
Herein, we integrated CRISPR/Cas12a with primer-assisted rolling circle amplification (PARCA) to specifically detect EGFR 19 from the genome. We fused the method into fluorescent and electrochemical detection systems forming a stable and sensitive dual-signal sensing platform. The fluorescent detection system stably detected EGFR 19 in a linear range from 500 fM to 10 nM with an ultra-low background signal. The electrochemical detection system possessed a detection limit as low as 42 aM due to the introduction of nanomaterial UIO-66-NH2. The dual-signal sensing platform showed superior performance in complex serum samples and real cell genomes and provided a flexible and dynamic approach for the ultra-sensitive detection of EGFR 19.
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Affiliation(s)
- Liyuan Deng
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China
| | - Jiangbo Dong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China
| | - Yin Liu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China
| | - Zhen Huang
- Key Laboratory of Bio-Resource and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, SeNA Research Institute and Szostak-CDHT Large Nucleic Acids Institute, Chengdu, 610000, PR China
| | - Human Sun
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China
| | - Liang Jin
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China.
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of 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.
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering, College of Chongqing University, Chongqing, 400044, PR China; National Facility for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, PR China.
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Lee M. Deep learning in CRISPR-Cas systems: a review of recent studies. Front Bioeng Biotechnol 2023; 11:1226182. [PMID: 37469443 PMCID: PMC10352112 DOI: 10.3389/fbioe.2023.1226182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/22/2023] [Indexed: 07/21/2023] Open
Abstract
In genetic engineering, the revolutionary CRISPR-Cas system has proven to be a vital tool for precise genome editing. Simultaneously, the emergence and rapid evolution of deep learning methodologies has provided an impetus to the scientific exploration of genomic data. These concurrent advancements mandate regular investigation of the state-of-the-art, particularly given the pace of recent developments. This review focuses on the significant progress achieved during 2019-2023 in the utilization of deep learning for predicting guide RNA (gRNA) activity in the CRISPR-Cas system, a key element determining the effectiveness and specificity of genome editing procedures. In this paper, an analytical overview of contemporary research is provided, with emphasis placed on the amalgamation of artificial intelligence and genetic engineering. The importance of our review is underscored by the necessity to comprehend the rapidly evolving deep learning methodologies and their potential impact on the effectiveness of the CRISPR-Cas system. By analyzing recent literature, this review highlights the achievements and emerging trends in the integration of deep learning with the CRISPR-Cas systems, thus contributing to the future direction of this essential interdisciplinary research area.
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Zhao Y, Wu W, Tang X, Zhang Q, Mao J, Yu L, Li P, Zhang Z. A universal CRISPR/Cas12a-powered intelligent point-of-care testing platform for multiple small molecules in the healthcare, environment, and food. Biosens Bioelectron 2023; 225:115102. [PMID: 36724657 DOI: 10.1016/j.bios.2023.115102] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
Growing studies focusing on nuclear acid detection via the emerging CRISPR technique demonstrate its promising application. However, limited works solve the identification of non-nucleic acid targets, especially multiple small molecules. To address challenges for point-of-care testing (POCT) in complex matrices for healthcare, environment, and food safety, we developed CRISPR Cas12a-powered highly sensitive, high throughput, intelligent POCT (iPOCT) for multiple small molecules based on a smartphone-controlled reader. As a proof of concept, aflatoxin B1 (AFB1), benzo[a]pyrene (BaP), and capsaicin (CAP) were chosen as multiple targets. First, three antigens were preloaded in independent microwells. Then, the antibody/antigen-induced fluorescent signals were consecutively transferred from the biotin-streptavidin to CRISPR/Cas12a system. Third, the fluorescent signals were recorded by a smartphone-controlled handheld dark-box readout. Under optimization, detection limits in AFB1, BaP, and CAP were 0.00257, 4.971, and 794.6 fg/mL with wide linear ranges up to four orders of magnitude. Using urine, water, soybean oil, wheat, and peanuts as the complex matrix, we recorded high selectivity, considerable recovery, repeatability, and high consistency comparison to HPLC-MS/MS methods. This work promises a practical intelligent POCT platform for multiple targets in lipid-soluble and water-soluble matrices and could be extensively applied for healthcare, environment, and food safety.
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Affiliation(s)
- Yuan Zhao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China
| | - Wenqin Wu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China
| | - Xiaoqian Tang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China
| | - Qi Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China; Hubei Hongshan Laboratory, Wuhan, 430070, PR China
| | - Jin Mao
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China; Hubei Hongshan Laboratory, Wuhan, 430070, PR China
| | - Li Yu
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China
| | - Peiwu Li
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China; Hubei Hongshan Laboratory, Wuhan, 430070, PR China; Zhejiang Xianghu Laboratory, Hangzhou, 311231, PR China
| | - Zhaowei Zhang
- Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Wuhan, 430062, PR China; Hubei Hongshan Laboratory, Wuhan, 430070, PR China.
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Li H, Xie Y, Chen F, Bai H, Xiu L, Zhou X, Guo X, Hu Q, Yin K. Amplification-free CRISPR/Cas detection technology: challenges, strategies, and perspectives. Chem Soc Rev 2023; 52:361-382. [PMID: 36533412 DOI: 10.1039/d2cs00594h] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Rapid and accurate molecular diagnosis is a prerequisite for precision medicine, food safety, and environmental monitoring. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-based detection, as a cutting-edged technique, has become an immensely effective tool for molecular diagnosis because of its outstanding advantages including attomolar level sensitivity, sequence-targeted single-base specificity, and rapid turnover time. However, the CRISPR/Cas-based detection methods typically require a pre-amplification step to elevate the concentration of the analyte, which may produce non-specific amplicons, prolong the detection time, and raise the risk of carryover contamination. Hence, various strategies for target amplification-free CRISPR/Cas-based detection have been developed, aiming to minimize the sensitivity loss due to lack of pre-amplification, enable detection for non-nucleic acid targets, and facilitate integration in portable devices. In this review, the current status and challenges of target amplification-free CRISPR/Cas-based detection are first summarized, followed by highlighting the four main strategies to promote the performance of target amplification-free CRISPR/Cas-based technology. Furthermore, we discuss future perspectives that will contribute to developing more efficient amplification-free CRISPR/Cas detection systems.
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Affiliation(s)
- Huimin Li
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Yi Xie
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Fumin Chen
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Huiwen Bai
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 220 South 33rd St., Philadelphia, Pennsylvania, USA
| | - Leshan Xiu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaonong Zhou
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Qinqin Hu
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
| | - Kun Yin
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, People's Republic of China. .,One Health Center, Shanghai Jiao Tong University-The University of Edinburgh, Shanghai, People's Republic of China
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10
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Ding L, Wu Y, Liu LE, He L, Yu S, Effah CY, Liu X, Qu L, Wu Y. Universal DNAzyme walkers-triggered CRISPR-Cas12a/Cas13a bioassay for the synchronous detection of two exosomal proteins and its application in intelligent diagnosis of cancer. Biosens Bioelectron 2023; 219:114827. [PMID: 36308835 DOI: 10.1016/j.bios.2022.114827] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/17/2022] [Indexed: 11/19/2022]
Abstract
Exosomal proteins are considered to be promising indicators of cancer. Herein, a novel DNAzyme walkers-triggered CRISPR-Cas12a/Cas13a strategy was proposed for the synchronous determination of exosomal proteins: serum amyloid A-1 protein (SAA1) and coagulation factor V (FV). In this design, the paired antibodies were used to recognize targets, thereby ensuring the specificity. DNAzyme walkers were employed to convert the contents of SAA1 and FV into activators (P1 and P2), and one target can produce abundant activators, thus achieving an initial amplification of signal. Furthermore, the P1 and P2 can activate CRISPR-Cas12a/Cas13a system, which in turn trans-cleaves the reporters, enabling a second amplification and generating two fluorescent signals. The assay is highly sensitive (limits of detection as low as 30.00 pg/mL for SAA1 and 200.00 pg/mL for FV), highly specific and ideally accurate. More importantly, it is universal and can be used to detect both non-membrane and membrane proteins in exosome. Besides, the method can be successfully applied to detect SAA1 and FV in plasma exosomes to differentiate between lung cancer patients and healthy individuals. To explore the application of the developed method in tumor diagnosis, a deep learning model based on the expressions of SAA1 and FV was developed. The accuracy of this model can achieve 86.96%, which proves that it has a promising practical application capacity. Thus, this study does not only provide a new tool for the detection of exosomal proteins and cancer diagnosis, but also propose a new strategy to detect non-nucleic acid analytes for CRISPR-Cas system.
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Affiliation(s)
- Lihua Ding
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Yan Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Li-E Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Songcheng Yu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Clement Yaw Effah
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Xia Liu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China
| | - Lingbo Qu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China; College of Chemistry, Zhengzhou University, Zhengzhou, 450001, China; Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, Zhengzhou University, Zhengzhou, 450001, China.
| | - Yongjun Wu
- College of Public Health, Zhengzhou University, Zhengzhou, 450001, China.
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11
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Gao L, Zhou Y, Cao L, Cui X, Zheng Y, Yin H, Ai S. Photoelectrochemical Biosensor for Histone Deacetylase Sirt1 Detection Based on Polyaspartic Acid-Engaged and Triggered Redox Cycling Amplification and Enhanced Photoactivity of BiVO 4 by Gold Nanoparticles and SnS 2. Anal Chem 2022; 94:16936-16944. [PMID: 36416225 DOI: 10.1021/acs.analchem.2c04380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A photoelectrochemical (PEC) biosensor was established for histone deacetylase Sirt1 detection based on the polyaspartic acid (PASP)-mediated redox cycling amplification and Sirt1 catalysis deacetylation-triggered recognition of the deacetylated substrate peptide, using PASP as the recognition reagent. After BiVO4 was composited with gold nanoparticles and SnS2, the photoactivity of the composite was greatly enhanced due to the matched energy band structure. Under the catalysis of Sirt1 enzyme, the acetylated substrate peptide was deacetylated to obtain a positive peptide, which was recognized by negative PASP. In addition to the recognition function, PASP also played other triple roles. First, PASP interacted with the positive peptide to form a double-stranded structure, which led to the electrode interface changing from irregular to regular, resulting in an improved PEC response. Second, PASP was involved into redox cycle amplification due to its reduction to dehydroascorbic acid. Further, it was used for repeated preparation of ascorbic acid to provide electron donors. This process enhanced the PEC response. Third, based on the matched energy band with BiVO4, PASP effectively improved the photoactivity of BiVO4. With multiplex signal amplification, the PEC biosensor showed a wide linear range (1.83-1830 pM) and high detection sensitivity with a low detection limit of 0.732 pM (S/N = 3). The applicability of this method was evaluated by studying the effects of a known inhibitor of nicotinamide and the heavy metal ions of Cd2+ and Pb2+ on Sirt1 enzyme activity, and the results showed that this method not only provided a new platform for screening Sirt1 enzyme inhibitors but also provided new biomarkers for evaluating the ecotoxicological effects of environmental pollutants.
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Affiliation(s)
- Lanlan Gao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Yunlei Zhou
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Lulu Cao
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Xiaoting Cui
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Yulin Zheng
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Huanshun Yin
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
| | - Shiyun Ai
- College of Chemistry and Material Science, Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Food Safety Analysis and Test Engineering Technology Research Center of Shandong Province, Shandong Agricultural University, Taian, Shandong271018, People’s Republic of China
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12
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Rapid screening of antimicrobial probiotics using CRISPR cascade. Biosens Bioelectron 2022; 216:114673. [DOI: 10.1016/j.bios.2022.114673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/23/2022] [Accepted: 08/28/2022] [Indexed: 11/29/2022]
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