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Wang Y, Zheng T, Li X, Wu P. Integrating Recombinase Polymerase Amplification and Photosensitization Colorimetric Detection in One Tube for Fast Screening of C. sakazakii in Formula Milk Powder. Anal Chem 2024; 96:5727-5733. [PMID: 38546834 DOI: 10.1021/acs.analchem.4c01130] [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
Cronobacter sakazakii (C. sakazakii) is a widely existing opportunistic pathogen and thus threatens people with low immunity, especially infants. To prevent the outbreak, a rapid and accurate on-site testing method is required. The current standard culture-based method is time-consuming (3-4 days), while the nucleic acid amplification (PCR)-based detection is mostly carried out in central laboratories. Herein, isothermal recombinase polymerase amplification (RPA) coupled with a photosensitization colorimetric assay (PCA) was adopted for the on-site detection of C. sakazakii in powdered infant formulas (PIFs). The lowest visual detection concentration of C. sakazakii is 800 cfu/mL and 2 cfu/g after 8 h bacteria pre-enrichment. Furthermore, to avoid typical cap opening-resulted aerosol pollution, the PCA reagents were lyophilized onto the cap of the RPA tube (containing lyophilized RPA reagents). After amplification, the tube was subjected to simple shaking to mix the PCA reagents with the amplification products for light-driven color development. Such a one-tube assay offered a lowest concentration of 1000 copies of genomic DNA of C. sakazakii within 1 h. After 8 h of bacterial enrichment, the lowest detecting concentration could be pushed down to 5 cfu/g bacteria in PIF. To facilitate on-site monitoring, a portable, battery-powered PCA device was designed to mount the typical RPA 8-tube strip, and a color analysis cellphone APP was further employed for facile readout.
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Affiliation(s)
- Yanying Wang
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Ting Zheng
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
| | - Xianming Li
- Department of Rheumatology and Immunology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Peng Wu
- Analytical & Testing Center, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu 610064, China
- School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang 453007, China
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2
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Li WM, Ren XD, Jiang YZ, Su N, Li BW, Sun XG, Li RX, Lu WP, Deng SL, Li J, Li MX, Huang Q. Rapid detection of EGFR mutation in CTCs based on a double spiral microfluidic chip and the real-time RPA method. Anal Bioanal Chem 2023:10.1007/s00216-023-04743-2. [PMID: 37254002 DOI: 10.1007/s00216-023-04743-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 06/01/2023]
Abstract
Circulating tumor cells (CTCs) are cells shed from primary or metastatic tumors and spread into the peripheral bloodstream. Mutation detection in CTCs can reveal vital genetic information about the tumors and can be used for "liquid biopsy" to indicate cancer treatment and targeted medication. However, current methods to measure the mutations in CTCs are based on PCR or DNA sequencing which are cumbersome and time-consuming and require sophisticated equipment. These largely limited their applications especially in areas with poor healthcare infrastructure. Here we report a simple, convenient, and rapid method for mutation detection in CTCs, including an example of a deletion at exon 19 (Del19) of the epidermal growth factor receptor (EGFR). CTCs in the peripheral blood of NSCLC patients were first sorted by a double spiral microfluidic chip with high sorting efficiency and purity. The sorted cells were then lysed by proteinase K, and the E19del mutation was detected via real-time recombinase polymerase amplification (RPA). Combining the advantages of microfluidic sorting and real-time RPA, an accurate mutation determination was realized within 2 h without professional operation or complex data interpretation. The method detected as few as 3 cells and 1% target variants under a strongly interfering background, thus, indicating its great potential in the non-invasive diagnosis of E19del mutation for NSCLC patients. The method can be further extended by redesigning the primers and probes to detect other deletion mutations, insertion mutations, and fusion genes. It is expected to be a universal molecular diagnostic tool for real-time assessment of relevant mutations and precise adjustments in the care of oncology patients.
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Affiliation(s)
- Wen-Man Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xiao-Dong Ren
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Yu-Zhu Jiang
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China
| | - Ning Su
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Bo-Wen Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Xian-Ge Sun
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Ruo-Xu Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Wei-Ping Lu
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Shao-Li Deng
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Jin Li
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China
| | - Meng-Xia Li
- Department of Cancer Center, Daping Hospital, Army Medical University, Chongqing, China.
| | - Qing Huang
- Department of Laboratory Medicine, Daping Hospital, Army Medical University, Chongqing, China.
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Dhandapani G, Nguyen VG, Kim MC, Noh JY, Jang SS, Yoon SW, Jeong DG, Huynh TML, Le VP, Song D, Kim HK. Magnetic-bead-based DNA-capture-assisted real-time polymerase chain reaction and recombinase polymerase amplification for the detection of African swine fever virus. Arch Virol 2023; 168:21. [PMID: 36593422 DOI: 10.1007/s00705-022-05681-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 11/20/2022] [Indexed: 01/04/2023]
Abstract
African swine fever (ASF) is a deadly disease in swine caused by African swine fever virus (ASFV). The global spread of ASFV has resulted in significant economic losses worldwide. Improved early detection has been the most important first line of defense for preventing ASF outbreaks and for activating control measures. Despite the availability of rapid amplification methods, nucleic acid extraction from specimens still needs to be performed in a laboratory. To facilitate this step, we exploited the strong affinity of biotin-streptavidin binding by functionalizing streptavidin-coated magnetic beads with biotinylated oligonucleotide capture probes to efficiently capture genotype II ASFV DNA directly from crude clinical samples. The captured DNA is suitable for detection using real-time quantitative PCR (qPCR) and recombinase polymerase amplification (RPA). In this study, ASFV DNA was efficiently captured from swine feces, serum, and tissue samples. Both DNA-capture-assisted qPCR and RPA-based detection methods have a limit of detection (LOD) of 102 copies/µl, which is comparable to those of commercially available kits. In addition, an RPA-SYBR Green I method was developed for the immediate visual detection of ASFV DNA, which is time-saving and efficient for resource-limited field settings. In summary, a rapid, versatile, sequence-specific DNA capture method was developed to efficiently capture ASFV DNA from swine clinical samples and subsequent detection by qPCR and RPA, which has the potential to be used for robust screening and surveillance of ASFV and in point-of-care (POC) diagnostics.
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Affiliation(s)
- Gowtham Dhandapani
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Van Giap Nguyen
- Department of Veterinary Microbiology and infectious diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Min Chan Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Ji Yeong Noh
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Seong Sik Jang
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea
| | - Sun-Woo Yoon
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- College of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Dae Gwin Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- College of Bioscience, University of Science and Technology, Daejeon, Republic of Korea
| | - Thi My Le Huynh
- Department of Veterinary Microbiology and infectious diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Van Phan Le
- Department of Veterinary Microbiology and infectious diseases, Faculty of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Daesub Song
- College of Veterinary Medicine, Seoul National University, Seoul, Republic of Korea.
| | - Hye Kwon Kim
- Department of Biological Sciences and Biotechnology, College of Natural Sciences, Chungbuk National University, Cheongju, Republic of Korea.
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4
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Zhao C, Yang L, Zhang X, Tang Y, Wang Y, Shao X, Gao S, Liu X, Wang P. Rapid and Sensitive Genotyping of SARS-CoV-2 Key Mutation L452R with an RPA- PfAgo Method. Anal Chem 2022; 94:17151-17159. [PMID: 36459151 PMCID: PMC9743015 DOI: 10.1021/acs.analchem.2c03563] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/21/2022] [Indexed: 12/05/2022]
Abstract
In the two years of COVID-19 pandemic, the SARS-CoV-2 variants have caused waves of infections one after another, and the pandemic is not ending. The key mutations on the S protein enable the variants with enhanced viral infectivity, immune evasion, and/or antibody neutralization resistance, bringing difficulties to epidemic prevention and control. In support of precise epidemic control and precision medicine of the virus, a fast and simple genotyping method for the key mutations of SARS-CoV-2 variants needs to be developed. By utilizing the specific recognition and cleavage property of the nuclease Argonaute from Pyrococcus furiosus (PfAgo), we developed a recombinase polymerase amplification (RPA) and PfAgo combined method for a rapid and sensitive genotyping of SARS-CoV-2 key mutation L452R. With a delicate design of the strategy, careful screening of the RPA primers and PfAgo gDNA, and optimization of the reaction, the method achieves a high sensitivity of a single copy per reaction, which is validated with the pseudovirus. This is the highest sensitivity that can be achieved theoretically and the highest sensitivity as compared to the available SARS-CoV-2 genotyping assays. Using RPA, the procedure of the method is finished within 1.5 h and only needs a minimum laboratorial support, suggesting that the method can be easily applied locally or on-site. The RPA-PfAgo method established in this study provides a strong support to the precise epidemic control and precision medicine of SARS-CoV-2 variants and can be readily developed for the simultaneous genotyping of multiple SARS-CoV-2 mutations.
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Affiliation(s)
- Chenjie Zhao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Lihong Yang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xue Zhang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yixin Tang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Yue Wang
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xiaofu Shao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Song Gao
- Jiangsu
Key Laboratory of Marine Biological Resources and Environment, Co-Innovation
Center of Jiangsu Marine Bio-industry Technology, Jiangsu Key Laboratory
of Marine Pharmaceutical Compound Screening, School of Pharmacy, Jiangsu Ocean University, Lianyungang 222005, China
| | - Xin Liu
- Key
Laboratory of Molecular Biophysics of Ministry of Education, College
of Life Science and Technology, Huazhong
University of Science and Technology, Wuhan 430074, China
| | - Pei Wang
- School
of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
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Xu Y, Wang Y, Hu J, Bao Z, Wang M. Development and Visualization Improvement for the Rapid Detection of Decapod Iridescent Virus 1 (DIV1) in Penaeus vannamei Based on an Isothermal Recombinase Polymerase Amplification Assay. Viruses 2022; 14:v14122752. [PMID: 36560756 PMCID: PMC9783574 DOI: 10.3390/v14122752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/14/2022] Open
Abstract
Viral diseases have seriously restricted the healthy development of aquaculture, and decapod iridescent virus 1 (DIV1) has led to heavy losses in the global shrimp aquaculture industry. Due to the lack of effective treatment, early detection and regular monitoring are the most effective ways to avoid infection with DIV1. In this study, a novel real-time quantitative recombinase polymerase amplification (qRPA) assay and its instrument-free visualization improvement were described for the rapid detection of DIV1. Optimum primer pairs, suitable reaction temperatures, and probe concentrations of a DIV1-qRPA assay were screened to determine optimal reaction conditions. Then, its ability to detect DIV1 was evaluated and compared with real-time quantitative polymerase chain reactions (qPCRs). The sensitivity tests demonstrated that the limit of detection (LOD) of the DIV1-qRPA assay was 1.0 copies μL-1. Additionally, the presentation of the detection results was improved with SYBR Green I, and the LOD of the DIV1-RPA-SYBR Green I assay was 1.0 × 103 copies μL-1. Both the DIV1-qRPA and DIV1-RPA-SYBR Green I assays could be performed at 42 °C within 20 min and without cross-reactivity with the following: white spot syndrome virus (WSSV), Vibrio parahaemolyticus associated with acute hepatopancreatic necrosis disease (VpAHPND), Enterocytozoon hepatopenaei (EHP), and infectious hypodermal and hematopoietic necrosis virus (IHHNV). In conclusion, this approach yields rapid, straightforward, and simple DIV1 diagnoses, making it potentially valuable as a reliable tool for the detection and prevention of DIV1, especially where there is a paucity of laboratory equipment.
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Affiliation(s)
- Yajin Xu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
| | - Yan Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Correspondence: (Y.W.); (M.W.)
| | - Jingjie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
- Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Sanya 572040, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao 266237, China
- Hainan Yazhou Bay Seed Laboratory, Sanya 572024, China
- Correspondence: (Y.W.); (M.W.)
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6
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Li F, Xiao J, Yang H, Yao Y, Li J, Zheng H, Guo Q, Wang X, Chen Y, Guo Y, Wang Y, Shen C. Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection. Front Microbiol 2022; 13:858806. [PMID: 35369478 PMCID: PMC8965353 DOI: 10.3389/fmicb.2022.858806] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
Mycoplasma pneumoniae (MP) is a one of most common pathogen in causing respiratory infection in children and adolescents. Rapid and efficient diagnostic methods are crucial for control and treatment of MP infections. Herein, we present an operationally simple, rapid and efficient molecular method for MP identification, which eliminates expensive instruments and specialized personnel. The method combines recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) 12a-based detection, with an optimal procedure less than 1 h from sample to result including DNA extraction (25 min), RPA reaction (39°C for 15-20 min), CRISPR/Cas12a detection (37°C for 10 min) and visual detection by naked eyes (2 min). This diagnostic method shows high sensitivity (two copies per reaction) and no cross-reactivity against other common pathogenic bacteria. Preliminary evaluation using 201 clinical samples shows sensitivity of 99.1% (107/108), specificity of 100% (93/93) and consistency of 99.5% (200/201), compared with real-time PCR method. The above data demonstrate that our developed method is reliable for rapid diagnosis of MP. In conclusion, the RPA-CRISPR/Cas12a has a great potential to be as a useful tool for reliable and quick diagnosis of MP infection, especially in primary hospitals with limited conditions.
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Affiliation(s)
- Feina Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Jing Xiao
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Haiming Yang
- Department of Respiratory Diseases II, Beijing Children's Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Yao Yao
- Department of Respiratory Diseases I, Beijing Children's Hospital, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Capital Medical University, Beijing, China
| | - Jieqiong Li
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Qian Guo
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Xiaotong Wang
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yuying Chen
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yajie Guo
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Yonghong Wang
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
| | - Chen Shen
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Center for Children's Health, Beijing, China
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7
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Yuan R, Tang W, Zhang H, You W, Hu X, Zhang H, Chen L, Nian W, Ding S, Luo Y. Palindromic-assisted self-annealing transcription amplification for reliable genotyping of epidermal growth factor receptor exon mutations. Biosens Bioelectron 2021; 194:113633. [PMID: 34543825 DOI: 10.1016/j.bios.2021.113633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 09/09/2021] [Accepted: 09/11/2021] [Indexed: 01/25/2023]
Abstract
Reliable discrimination of specific epidermal growth factor receptor (EGFR) gene mutations plays a critical role in guiding lung cancer therapeutics. Until now, convenient and accurate recognition of the specific deletion of EGFR exons has remained particularly challenging. Herein, we propose a palindromic-assisted self-annealing transcription amplification (PASTA) strategy for the reliable detection of circulating EGFR exon mutations. We designed a palindromic DNA hairpin nanorobot consisting of a palindromic tail, a T7 promoter, a target recognition region, and a transcription template. The nanorobot enabled prompt self-assembly into a target-hairpin/hairpin-target dimer in the presence of single-stranded DNA target and further triggered in vitro transcription. In a proof-of-concept experiment for detecting circulating 15n-del EGFR mutation, a detection limit of 0.8 fM and a linear detection range of 1 fM to 100 pM was achieved, and an accuracy of 100% was reached in clinical validation by analyzing 20 samples from clinical lung cancer patients. Empowered by the intrinsic sensitivity and selectivity, the proposed PASTA approach will lead to the development of a universal platform for reliable molecular subtyping.
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Affiliation(s)
- Rui Yuan
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China; College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Wanyan Tang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China
| | - Hong Zhang
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China; College of Bioengineering, Chongqing University, Chongqing, 400044, PR China
| | - Wenxin You
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China; Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Xiaolin Hu
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China
| | - Haiwei Zhang
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China
| | - Ling Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China
| | - Weiqi Nian
- Chongqing Key Laboratory of Translational Research for Cancer Metastasis and Individualized Treatment, Chongqing University Cancer Hospital, Chongqing, 400030, PR China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, PR China.
| | - Yang Luo
- Center of Smart Laboratory and Molecular Medicine, School of Medicine, Chongqing University, Chongqing, 400044, PR China.
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8
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Fujita T, Nagata S, Fujii H. Protein or ribonucleoprotein-mediated blocking of recombinase polymerase amplification enables the discrimination of nucleotide and epigenetic differences between cell populations. Commun Biol 2021; 4:988. [PMID: 34413466 PMCID: PMC8376914 DOI: 10.1038/s42003-021-02503-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/28/2021] [Indexed: 12/27/2022] Open
Abstract
Isothermal DNA amplification, such as recombinase polymerase amplification (RPA), is well suited for point-of-care testing (POCT) as it does not require lengthy thermal cycling. By exploiting DNA amplification at low temperatures that do not denature heat-sensitive molecules such as proteins, we have developed a blocking RPA method to detect gene mutations and examine the epigenetic status of DNA. We found that both nucleic acid blockers and nuclease-dead clustered regularly interspaced short palindromic repeats (CRISPR) ribonucleoproteins suppress RPA reactions by blocking elongation by DNA polymerases in a sequence-specific manner. By examining these suppression events, we are able to discriminate single-nucleotide mutations in cancer cells and evaluate genome-editing events. Methyl-CpG binding proteins similarly inhibit elongation by DNA polymerases on CpG-methylated template DNA in our RPA reactions, allowing for the detection of methylated CpG islands. Thus, the use of heat-sensitive molecules such as proteins and ribonucleoprotein complexes as blockers in low-temperature isothermal DNA amplification reactions markedly expands the utility and application of these methods. Fujita et al. investigate the use of oligoribonucleotides, proteins, and ribonucleoprotein complexes as sequence-specific blockers of DNA extension by DNA polymerases. They demonstrate the value of proteins and ribonucleoprotein complexes as blockers in low-temperature isothermal DNA amplification reactions for discrimination of nucleotide and epigenetic differences.
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Affiliation(s)
- Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan.
| | - Shoko Nagata
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, Aomori, Japan.
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9
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Yang H, Yan M, Xu G, Qian X, Zhao R, Han Y, Zhang L, Gu H, Xu H. A tailored LNA clamping design principle: Efficient, economized, specific and ultrasensitive for the detection of point mutations. Biotechnol J 2021; 16:e2100233. [PMID: 34278717 DOI: 10.1002/biot.202100233] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 07/12/2021] [Accepted: 07/16/2021] [Indexed: 11/07/2022]
Abstract
In the development of personalized medicine, the ultrasensitive detection of point mutations that correlate with diseases is important to improve the efficacy of treatment and guide clinical medication. In this study, locked nucleic acid (LNA) was introduced as an amplification suppressor of a massive number of wild-type alleles in an amplification refractory mutation system (ARMS) to achieve the detection of low-abundance mutations with high specificity and sensitivity of at least 0.1%. By integrating the length of clamp, base type, number and position of LNA modifications, we have established a "shortest length with the fewest LNA bases" principle from which each LNA base would play a key role in the affinity and the ability of single base discrimination could be improve. Finally, based on this LNA design guideline, a series of the most important single point mutation sites of epidermal growth factor receptor (EGFR) was verified to achieve the optimal amplification state which as low as 0.1% mutation gene amplification was not affected under the wild gene amplification was completely inhibited, demonstrating that the proposed design principle has good applicability and versatility and is of great significance for the detection of circulating tumor DNA.
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Affiliation(s)
- Hao Yang
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
| | - Mengqiu Yan
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
| | - Gaolian Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
| | - Xiaohua Qian
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
| | - Ruiying Zhao
- Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, PR China
| | - Yuchen Han
- Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, PR China
| | - Lin Zhang
- Shanghai Mag-Gene Nano Tech Co., Ltd, Shanghai, PR China
| | - Hongchen Gu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
| | - Hong Xu
- School of Biomedical Engineering/Med-X Research Institute, Shanghai Jiao Tong University, Shanghai, PR China
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10
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Rapid detection of multidrug-resistant tuberculosis based on allele-specific recombinase polymerase amplification and colorimetric detection. PLoS One 2021; 16:e0253235. [PMID: 34115793 PMCID: PMC8195408 DOI: 10.1371/journal.pone.0253235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) poses a serious threat to TB control. Early diagnosis and proper treatment are essential factors to limit the spread of the disease. The existing molecular tests for MDR-TB usually require specific instruments, steady power supply, and routine maintenance, which might be obstacles for low-resource settings. This study aimed to develop allele-specific isothermal recombinase polymerase amplification (allele-specific RPA) to simultaneously detect the most common mutations in the rpoB gene at codons 516, 526, and 531, which are associated with rifampicin resistance, and in the katG gene at codon 315, which is related to isoniazid resistance. Allele-specific primers targeting four major mutations, rpoB516, rpoB526, rpoB531, and katG315, were constructed and used in individual RPA reactions. The RPA amplicons were endpoints detected by the naked eye immediately after applying SYBR Green I. The optimised RPA assay was evaluated with the Mycobacterium tuberculosis wild-type strain H37Rv and 141 clinical M. tuberculosis isolates. The results revealed that allele-specific RPA combined with SYBR Green I detection (AS-RPA/SYBR) detected these four major mutations with 100% sensitivity and specificity relative to DNA sequencing. The limits of detection for these particular mutations with AS-RPA/SYBR were 5 ng. As a result of the outstanding performance of AS-RPA/SYBR, including its easy setup, speed, lack of a specific instrument requirement, and lack of cross-reaction with other bacteria, this technique may be integrated for the molecular diagnosis of MDR-TB, especially in low-resource settings.
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11
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Jia Z, Yuan H, Zhao X, Yin J, Cong H, Gao W, Jin Q, Jia C, Zhao J. Single-cell genetic analysis of lung tumor cells based on self-driving micro-cavity array chip. Talanta 2021; 226:122172. [PMID: 33676714 DOI: 10.1016/j.talanta.2021.122172] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 11/24/2022]
Abstract
Lung cancer is one of the common malignant tumors with a high incidence and mortality rate. Targeted therapies are efficient on lung cancer patients with specific gene mutations. Circulating tumor cells (CTCs) are used for liquid biopsy, providing genetic information for lung cancer treatment selection and prognosis. We developed a less costly self-driving micro-cavity array for simple molecular analysis at a single cell level to examine the genetic make-up of CTCs. This chip integrated sample detection structure and vacuum driving system to achieve cell loading, lysing, isothermal amplification (LAMP), and signal read-out on one chip. We used the "film-polydimethylsiloxane (PDMS) chip-film" structure and oil sealing method during amplification reaction to minimize water loss. We then conducted a LAMP assay using the self-driving device to detect epidermal growth factor receptor (EGFR) L858R mutation and identified an excellent linear in the range between 101-104 copies/μL (R2 = 0.997). We finally assessed the EGFR L858R gene expression of lung tumor cells (H1975 cells) as putative CTCs using the proposed detection platform. We discovered its ability to perform genetic analysis at the single-cell level. The EGFR L858R mutational gene expression levels were different in H1975 cells. In conclusion, the self-driving micro-cavity array is a less costly and simple tool for mutational gene profiling of single lung CTC. Besides, it can be used in personalized therapy and efficacy monitoring.
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Affiliation(s)
- Zhisen Jia
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
| | - Haojun Yuan
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xuefei Zhao
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Jiawen Yin
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hui Cong
- Center of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, 226000, China
| | - Wanlei Gao
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Qinghui Jin
- The Faculty of Electrical Engineering and Computer Science, Ningbo University, Ningbo, Zhejiang, 315211, China; State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Chunping Jia
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China.
| | - Jianlong Zhao
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, 200050, China
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12
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Bushmeat Species Identification: Recombinase Polymerase Amplification (RPA) Combined with Lateral Flow (LF) Strip for Identification of Formosan Reeves' Muntjac ( Muntiacus reevesi micrurus). Animals (Basel) 2021; 11:ani11020426. [PMID: 33562213 PMCID: PMC7914887 DOI: 10.3390/ani11020426] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 11/16/2022] Open
Abstract
Simple Summary Illegal hunting of wild animals and the consumption of bushmeat are recognized not only as a threat to biodiversity, but also as a risk for transmitting zoonotic diseases. Illegal sales of meat products from Formosan Reeves’ muntjac (Muntiacus reevesi micrurus) is a growing issue in Taiwan, bringing forth the demand for a fast and cost-effective technique for meat species identification. In this study, a new recombinase polymerase amplification combined with a lateral flow strip to identify Formosan Reeves’ muntjac in meat products was described. This method only requires minimal sample preparation and an isothermal heating process. The result can be interpreted by the naked eye within 30 min. The system we designed efficiently detected a variety of meat products, and no cross-reactions were observed with other animal species. This simple assay provides a sensitive and specific method to identify bushmeat sources in various meat products, which holds the potential for on-field application in the future. Abstract The identification of animal species of meat in meat products is of great concern for various reasons, such as public health, religious beliefs, food allergies, legal perspectives, and bushmeat control. In this study, we developed a new technique to identify Formosan Reeves’ muntjac in meat using recombinase polymerase amplification (RPA) in combination with a lateral flow (LF) strip. The DNA extracted from a piece of Formosan Reeves’ muntjac meat was amplified by a pair of specific primers based on its mitochondrial cytochrome b gene for 10 min at a constant temperature ranging from 30 to 45 °C using RPA. Using the specific probe added to the RPA reaction system, the amplified products were visualized on the LF strip within 5 min. The total operating time from quick DNA extraction to visualizing the result was approximately 30 min. The RPA-LF system we designed was efficient when using boiled, pan-fried, roasted, stir-fried, or stewed samples. The advantages of simple operation, speediness, and cost-effectiveness make our RPA-LF method a promising molecular detection tool for meat species identification of either raw or variously cooked Formosan Reeves’ muntjac meat. It is also possible to apply this method to identify the meat of other wildlife sources.
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13
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Zhang S, Sun A, Wan B, Du Y, Wu Y, Zhang A, Jiang D, Ji P, Wei Z, Zhuang G, Zhang G. Development of a Directly Visualized Recombinase Polymerase Amplification-SYBR Green I Method for the Rapid Detection of African Swine Fever Virus. Front Microbiol 2020; 11:602709. [PMID: 33424805 PMCID: PMC7793706 DOI: 10.3389/fmicb.2020.602709] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/27/2020] [Indexed: 11/13/2022] Open
Abstract
African swine fever (ASF) is a lethal disease in swine caused by etiologic African swine fever virus (ASFV). The global spread of ASFV has resulted in huge economic losses globally. In the absence of effective vaccines or drugs, pathogen surveillance has been the most important first-line intervention to prevent ASF outbreaks. Among numerous diagnostic methods, recombinase polymerase amplification (RPA)-based detection is capable of producing sensitive and specific results without relying on the use of expensive instruments. However, currently used gene-specific, probe-based RPA for ASFV detection is expensive and time-consuming. To improve the efficiency of ASFV surveillance, a novel directly visualized SYBR Green I-staining RPA (RPAS) method was developed to detect the ASFV genome. SYBR Green I was added to the amplified RPA products for direct visualization by the naked eye. The sensitivity and specificity of this method were confirmed using standard plasmid and inactivated field samples. This method was shown to be highly specific with a detection limit of 103 copies/μl of ASFV in 15 min at 35°C without any cross-reactions with other important porcine viruses selected. In summary, this method enables direct sample visualization with reproducible results for ASFV detection and hence has the potential to be used as a robust tool for ASF prevention and control.
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Affiliation(s)
- Shuai Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Aijun Sun
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Bo Wan
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yongkun Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Yanan Wu
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Angke Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Dawei Jiang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Pengchao Ji
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Zhanyong Wei
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Guoqing Zhuang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Gaiping Zhang
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China.,Key laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou, China
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14
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Rungkamoltip P, Temisak S, Piboonprai K, Japrung D, Thangsunan P, Chanpanitkitchot S, Chaowawanit W, Chandeying N, Tangjitgamol S, Iempridee T. Rapid and ultrasensitive detection of circulating human papillomavirus E7 cell-free DNA as a cervical cancer biomarker. Exp Biol Med (Maywood) 2020; 246:654-666. [PMID: 33307803 DOI: 10.1177/1535370220978899] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Circulating cell-free DNA (cfDNA) has attracted attention as a non-invasive biomarker for diagnosing and monitoring various cancers. Given that human papillomavirus (HPV) DNA integration and overexpression of E6/E7 oncogenes are pivotal events for carcinogenesis, we sought to determine if HPV E7 cfDNA could serve as a specific biomarker for cervical cancer detection. We applied droplet digital PCR (ddPCR) to quantify HPV16/18 E7 cfDNA from the serum of patients with cervical cancer, cervical intraepithelial neoplasia, and controls. HPV16/18 E7 cfDNA was highly specific for cervical cancer, displaying 30.77% sensitivity, 100% specificity, and an area under the curve of 0.65. Furthermore, we developed a sensitive isothermal detection of HPV16/18 E7 and the PIK3CA WT reference gene based on recombinase polymerase amplification combined with a lateral flow strip (RPA-LF). The assay took less than 30 min and the detection limit was 5-10 copies. RPA-LF exhibited 100% sensitivity and 88.24% specificity towards HPV16/18 E7 cfDNA in clinical samples. The agreement between RPA-LF and ddPCR was 83.33% (κ = 0.67) for HPV16 E7 and 100% (κ = 1.0) for HPV18 E7, indicating a good correlation between both tests. Therefore, we conclude that HPV E7 cfDNA represents a potential tumor marker with excellent specificity and moderate sensitivity for minimally invasive cervical cancer monitoring. Moreover, the RPA-LF assay provides an affordable, rapid, and ultrasensitive tool for detecting HPV cfDNA in resource-limited settings.
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Affiliation(s)
- Phetploy Rungkamoltip
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Sasithon Temisak
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Kitiya Piboonprai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand.,Laboratory of Host Defense, The World Premier International Research Center Initiative (WPI) Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0871, Japan
| | - Deanpen Japrung
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Pattanapong Thangsunan
- Chemical Metrology and Biometry Department, National Institute of Metrology (NIMT), Pathum Thani 12120, Thailand
| | - Saranya Chanpanitkitchot
- Department of Obstetrics and Gynecology, Rajavithi Hospital, College of Medicine, Rangsit University, Bangkok 10400, Thailand
| | - Woraphot Chaowawanit
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Nutthaporn Chandeying
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand
| | - Siriwan Tangjitgamol
- Department of Obstetrics and Gynecology, Faculty of Medicine Vajira Hospital, Navamindhadhiraj University, Bangkok 10300, Thailand.,Obstetrics and Gynecology Section, MedPark Hospital, Bangkok 10110, Thailand
| | - Tawin Iempridee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani 12120, Thailand
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15
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Duan Q, Li X, He X, Shen X, Cao Y, Zhang R, Bai X, Zhang J, Ma X. A duplex probe-directed recombinase amplification assay for detection of single nucleotide polymorphisms on 8q24 associated with prostate cancer. ACTA ACUST UNITED AC 2020; 54:e9549. [PMID: 33263645 PMCID: PMC7695445 DOI: 10.1590/1414-431x20209549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 09/09/2020] [Indexed: 12/12/2022]
Abstract
Single nucleotide polymorphisms (SNPs) have important application value in the research of population genetics, hereditary diseases, tumors, and drug development. Conventional methods for detecting SNPs are typically based on PCR or DNA sequencing, which is time-consuming, costly, and requires complex instrumentation. In this study, we present a duplex probe-directed recombinase amplification (duplex-PDRA) assay that can perform real-time detection of two SNPs (rs6983267 and rs1447295) in four reactions in two tubes at 39°C within 30 min. The sensitivity of duplex-PDRA was 2×103-104 copies per reaction and no cross-reactivity was observed. A total of 382 clinical samples (179 prostate cancer patients and 203 controls) from northern China were collected and tested by duplex-PDRA assay and direct sequencing. The genotyping results were completely identical. In addition, the association analysis of two SNPs with prostate cancer risk and bone metastasis was conducted. We found that the TT genotype of rs6983267 (OR: 0.42; 95%CI: 0.23-0.78; P=0.005) decreased the risk of prostate cancer, while the CA genotype of rs1447295 (OR: 1.89; 95%CI: 1.20-2.96; P=0.005) increased the risk of prostate cancer. However, no association between the two SNPs (rs6983267 and rs1447295) and bone metastasis in prostate cancer was found in this study (P>0.05). In conclusion, the duplex-PDRA assay is an effective method for the simultaneous detection of two SNPs and shows great potential for widespread use in research and clinical settings.
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Affiliation(s)
- Qingxia Duan
- Hebei Medical University, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xinna Li
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China.,Yangzhou Center for Disease Control and Prevention, Yangzhou, Jiangsu, China
| | - Xiaozhou He
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xinxin Shen
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Yu Cao
- Hebei Medical University, Shijiazhuang, Hebei, China
| | - Ruiqing Zhang
- Hebei Medical University, Shijiazhuang, Hebei, China.,NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Xueding Bai
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
| | - Jinyan Zhang
- Hebei Medical University Fourth Affiliated Hospital, Shijiazhuang, Hebei, China
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping District, Beijing, China
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16
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Direct detection of methicillin-resistant in Staphylococcus spp. in positive blood culture by isothermal recombinase polymerase amplification combined with lateral flow dipstick assay. World J Microbiol Biotechnol 2020; 36:162. [PMID: 32989593 DOI: 10.1007/s11274-020-02938-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/17/2020] [Indexed: 12/14/2022]
Abstract
Methicillin-resistant staphylococci (MRS) are important antimicrobial-resistant pathogens in sepsis. Conventional blood cultures take 24-72 h. The polymerase chain reaction (PCR)-based methods give faster results (2-3 h) but need expensive thermal cyclers. We therefore developed an isothermal recombinase polymerase amplification (RPA) combined with lateral flow dipstick (LFD) assay for rapid detection of MRS in spiked blood culture samples. Fifty-six clinical isolates including 38 mecA-carrying staphylococci and 18 non-mecA-carrying organisms as confirmed by PCR methods were studied. RPA primer set and probe specific for mecA gene (encoding penicillin-binding protein 2a) were designed. RPA reaction was carried out under isothermal condition (45 °C) within 20 min and read by LFD in 5 min. The RPA-LFD provided 92.1% (35/38) sensitivity for identifying MRS in positive blood culture samples, and no cross-amplification was found (100% specificity). This test failed to detect three mecA-carrying S.sciuri isolates. The detection limits of RPA-LFD method for identifying MRS were equal to those of PCR method. The RPA-LFD is simple, fast, and user-friendly. This method could detect the mecA gene directly from the positive blood culture samples without requirement for special equipment. This method would be useful for appropriate antibiotic therapy and infection control, particularly in a low-resource setting.
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17
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A probe directed recombinase amplification assay for detection of MTHFR A1298C polymorphism associated with congenital heart disease. Biotechniques 2019; 64:211-217. [PMID: 29793361 DOI: 10.2144/btn-2018-2010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) play an important role in susceptibility to complex diseases, treatment efficacy and adverse drug responses. Conventional methods to detect SNPs are usually based on PCR or DNA sequencing, which are typically time-consuming and require sophisticated equipment. In this proof-of-concept study, a probe-directed recombinase amplification (PDRA) assay was developed to detect the A1298C polymorphism of 5,10-methylenetetrahydrofolate reductase (MTHFR). The PDRA assay included two real-time reactions to detect the A and C nucleotides of A1298C polymorphism. Each reaction contained only one primer and one probe and was finished at 39°C within 35 min. The results of genotyping of 150 clinical samples using PDRA were completely consistent with those by direct sequencing. Additionally, when the 1000 Genomes Project HCB frequencies were used as the control group, MTHFR A1298C was found to be associated with congenital heart disease. In conclusion, the proposed novel PDRA assay is a valuable tool for the detection of SNPs and demonstrates significant potential to be widely applicable in both research and clinical settings.
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18
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Singpanomchai N, Akeda Y, Tomono K, Tamaru A, Santanirand P, Ratthawongjirakul P. Naked eye detection of the Mycobacterium tuberculosis complex by recombinase polymerase amplification-SYBR green I assays. J Clin Lab Anal 2018; 33:e22655. [PMID: 30129085 DOI: 10.1002/jcla.22655] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 07/19/2018] [Accepted: 07/28/2018] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Rapid diagnosis of Mycobacterium tuberculosis (Mtb) is key to controlling the spread of tuberculosis, which is a global health concern. In this study, isothermal recombinase polymerase amplification (RPA) was developed to detect specific targets of Mtb, IS6110 and IS1081. Additionally, SYBR Green I was used for endpoint detection of the RPA products by the naked eye. METHOD A total of 146 genomic Mtb DNA samples and 24 genomic nontuberculous mycobacteria (NTM) DNA samples were amplified at IS6110 and IS1081 by RPA. After a complete amplification, the RPA amplicons were examined by agarose gel electrophoresis (RPA-AGE) and SYBR Green I (RPA-S) assays. The performance of the RPA assays was evaluated by comparing them to a conventional PCR. RESULTS The RPA assay demonstrated to have a good capability to differentiate Mtb from NTM with a very short turnaround time at a constant temperature. Compared to conventional PCR, the sensitivities and specificities of RPA-AGE for IS6110 and IS1081 were 100%. The specificity of RPA-S was 100% for both targets; however, its sensitivities for IS6110 and IS1081 were 97.95% and 99.32%, respectively. The limits of detection of IS6110 RPA-AGE and RPA-S were 0.05 and 0.5 ng, respectively, while the LODs of IS1081 RPA-AGE and RPA-S were 0.00005 and 0.05 ng, respectively. Both RPA assays showed a satisfying diagnostic specificity, with no cross-reaction with other bacteria. CONCLUSION A rapid, sensitive, naked eye RPA assay can be integrated into point-of-care diagnosis for Mtb detection, especially in remote areas where laboratory instrument resources are limited.
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Affiliation(s)
- Nuntita Singpanomchai
- Program of Molecular sciences in Medical Microbiology and Immunology, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Yukihiro Akeda
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka University, Osaka, Japan
| | - Kazunori Tomono
- Division of Infection Control and Prevention, Osaka University Hospital, Osaka University, Osaka, Japan
| | - Aki Tamaru
- Department of Bacteriology, Osaka Prefectural Institute of Public Health, Osaka, Japan
| | - Pitak Santanirand
- Microbiology Unit, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Panan Ratthawongjirakul
- Research Group of Innovative Diagnosis of Antimicrobial Resistance, Department of Transfusion Medicine and Clinical Microbiology, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
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19
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Blocked recombinase polymerase amplification for mutation analysis of PIK3CA gene. Anal Biochem 2018; 544:49-56. [DOI: 10.1016/j.ab.2017.12.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/08/2017] [Accepted: 12/09/2017] [Indexed: 12/12/2022]
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20
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Abstract
Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.
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Affiliation(s)
- Ivan Magriñá Lobato
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain
| | - Ciara K O'Sullivan
- INTERFIBIO Consolidated Research Group, Departament d'Enginyeria Química, Universitat Rovira i Virgili, Països Catalans, 26, 43007, Tarragona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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Mo Y, Cui F, Li D, Dai Y, Li X, Zhang X, Qiu Y, Yin Y, Zhang X, Xu W. Establishment of a rapid and sensitive method based on recombinase polymerase amplification to detect mts90, a new molecular target of Mycobacterium tuberculosis. RSC Adv 2017. [DOI: 10.1039/c7ra09999a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The paper is about rapid screening of tuberculosis for detecting mts90, a new molecular target ofMycobacterium tuberculosis.
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