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Ma Z, Xu J, Hou W, Lei Z, Li T, Shen W, Yu H, Liu C, Zhang J, Tang S. Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography. Anal Chem 2024; 96:5195-5204. [PMID: 38520334 DOI: 10.1021/acs.analchem.3c05500] [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: 03/25/2024]
Abstract
The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.
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Affiliation(s)
- Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Junjie Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Weilin Hou
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Zi Lei
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438, Jiefang Road, Zhenjiang 212000, Jiangsu, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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Wang M, Liu H, Ren J, Huang Y, Deng Y, Liu Y, Chen Z, Chow FWN, Leung PHM, Li S. Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review. BIOSENSORS 2023; 13:bios13020160. [PMID: 36831926 PMCID: PMC9953907 DOI: 10.3390/bios13020160] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 06/12/2023]
Abstract
Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.
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Affiliation(s)
- Meiling Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Hongna Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Jie Ren
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yunqi Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Yuan Liu
- Hengyang Medical School, University of South China, Hengyang 421001, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
| | - Franklin Wang-Ngai Chow
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Polly Hang-Mei Leung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China
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Yang Z, Shen B, Yue L, Miao Y, Hu Y, Ouyang R. Application of Nanomaterials to Enhance Polymerase Chain Reaction. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27248854. [PMID: 36557991 PMCID: PMC9781713 DOI: 10.3390/molecules27248854] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/27/2022] [Accepted: 12/05/2022] [Indexed: 12/15/2022]
Abstract
Polymerase Chain Reaction (PCR) is one of the most common technologies used to produce millions of copies of targeted nucleic acid in vitro and has become an indispensable technique in molecular biology. However, it suffers from low efficiency and specificity problems, false positive results, and so on. Although many conditions can be optimized to increase PCR yield, such as the magnesium ion concentration, the DNA polymerases, the number of cycles, and so on, they are not all-purpose and the optimization can be case dependent. Nano-sized materials offer a possible solution to improve both the quality and productivity of PCR. In the last two decades, nanoparticles (NPs) have attracted significant attention and gradually penetrated the field of life sciences because of their unique chemical and physical properties, such as their large surface area and small size effect, which have greatly promoted developments in life science and technology. Additionally, PCR technology assisted by NPs (NanoPCR) such as gold NPs (Au NPs), quantum dots (QDs), and carbon nanotubes (CNTs), etc., have been developed to significantly improve the specificity, efficiency, and sensitivity of PCR and to accelerate the PCR reaction process. This review discusses the roles of different types of NPs used to enhance PCR and summarizes their possible mechanisms.
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Affiliation(s)
- Zhu Yang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Institut Pasteur of Shanghai, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Bei Shen
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
| | - Lihuan Yue
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yuqing Miao
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
| | - Yihong Hu
- CAS Key Laboratory of Molecular Virology & Immunology, Institutional Center for Shared Technologies and Facilities, Pathogen Discovery and Big Data Platform, Institute Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
| | - Ruizhuo Ouyang
- Institute of Bismuth and Rhenium Science, School Materials and Chemistry, University of Shanghai for Science and Technology, Shanghai 200093, China
- Correspondence: (Y.M.); (Y.H.); (R.O.)
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Faisal Hamdi AI, How SH, Islam MK, Lim JCW, Stanslas J. Adaptive therapy to circumvent drug resistance to tyrosine kinase inhibitors in cancer: is it clinically relevant? Expert Rev Anticancer Ther 2022; 22:1309-1323. [PMID: 36376248 DOI: 10.1080/14737140.2022.2147671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
INTRODUCTION Cancer is highly adaptable and is constantly evolving against current targeted therapies such as tyrosine kinase inhibitors. Despite advances in recent decades, the emergence of drug resistance to tyrosine kinase inhibitors constantly hampers therapeutic efficacy of cancer treatment. Continuous therapy versus intermittent clinical regimen has been a debate in drug administration of cancer patients. An ecologically-inspired shift in cancer treatment known as 'adaptive therapy' intends to improve the drug administration of drugs to cancer patients that can delay emergence of drug resistance. AREAS COVERED We discuss improved understanding of the concept of drug resistance, the basis of continuous therapy, intermittent clinical regimens, and adaptive therapy will be reviewed. In addition, we discuss how adaptive therapy provides guidance for future cancer treatment. EXPERT OPINION The current understanding of drug resistance in cancer leads to poor prognosis and limited treatment options in patients. Fighting drug resistance mutants is constantly followed by new forms of resistance. In most reported cases, continuous therapy leads to drug resistance and an intermittent clinical regimen vaguely delays it. However, adaptive therapy, conceptually, exploits multiple parameters that can suppress the growth of drug resistance and provides safe treatment for cancer patients in the future.
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Affiliation(s)
- Amir Imran Faisal Hamdi
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
| | - Soon Hin How
- Kuliyyah of Medicine, International Islamic University Malaysia, Kuantan Campus, Kuliyyah of Medicine, 25200, Kuantan, Malaysia
| | | | - Jonathan Chee Woei Lim
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
| | - Johnson Stanslas
- Pharmacotherapeutics Unit, Department of Medicine, Universiti Putra MalaysiaMedicine, 43400, Serdang, Malaysia
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Wang Y, Chen H, Wei H, Rong Z, Wang S. Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader. LAB ON A CHIP 2022; 22:1531-1541. [PMID: 35266944 DOI: 10.1039/d1lc01167g] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Several virulent variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged along with the spread of this virus throughout the population. Some variants can exhibit increased transmissibility and reduced immune neutralization reactivity. These changes are deeply concerning issues that may hinder the ongoing effort of epidemic control measures, especially mass vaccination campaigns. The accurate discrimination of SARS-CoV-2 and its emerging variants is essential to contain the coronavirus disease 2019 pandemic. Herein, we report a low-cost, facile, and highly sensitive diagnostic platform that can simultaneously distinguish wild-type (WT) SARS-CoV-2 and its two mutations, namely, D614G and N501Y, within 2 h. WT or mutant (M) nucleic acid fragments at each allelic locus were selectively amplified by the tetra-primer amplification refractory mutation system (ARMS)-PCR assay. Allele-specific amplicons were simultaneously detected by two test lines on a quantum dot nanobead (QB)-based dual-color fluorescent test strip, which could be interpreted by the naked eye or by a home-made fluorescent strip readout device that was wirelessly connected to a smartphone for quantitative data analysis and result presentation. The WT and M viruses were indicated and were strictly discriminated by the presence of a green or red band on test line 1 for the D614G site and test line 2 for the N501Y site. The limits of detection (LODs) for the WT and M D614G were estimated as 78.91 and 33.53 copies per μL, respectively. This assay was also modified for the simultaneous detection of the N and ORF1ab genes of SARS-CoV-2 with LODs of 1.90 and 6.07 copies per μL, respectively. The proposed platform can provide a simple, accurate, and affordable diagnostic approach for the screening of SARS-CoV-2 and its variants of concern even in resource-limited settings.
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Affiliation(s)
- Yunxiang Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Hong Chen
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Hongjuan Wei
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Zhen Rong
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
| | - Shengqi Wang
- Beijing Institute of Radiation Medicine, Beijing 100850, P. R. China.
- Beijing Key Laboratory of New Molecular Diagnosis Technologies for Infectious Diseases, Beijing 100850, P. R. China
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Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology. MICROMACHINES 2022; 13:mi13020145. [PMID: 35208270 PMCID: PMC8879704 DOI: 10.3390/mi13020145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/03/2022] [Accepted: 01/04/2022] [Indexed: 11/17/2022]
Abstract
Purpose: This study aims to establish a competitive allele-specific PCR based on penta-primer amplification refractory mutation system (PARMS) technology to detect the key mutation sites of variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus for rapid typing. Methods: Competitive allele-specific primers and universal primers were designed for the key gene mutation sites N501Y, E484K, L452R, and K417N of SARS-CoV-2 VOCs, respectively.Using the principle of allele-specific polymerase chain reaction and fluorescence energy resonance transfer, different VOCs can be differentiated. Results: Using reverse transcribed cDNA of different VOCs as specimens, through double-blind detection, different VOC types can be effectively identified, with an accuracy rate of 100%. Through the identification and detection of different VOCs, effective differentiation can be achieved. Conclusions: The system has high specificity and sensitivity, with a detection limit of 1.28 copies/reaction.PARMS technology is fast, efficient, and low-cost. It is used for the identification and detection of the popular SARS-CoV-2 VOCs, which is helpful for the rapid and accurate prevention and control of COVID-19 epidemic.
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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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