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Zhang Y, Xu S, Luo M, Chen J, Wang L, Yang F, Ye J, Liu J, He B, Weng L, Li S, Zhang D. Hairpin-Empowered Invasive Reaction Combined with Catalytic Hairpin Assembly Cascade Amplification for the Specific Detection of Single-Nucleotide Polymorphisms. Anal Chem 2024; 96:10283-10293. [PMID: 38864304 DOI: 10.1021/acs.analchem.4c01049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Single-nucleotide polymorphism (SNP) is widely used in the study of disease-related genes and in the genetic study of animal and plant strains. Therefore, SNP detection is crucial for biomedical diagnosis and treatment as well as for molecular design breeding of animals and plants. In this regard, this article describes a novel technique for detecting SNP using flap endonuclease 1 (FEN 1) as a specific recognition element and catalytic hairpin assembly (CHA) cascade reaction as a signal amplification strategy. The mutant target (MT) was hybridized with a biotin-modified upstream probe and hairpin-type downstream probe (DP) to form a specific three-base overlapping structure. Then, FEN 1 was employed for three-base overlapping structure-specific recognition, namely, the precise SNP site identification and the 5' flap of DP dissociation. After dissociation, the hybridized probes were magnetically separated by a streptavidin-biotin complex. Especially, the ability to establish such a hairpin-type DP provided a powerful tool that could be used to hide the cut sequence (CS) and avoid false-positive signals. The cleaved CS initiated the CHA reaction and allowed superior fluorescence signal generation. Owing to the high specificity of FEN 1 for single base recognition, only the MT could be distinguished from the wild-type target and mismatched DNA. Owing to the dual signal amplification, as low as 0.36 fM MT and 1% mutation abundance from the mixtures could be detected, respectively. Furthermore, it could accurately identify SNPs from human cancer cells, as well as soybean leaf genome extracts. This strategy paves the way for the development of more precise and sensitive tools for diagnosing early onset diseases as well as molecular design breeding tools.
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Affiliation(s)
- Yunshan Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shijie Xu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Ma Luo
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jian Chen
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Lanyue Wang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Fang Yang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
- School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, Hunan 411201, China
| | - Jing Ye
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Jichong Liu
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Bingxiao He
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Lin Weng
- Research Center for Intelligent Computing Platforms, Research Institute of Intelligent Computing, Zhejiang Laboratory, Hangzhou 311121, China
| | - Shuang Li
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin 300072, China
| | - Diming Zhang
- Research Center for Novel Computational Sensing and Intelligent Processing, Zhejiang Laboratory, Hangzhou 311121, China
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Luo Y, Hu Q, Yu Y, Lyu W, Shen F. Experimental investigation of confinement effect in single molecule amplification via real-time digital PCR on a multivolume droplet array SlipChip. Anal Chim Acta 2024; 1304:342541. [PMID: 38637051 DOI: 10.1016/j.aca.2024.342541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Digital polymerase chain reaction (digital PCR) is an important quantitative nucleic acid analysis method in both life science research and clinical diagnostics. One important hypothesis is that by physically constraining a single nucleic acid molecule in a small volume, the relative concentration can be increased therefore further improving the analysis performance, and this is commonly defined as the confinement effect in digital PCR. However, experimental investigation of this confinement effect can be challenging since it requires a microfluidic device that can generate partitions of different volumes and an instrument that can monitor the kinetics of amplification. (96). RESULTS Here, we developed a real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip) that can generate droplet of 125 nL, 25 nL, 5 nL, and 1 nL by a simple "load-slip" operation. In the digital region, by reducing the volume, the relative concentration is increased, the amplification kinetic can be accelerated, and the time to reach the fluorescence threshold, or Cq value, can be reduced. When the copy number per well is much higher than one, the relative concentration is independent of the partition volume, thus the amplification kinetics are similar in different volume partitions. This system is not limited to studying the kinetics of digital nucleic acid amplification, it can also extend the dynamic range of the digital nucleic acid analysis by additional three orders of magnitude by combining a digital and an analog quantification algorithm. (140). SIGNIFICANCE In this study, we experimentally investigated for the first time the confinement effect in the community of digital PCR via a new real-time digital PCR system with a multivolume droplet array SlipChip (Muda-SlipChip). And a wider dynamic range of quantification methods compared to conventional digital PCR was validated by this system. This system provides emerging opportunities for life science research and clinical diagnostics. (63).
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Affiliation(s)
- Yang Luo
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Yan Yu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai, 200030, PR China.
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Takahara H, Tanaka H, Hashimoto M. Fast Thermocycling in Custom Microfluidic Cartridge for Rapid Single-Molecule Droplet PCR. SENSORS (BASEL, SWITZERLAND) 2023; 23:9884. [PMID: 38139729 PMCID: PMC10747138 DOI: 10.3390/s23249884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/13/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]
Abstract
The microfluidic droplet polymerase chain reaction (PCR), which enables simultaneous DNA amplification in numerous droplets, has led to the discovery of various applications that were previously deemed unattainable. Decades ago, it was demonstrated that the temperature holding periods at the denaturation and annealing stages in thermal cycles for PCR amplification could be essentially eliminated if a rapid change of temperature for an entire PCR mixture was achieved. Microfluidic devices facilitating the application of such fast thermocycling protocols have significantly reduced the time required for PCR. However, in microfluidic droplet PCR, ensuring successful amplification from single molecules within droplets has limited studies on accelerating assays through fast thermocycling. Our developed microfluidic cartridge, distinguished for its convenience in executing single-molecule droplet PCR with common laboratory equipment, features droplets positioned on a thin glass slide. We hypothesized that applying fast thermocycling to this cartridge would achieve single-molecule droplet PCR amplification. Indeed, the application of this fast protocol demonstrated successful amplification in just 22 min for 30 cycles (40 s/cycle). This breakthrough is noteworthy for its potential to expedite microfluidic droplet PCR assays, ensuring efficient single-molecule amplification within a remarkably short timeframe.
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Affiliation(s)
| | | | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe 610-0321, Kyoto, Japan
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Hu Q, Kanwal F, Lyu W, Zhang J, Liu X, Qin K, Shen F. Multiplex Digital Polymerase Chain Reaction on a Droplet Array SlipChip for Analysis of KRAS Mutations in Pancreatic Cancer. ACS Sens 2023; 8:114-121. [PMID: 36520653 DOI: 10.1021/acssensors.2c01776] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pancreatic cancer is a terminal disease with high mortality and very poor prognosis. A sensitive and quantitative analysis of KRAS mutations in pancreatic cancer provides a tool not only to understand the biological mechanisms of pancreatic cancer but also for diagnosis and treatment monitoring. Digital polymerase chain reaction (PCR) is a promising tool for KRAS mutation analysis, but current methods generally require a complex microfluidic handling system, which can be challenging to implement in routine research and point-of-care clinical diagnostics. Here, we present a droplet-array SlipChip (da-SlipChip) for the multiplex quantification of KRAS G12D, V, R, and C mutant genes with the wild-type (WT) gene background by dual color (FAM/ROX) fluorescence detection. This da-SlipChip is a high-density microwell array of 21,696 wells of 200 pL in 4 by 5424 microwell format with simple loading and slipping operation. It does not require the same precise alignment of microfeatures on the different plates that are acquired by the traditional digital PCR SlipChip. This device can provide accurate quantification of both mutant genes and the WT KRAS gene. We collected tumor tissue, paired normal pancreatic tissue, and other normal tissues from 18 pancreatic cancer patients and analyzed the mutation profiles of KRAS G12D, V, R, and C in these samples; the results from the multiplex digital PCR on da-SlipChip agree well with those of next-generation sequencing (NGS). This da-SlipChip moves digital PCR closer to the practical point-of-care applications not only for detecting KRAS mutations in pancreatic cancer but also for other applications that require precise nucleic acid quantification with high sensitivity.
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Affiliation(s)
- Qixin Hu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Fariha Kanwal
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Weiyuan Lyu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Jiajie Zhang
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Xu Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
| | - Kai Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200031, China
| | - Feng Shen
- School of Biomedical Engineering, Shanghai Jiao Tong University, 1954 Hua Shan Road, Shanghai 200030, China
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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Rapid Multiplex Strip Test for the Detection of Circulating Tumor DNA Mutations for Liquid Biopsy Applications. BIOSENSORS 2022; 12:bios12020097. [PMID: 35200357 PMCID: PMC8869478 DOI: 10.3390/bios12020097] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/26/2022] [Accepted: 02/01/2022] [Indexed: 01/16/2023]
Abstract
In the era of personalized medicine, molecular profiling of patient tumors has become the standard practice, especially for patients with advanced disease. Activating point mutations of the KRAS proto-oncogene are clinically relevant for many types of cancer, including colorectal cancer (CRC). While several approaches have been developed for tumor genotyping, liquid biopsy has been gaining much attention in the clinical setting. Analysis of circulating tumor DNA for genetic alterations has been challenging, and many methodologies with both advantages and disadvantages have been developed. We here developed a gold nanoparticle-based rapid strip test that has been applied for the first time for the multiplex detection of KRAS mutations in circulating tumor DNA (ctDNA) of CRC patients. The method involved ctDNA isolation, PCR-amplification of the KRAS gene, multiplex primer extension (PEXT) reaction, and detection with a multiplex strip test. We have optimized the efficiency and specificity of the multiplex strip test in synthetic DNA targets, in colorectal cancer cell lines, in tissue samples, and in blood-derived ctDNA from patients with advanced colorectal cancer. The proposed strip test achieved rapid and easy multiplex detection (normal allele and three major single-point mutations) of the clinically relevant KRAS mutations in ctDNA in blood samples of CRC patients with high specificity and repeatability. This multiplex strip test represents a minimally invasive, rapid, low-cost, and promising diagnostic tool for the detection of clinically relevant mutations in cancer patients.
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7
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Xue C, Wang L, Huang H, Wang R, Yuan P, Wu ZS. Stimuli-Induced Upgrade of Nuclease-Resistant DNA Nanostructure Composed of a Single Molecular Beacon for Detecting Mutant Genes. ACS Sens 2021; 6:4029-4037. [PMID: 34731570 DOI: 10.1021/acssensors.1c01423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
As a kind of cell-free DNA in the bloodstream liberated from tumor cells, circulating tumor DNAs (ctDNAs) have been recognized as promising biomarkers in the field of early cancer diagnosis. However, robust, sensitive, and accurate detection of ctDNA in serum remains extremely challenging, especially toward the mutant KRAS gene, one of the most frequently mutated genes. Although DNA oligonucleotides as emerging practical signaling materials have been developed as sensitive and accurate tools, some intrinsic defects need to be overcome, such as fragility in complex biological environments. In this work, on the basis of the hydrophilicity-promoted assembly, a core/shell DNA nanostructure (DNS-MB) probe is constructed from only one hairpin-shaped probe (cholesterol-modified palindromic molecular beacon, Chol-PMB) for the amplification detection of KRAS mutation in serum without the need for any auxiliary probe. Chol-PMB is designed to recognize target DNA and serve as a polymerization primer and template, and thus target species can initiate polymerization-based strand displacement amplification (SDA). Moreover, target DNA is able to induce further aggregation of DNS-MB particles due to the enzymatic cross-linking effect, leading to a structural upgrade. The DNS-MB probe exhibits a detection limit of 50 fM and a wide quantitative range (from 50 fM to 160 nM). In addition, single nucleotide polymorphisms can be discriminated, such as mutant KRAS G12D (KRAS-M), providing a desirable platform for screening ctDNAs. More excitingly, because the termini of DNA components are hidden inward from nuclease attack, DNS-MB circumvents a false-positive signal even in freshly sampled serum and is suitable for application in the complex biological milieu. As a proof of concept, the DNS-MB probe is expected to provide useful insight into the development of simple and degradation-resistant DNA probes for substantially amplified detection of ctDNAs in complex serum, showing potential applications in the field of early tumor diagnosis.
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Affiliation(s)
- Chang Xue
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Lei Wang
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Hong Huang
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ruozhong Wang
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha 410128, China
| | - Pei Yuan
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- College of Chemical Engineering, Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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8
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Hao Q, Xu Q, Niu S, Ding C, Luo X. Anti-Fouling Magnetic Beads Combined with Signal Amplification Strategies for Ultra-Sensitive and Selective Electrochemiluminescence Detection of MicroRNAs in Complex Biological Media. Anal Chem 2021; 93:10679-10687. [PMID: 34288646 DOI: 10.1021/acs.analchem.1c02186] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Herein, an electrochemiluminescence (ECL) microRNA biosensor based on anti-fouling magnetic beads (MBs) and two signal amplification strategies was developed. The newly designed anti-fouling dendritic peptide was wrapped on the surfaces of MBs to make them resistant to nonspecific adsorption of biomolecules in complex biological samples so as to realize accurate and selective target recognition. One of the amplification strategies was achieved through nucleic acid cycle amplification based on the DNAzyme on the surfaces of MBs. Then, the output DNA generated by the nucleic acid cycle amplification program stimulated the hybrid chain reaction (HCR) process on the modified electrode surface to generate the other amplification of the ECL response. Titanium dioxide nanoneedles (TiO2 NNs), as a co-reaction accelerator of the Ru(bpy)2(cpaphen)2+ and tripropylamine (TPrA) system, were wrapped with the electrodeposited polyaniline (PANI) on the electrode surface to enhance the ECL intensity of Ru(bpy)2(cpaphen)2+. The conducting polymer PANI can not only immobilize the TiO2 NNs but also improve the conductivity of the modified electrodes. The biosensor exhibited ultra-high sensitivity and excellent selectivity toward the detection of miRNA 21, with a detection limit of 0.13 fM. More importantly, with the anti-fouling MBs as a unique separation tool, this ECL biosensor was capable of assaying targets in complex biological media such as serum and cell lysate.
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Affiliation(s)
- Qiuxia Hao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Qingzhang Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Shuyan Niu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Caifeng Ding
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education; Shandong Key Laboratory of Biochemical Analysis; Key Laboratory of Analytical Chemistry for Life Science in Universities of Shandong; College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao 266042, PR China
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Fan Z, Zhou Z, Zhang W, Zhang X, Lin JM. Inkjet printing based ultra-small MnO 2 nanosheets synthesis for glutathione sensing. Talanta 2021; 225:121989. [PMID: 33592737 DOI: 10.1016/j.talanta.2020.121989] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 11/25/2020] [Accepted: 12/05/2020] [Indexed: 11/29/2022]
Abstract
Manganese dioxide (MnO2) with small size is competent in sensing applications, but its synthesis generally adopts templates or in complex ways. Inkjet printing technique with excellent performance offers a versatile tool due to its stability, flexibility, economy. Herein, an inkjet printing method was developed for rapid synthesis of ultra-small MnO2 nanosheets. The findings validated the feasibility of inkjet printing method for MnO2 nanosheets synthesis and achieved the demand of small size and facile mode. Additionally, the limit of detection (LOD) of ultra-small MnO2 nanosheets in glutathione (GSH) sensing achieved 0.26 μM, which was about 40% more sensitive than that of the typical MnO2 nanosheets, enabling the establishment of a rapid and efficient modality for sensitive and selective GSH sensing. By virtue of the inkjet printing approach, the ultra-small MnO2 nanosheets was obtained in a short time without complicated fabricating process. It can be foreseen that the proposed inkjet printing approach would facilitate the application prospects of ultra-small MnO2 nanosheets in diverse fields. Such a facile approach may open new avenues for synthesis of ultra-small or ultrafine nanomaterials.
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Affiliation(s)
- Zhaoxuan Fan
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Ziping Zhou
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China
| | - Weifei Zhang
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China
| | - Xueji Zhang
- Research Center for Bioengineering and Sensing Technology, School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, PR China; School of Biomedical Engineering, Shenzhen University, Shenzhen, 518060, PR China.
| | - Jin-Ming Lin
- Department of Chemistry, Beijing Key Laboratory of Microanalytical Methods and Instrumentation, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, Tsinghua University, Beijing, 100084, PR China.
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Takahara H, Matsushita H, Inui E, Ochiai M, Hashimoto M. Convenient microfluidic cartridge for single-molecule droplet PCR using common laboratory equipment. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2021; 13:974-985. [PMID: 33533381 DOI: 10.1039/d0ay01779e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We have previously established a cost-efficient in-house system for single-molecule droplet polymerase chain reaction (PCR) using a polydimethylsiloxane microfluidic cartridge and common laboratory equipment. However, the microfluidic cartridge was only capable of generating monodisperse water-in-oil droplets. Therefore, careful and time-consuming manual droplet handling using a micropipette was required to transfer droplets between the three discrete steps involved in the workflow of droplet PCR-i.e., (1) droplet generation; (2) PCR amplification; and (3) determination of the fluorescence intensity of the thermocycled droplets. In the current study, we developed a new microfluidic cartridge consisting of four layers, with a thin glass slide as the bottom layer. In this cartridge, droplets generated in the uppermost polydimethylsiloxane microfluidic layer are delivered to the glass slide in an online fashion. After the accumulation of many droplets on the glass slide, the cartridge is placed on the flatbed heat block of a thermocycler for PCR amplification. Direct fluorescence imaging of the thermocycled droplets on the glass slide is then carried out using a conventional fluorescence microscope. Efficient heat transfer from the heat block to the settled droplets through the thin glass slide was confirmed by successful PCR amplification inside the droplets, even from single template molecules. The new cartridge eliminates the need for manual droplet transfer between the major steps of droplet PCR analysis, allowing more convenient single-molecule droplet PCR than in our previous studies.
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Affiliation(s)
- Hirokazu Takahara
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Hiroo Matsushita
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Erika Inui
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Masashi Ochiai
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
| | - Masahiko Hashimoto
- Department of Chemical Engineering and Materials Science, Faculty of Science and Engineering, Doshisha University, 1-3 Tataramiyakodani, Kyotanabe, Kyoto 610-0321, Japan.
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11
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Zhang W, Bream JH, Leng SX, Margolick JB. Validation of Preamplification to Improve Quantification of Cytomegalovirus DNA Using Droplet Digital Polymerase Chain Reaction. Anal Chem 2021; 93:3710-3716. [PMID: 33596050 PMCID: PMC10074994 DOI: 10.1021/acs.analchem.0c02890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Subclinical cytomegalovirus (CMV) replication is associated with strong cellular immune response and chronic inflammation, which could contribute to aging-related conditions such as cardiovascular disease and frailty. However, because of very low levels of CMV DNA present in people with chronic CMV infection, it has been difficult to explore the virologic and immunologic mechanisms of chronic low-level CMV infection and a sensitive method to monitor CMV replication is needed. Droplet digital PCR (ddPCR) has been shown to have higher precision and reproducibility than real-time quantitative PCR (qPCR) in quantifying low levels of CMV DNA, but it is not always sensitive enough for this purpose. Through rigorous validation experiments, we demonstrated that sensitivity and precision of quantification of very low levels of CMV DNA by ddPCR can be significantly increased by preamplification of samples with 10-20 cycles of conventional PCR, especially when testing CMV DNA in the presence of cellular DNA. With preamplification, we could reliably quantify down to two copies of CMV DNA, as opposed to five copies without preamplification. Further studies are needed to determine if ddPCR with preamplification can facilitate mechanistic studies of the characteristics and consequences of chronic CMV infection in aging adults.
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Affiliation(s)
- Weiying Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Jay H. Bream
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
- Graduate Program in Immunology, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Sean X. Leng
- Division of Geriatric Medicine and Gerontology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland
| | - Joseph B. Margolick
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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Sivapalan L, Kocher H, Ross-Adams H, Chelala C. Molecular profiling of ctDNA in pancreatic cancer: Opportunities and challenges for clinical application. Pancreatology 2021; 21:363-378. [PMID: 33451936 PMCID: PMC7994018 DOI: 10.1016/j.pan.2020.12.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 01/10/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is predicted to become the second leading cause of cancer-related mortality within the next decade, with limited effective treatment options and a dismal long-term prognosis for patients. Genomic profiling has not yet manifested clinical benefits for diagnosis, treatment or prognosis in PDAC, due to the lack of available tissues for sequencing and the confounding effects of low tumour cellularity in many biopsy specimens. Increasing focus is now turning to the use of minimally invasive liquid biopsies to enhance the characterisation of actionable PDAC tumour genomes. Circulating tumour DNA (ctDNA) is the most comprehensively studied liquid biopsy analyte in blood and can provide insight into the molecular profile and biological characteristics of individual PDAC tumours, in real-time and in advance of traditional imaging modalities. This can pave the way for identification of new therapeutic targets, novel risk variants and markers of tumour response, to supplement diagnostic screening and provide enhanced scrutiny in treatment stratification. In the roadmap towards the application of precision medicine for clinical management in PDAC, ctDNA analyses may serve a leading role in streamlining candidate biomarkers for clinical integration. In this review, we highlight recent developments in the use of ctDNA-based liquid biopsies for PDAC and provide new insights into the technical, analytical and biological challenges that must be overcome for this potential to be realised.
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Affiliation(s)
- L. Sivapalan
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H.M. Kocher
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - H. Ross-Adams
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK
| | - C. Chelala
- Centre for Cancer Biomarkers and Biotherapeutics, Barts Cancer Institute, Queen Mary University of London, EC1M 6BQ, UK,Corresponding author.
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13
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Varona M, Anderson JL. Advances in Mutation Detection Using Loop-Mediated Isothermal Amplification. ACS OMEGA 2021; 6:3463-3469. [PMID: 33585732 PMCID: PMC7876693 DOI: 10.1021/acsomega.0c06093] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 05/25/2023]
Abstract
Detection of mutations and single-nucleotide polymorphisms is highly important for diagnostic applications. Loop-mediated isothermal amplification (LAMP) is a powerful technique for the rapid and sensitive detection of nucleic acids. However, LAMP traditionally does not possess the ability to resolve single-nucleotide differences within the target sequence. Because of its speed and isothermal nature, LAMP is ideally suited for point-of-care applications in resource-limited settings. Recently, different approaches have been developed and applied to enable single-nucleotide differentiation within target sequences. This Mini-Review highlights advancements in mutation detection using LAMP. Methods involving primer design and modification to enable sequence differentiation are discussed. In addition, the development of probe-based detection methods for mutation detection are also covered.
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14
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Lueong SS, Herbst A, Liffers ST, Bielefeld N, Horn PA, Tannapfel A, Reinacher-Schick A, Hinke A, Hegewisch-Becker S, Kolligs FT, Siveke JT. Serial Circulating Tumor DNA Mutational Status in Patients with KRAS-Mutant Metastatic Colorectal Cancer from the Phase 3 AIO KRK0207 Trial. Clin Chem 2020; 66:1510-1520. [PMID: 33257977 DOI: 10.1093/clinchem/hvaa223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/28/2020] [Indexed: 12/31/2022]
Abstract
BACKGROUND We assessed the usefulness of circulating tumor DNA (ctDNA) pre- or post-treatment initiation for outcome prediction and treatment monitoring in metastatic colorectal cancer (mCRC). METHODS Droplet digital PCR was used to measure absolute mutant V-Ki-ras2 Kirsten rat sarcoma viral oncogene ((mut)KRAS) ctDNA concentrations in 214 healthy controls (plasma and sera) and in 151 tissue-based mutKRAS positive patients with mCRC from the prospective multicenter phase 3 trial AIO KRK0207. Serial mutKRAS ctDNA was analyzed prior to and 2-3 weeks after first-line chemotherapy initiation with fluoropyrimidine, oxaliplatin, and bevacizumab in patients with mCRC and correlated with clinical parameters. RESULTS mut KRAS ctDNA was detected in 74.8% (113/151) of patients at baseline and in 59.6% (90/151) at follow-up. mutKRAS ctDNA at baseline and follow-up was associated with poor overall survival (OS) (hazard ratio [HR] =1.88, 95% confidence interval [CI] 1.20-2.95; HR = 2.15, 95% CI 1.47-3.15) and progression-free survival (PFS) (HR = 2.53, 95% CI 1.44-4.46; HR = 1.90, 95% CI 1.23-2.95), respectively. mutKRAS ctDNA clearance at follow-up conferred better disease control (P = 0.0075), better OS (log-rank P = 0.0018), and PFS (log-rank P = 0.0018). Measurable positive mutKRAS ctDNA at follow-up was the strongest and most significant independent prognostic factor on OS in multivariable analysis (HR = 2.31, 95% CI 1.40-3.25). CONCLUSIONS Serial analysis of circulating mutKRAS concentrations in mCRC has prognostic value. Post treatment mutKRAS concentrations 2 weeks after treatment initiation were associated with therapeutic response in multivariable analysis and may be an early response predictor in patients receiving first-line combination chemotherapy. CLINICALTRIALSGOV IDENTIFIER NCT00973609.
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Affiliation(s)
- Smiths S Lueong
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Andreas Herbst
- Institute of Laboratory Medicine, University of Munich, Munich, Germany.,German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Sven-Thorsten Liffers
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Nicola Bielefeld
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
| | - Peter A Horn
- Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Institute for Transfusion Medicine, University Hospital Essen, Essen, Germany
| | | | - Anke Reinacher-Schick
- Department of Hematology, Oncology and Palliative Care, St. Josef-Hospital, Ruhr-University Bochum
| | - Axel Hinke
- CCRC: Cancer Clinical Research Consulting, Düsseldorf, Germany
| | | | - Frank T Kolligs
- German Cancer Consortium (DKTK, Partner Site Munich) and German Cancer Research Center, DKFZ, Heidelberg, Germany.,Department of Medicine, Division of- Gastroenterology, Hepatology & Infectiology, Helios Clinic Berlin-Buch, Berlin, Germany.,Department of Medicine II, University of Munich, Munich, Germany
| | - Jens T Siveke
- Institute for Developmental Cancer Therapeutics, West German Cancer Center, University Medicine Essen, Essen, Germany.,Division of Solid Tumor Translational Oncology, German Cancer Consortium (DKTK, Partner Site Essen) and German Cancer Research Center, DKFZ, Heidelberg, Germany
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15
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Biocomputing label-free security system based on homogenous ligation chain reaction-induced dramatic change in melting temperature for screening single nucleotide polymorphisms. Talanta 2020; 218:121141. [PMID: 32797898 DOI: 10.1016/j.talanta.2020.121141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/03/2020] [Accepted: 05/07/2020] [Indexed: 12/17/2022]
Abstract
The development of smart platform with accurate, inexpensive and reliable detection of single-nucleotide polymorphisms (SNPs) has long been concerned in the fields of medical diagnosis and basic research. Here, we present a ligation chain reaction (LCR)-based sensing system for the cost-effective screening of SNPs by simply conducting DNA melting analysis. No chemical modification is required and the signaling operation is accomplished in homogeneous solution, circumventing the complex modification process and possibly compromised enzymatic activity associated with heterogeneous materials, such as quantum dot (QD) and gold nanoparticle (GNP). Due to the enzymatic catalysis and high fidelity of ligase, the system is capable of executing signal amplification, providing a high sensitivity and selectivity. KRAS gene is easily recognized and the site-specific mutation of guanine (G) to adenine (A), thymine (T) or cytosine (C) is accurately screened. Moreover, the excellent reliability was demonstrated by blind test and recovery test. LCR-based signaling mechanism was further used to develop the biocomputing security system, and two logic gates consisting of four single-stranded DNAs (ssDNAs) offer a double insurance to protect the information against illegal invasion, guaranteeing the reliability of output information. Once in the absence of one essential factor, the security system was always locked regardless of target key, serving as a novel strategy to ensure the safety of output information at molecular level. As a proof-of-concept scheme, this contribution introduces new insight into the development of DNA security systems and the exploitation of powerful signal transduction strategy suitable for rapid and convenient disease diagnosis.
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16
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Tang Z, Huang J, He H, Ma C, Wang K. Contributing to liquid biopsy: Optical and electrochemical methods in cancer biomarker analysis. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2020.213317] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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17
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Abdallah R, Taly V, Zhao S, Pietrasz D, Bachet JB, Basile D, Mas L, Zaanan A, Laurent-Puig P, Taieb J. Plasma circulating tumor DNA in pancreatic adenocarcinoma for screening, diagnosis, prognosis, treatment and follow-up: A systematic review. Cancer Treat Rev 2020; 87:102028. [PMID: 32485509 DOI: 10.1016/j.ctrv.2020.102028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 04/27/2020] [Accepted: 04/29/2020] [Indexed: 12/19/2022]
Abstract
While no biomarker is currently recommended for the management of pancreatic adenocarcinoma (PA), circulating tumor DNA (ctDNA) seems promising but little is known on how it may help to manage our patients in the near future. This systematic review of literature was designed to explore the current knowledge on ctDNA as a screening, diagnostic, prognostic, predictive and theranostic biomarker in the management of PA. We retrieved 62 full-text articles, 3 meta-analyses, 2 clinical trials, 1 abstract and 13 ongoing trials. Results were categorized into sections about screening, diagnosis, prognosis and follow-up of localized and advanced PA together with possible theranostics applications. Although its specificity is excellent, the current sensitivity of ctDNA remains a limitation especially in patients without metastatic disease. Therefore, this biomarker cannot be currently used as a screening or diagnostic tool. Increasing evidence suggests that ctDNA is a relevant candidate biomarker to assess minimal residual disease after radical surgery, but also a strong independent biomarker linked to a poor prognosis in advanced PA. Some recent data also indicates that ctDNA is an attractive biomarker for longitudinal follow-up and possibly early treatment adaptation. Its role in tumor profiling in advanced disease to decide targeted treatments remains to be explored. Altogether, ctDNA appears to be a reliable prognostic tool. Though promising results have been reported, further studies are still needed to define exactly how ctDNA can help physicians in the screening, diagnosis and treatment, as PA is expected to become a major cause of cancer-related deaths in the forthcoming decade.
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Affiliation(s)
- Raëf Abdallah
- Université de Paris, Department of Hepatogastroenterology and GI Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France; Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Valérie Taly
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Shulin Zhao
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Daniel Pietrasz
- Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Jean-Baptiste Bachet
- Department of Hepatogastroenterology and GI Oncology, La Pitié-Salpêtrière Hospital, Paris, INSERM UMRS 1138, Université de Paris, Paris, France
| | - Debora Basile
- Université de Paris, Department of Hepatogastroenterology and GI Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France; Department of Medicine (DAME), University of Udine, Italy
| | - Léo Mas
- Department of Hepatogastroenterology and GI Oncology, La Pitié-Salpêtrière Hospital, Paris, INSERM UMRS 1138, Université de Paris, Paris, France
| | - Aziz Zaanan
- Université de Paris, Department of Hepatogastroenterology and GI Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France; Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France
| | - Pierre Laurent-Puig
- Université de Paris, Department of Hepatogastroenterology and GI Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France
| | - Julien Taieb
- Université de Paris, Department of Hepatogastroenterology and GI Oncology, Georges Pompidou European Hospital, APHP Centre, Paris, France; Centre de Recherche des Cordeliers, INSERM, CNRS, Sorbonne Université, USPC, Université Paris Descartes, Université Paris Diderot, Equipe labellisée Ligue Nationale contre le cancer, Paris, France.
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18
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Dhayat SA, Yang Z. Impact of circulating tumor DNA in hepatocellular and pancreatic carcinomas. J Cancer Res Clin Oncol 2020; 146:1625-1645. [PMID: 32338295 PMCID: PMC7256092 DOI: 10.1007/s00432-020-03219-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
Hepatocellular carcinoma (HCC) and pancreatic cancer (PC) belong to the most lethal malignancies worldwide. Despite advances in surgical techniques and perioperative multidisciplinary management, the prognosis of both carcinoma entities remains poor mainly because of rapid tumor progression and early dissemination with diagnosis in advanced tumor stages with poor sensitivity to current therapy regimens. Both highly heterogeneous visceral carcinomas exhibit unique somatic alterations, but share common driver genes and mutations as well. Recently, circulating tumor DNA (ctDNA) could be identified as a liquid biopsy tool with huge potential as non-invasive biomarker in early diagnosis and prognosis. CtDNA released from necrotic or apoptotic cells of primary tumors, metastasis, and circulating tumor cells can reveal genetic and epigenetic alterations with tumor-specific and individual mutation and methylation profiles. In this article, we focus on clinical impact of ctDNA as potential biomarker in patients with HCC and PC.
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Affiliation(s)
- Sameer A Dhayat
- Department of General, Visceral and Transplantation Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1 (W1), 48149, Munster, Germany.
| | - Zixuan Yang
- Department of General, Visceral and Transplantation Surgery, University Hospital Muenster, Albert-Schweitzer-Campus 1 (W1), 48149, Munster, Germany
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19
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Varona M, Eitzmann DR, Pagariya D, Anand RK, Anderson JL. Solid-Phase Microextraction Enables Isolation of BRAF V600E Circulating Tumor DNA from Human Plasma for Detection with a Molecular Beacon Loop-Mediated Isothermal Amplification Assay. Anal Chem 2020; 92:3346-3353. [PMID: 31950824 PMCID: PMC7155775 DOI: 10.1021/acs.analchem.9b05323] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Circulating tumor DNA (ctDNA) is a promising biomarker that can provide a wealth of information regarding the genetic makeup of cancer as well as provide a guide for monitoring treatment. Methods for rapid and accurate profiling of ctDNA are highly desirable in order to obtain the necessary information from this biomarker. However, isolation of ctDNA and its subsequent analysis remains a challenge due to the dependence on expensive and specialized equipment. In order to enable widespread implementation of ctDNA analysis, there is a need for low-cost and highly accurate methods that can be performed by nonexpert users. In this study, an assay is developed that exploits the high specificity of molecular beacon (MB) probes with the speed and simplicity of loop-mediated isothermal amplification (LAMP) for the detection of the BRAF V600E single-nucleotide polymorphism (SNP). Furthermore, solid-phase microextraction (SPME) is applied for the successful isolation of clinically relevant concentrations (73.26 fM) of ctDNA from human plasma. In addition, the individual effects of plasma salts and protein on the extraction of ctDNA with SPME are explored. The performed work expands the use of MB-LAMP for SNP detection as well as demonstrates SPME as a sample preparation tool for nucleic acid analysis in plasma.
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Affiliation(s)
- Marcelino Varona
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Derek R. Eitzmann
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Darshna Pagariya
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Robbyn K. Anand
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
| | - Jared L. Anderson
- Department of Chemistry, Iowa State University, Ames, Iowa 50011, United States
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20
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Affiliation(s)
- Yun Ding
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Philip D. Howes
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
| | - Andrew J. deMello
- Institute for Chemical and Bioengineering, Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zürich, Switzerland
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21
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Feng W, Ding Y, Zong W, Ju S. Non-coding RNAs in regulating gastric cancer metastasis. Clin Chim Acta 2019; 496:125-133. [PMID: 31276633 DOI: 10.1016/j.cca.2019.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/01/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022]
Abstract
Gastric cancer is one of the leading causes of cancer-related deaths worldwide, and mortality remains high, especially in East Asia. At present, the main method to diagnose gastric cancer is pathological biopsy. At the time of diagnosis, most patients have been diagnosed with advanced cancer and metastasis. The treatment of gastric cancer patients is mainly radical surgical resection and chemoradiotherapy, while patients with metastatic tumor have great challenges to radical surgery and are prone to drug resistance. Metastasis is an important factor affecting tumor development. In addition, evidence accumulated in the literature indicates that non-coding RNA plays a key role in tumor metastasis. This article reviews the role of ncRNAs in gastric cancer metastasis and discusses the regulatory mechanism in the development and treatment of gastric cancer.
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Affiliation(s)
- Wei Feng
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Ye Ding
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Wei Zong
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, China.
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