1
|
Zhang Z, Guan L, Yao J, Li L, Liu C, Guo Y, Xie G. RART-LAMP: One-Step Extraction-Free Method for Genotyping within 40 min. Anal Chem 2023; 95:12487-12496. [PMID: 37534990 DOI: 10.1021/acs.analchem.3c02232] [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: 08/04/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a commonly used alternative to PCR for point-of-care detection of nucleic acids due to its rapidity, sensitivity, specificity, and simpler instrumentation. While dual-labeled TaqMan probes are widely used in PCR for single-nucleotide polymorphism (SNP) genotyping, real-time LAMP primarily relies on turbidimetry or intercalator fluorescence measurements, which can be non-specific and generate false-positive results. In this study, we propose a closed-tube, dual-labeled RNA-modified probes and RNase H II-assisted real-time LAMP (RART-LAMP) method for SNP genotyping. Our findings indicate that (1) fluorescence signals were predominantly derived from probe hydrolysis rather than hybridization, (2) temperature-controlled hybridization between the probe and template ensured the specificity of SNP analysis, and (3) RNase H II hydrolysis between the target containing SNP sites and probes did not exhibit sequence specificity. Our RART-LAMP approach demonstrated excellent performance in genotyping C677T clinical samples, including gDNA extracted from blood, saliva, and swabs. More importantly, saliva and swab samples could be directly analyzed without any pretreatment, indicating promising prospects for nucleic acid analysis at the point of care in resource-limited settings.
Collapse
Affiliation(s)
- Zhang Zhang
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
| | - Luhao Guan
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
- Department of Laboratory Medicine, Luzhou Traditional Chinese Medicine Hospital, Luzhou 646000, China
| | - Juan Yao
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Lijia Li
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Chunfang Liu
- Zhuhai Biori Biotechnology Company Limited, Zhuhai 519000, China
| | - Yongcan Guo
- Department of Laboratory Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou 646000, China
| | - Guoming Xie
- Key Laboratory of Clinical Laboratory Diagnostics (Chinese Ministry of Education), College of Laboratory Medicine, Chongqing Medical Laboratory Microfluidics and SPRi Engineering Research Center, Chongqing Medical University, Chongqing 400016, China
| |
Collapse
|
2
|
Liu H, Lai Y, Xu Z, Yang Z, Yu Y, Yan P. Expression Characteristics and Sequence Variation Analysis of Rice Starch Regulator 1 Gene in Japonica Rice With Transgressive Variation. INTERNATIONAL JOURNAL OF AGRICULTURAL AND ENVIRONMENTAL INFORMATION SYSTEMS 2023. [DOI: 10.4018/ijaeis.317417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The parents and transgressive variation lines of hybrids with significant difference in amylose content were selected to compare and analyze the accumulation characteristics of amylose and the change of OsRSR1 expression in grains in the process of grain filling, and the PCR technology was used to clone the OsRSR1 gene base sequence of four varieties. The results showed that the amylose content in grains increased gradually with grain filling process, the amylose content of offspring and parents with high amylose content were higher than the offspring and parents with low amylose content, hybrids could obtain the transgressive variation lines through the continuous directional selection of amylose content in grain, and the accumulation of amylose content in grain was closely related to genotypes. The expression quantity of OsRSR1 gene in grain was increasing during the grain filling process, the amylose content of grain was closely related to the activity of OsRSR1 gene, and the expression of grain OsRSR1 gene could also produce transgressive variation.
Collapse
Affiliation(s)
- Haiying Liu
- Heilongjiang Academy of Agricultural Sciences, China
| | - Yongcai Lai
- Heilongjiang Academy of Agricultural Sciences, China
| | - Zhenhua Xu
- Biotechnogogy Research Institute, Heilongjiang Academy of Agricultural Sciences, China
| | - Zhonliang Yang
- Biotechnogogy Research Institute, Heilongjiang Academy of Agricultural Sciences, China
| | - Yanmin Yu
- Biotechnogogy Research Institute, Heilongjiang Academy of Agricultural Sciences, China
| | - Ping Yan
- Biotechnogogy Research Institute, Heilongjiang Academy of Agricultural Sciences, China
| |
Collapse
|
3
|
Cao G, Long K, Qiu Y, Ma Y, Qin H, Huo D, Yang M, Shen C, Hou C. Inducible positive amplification regulation coupled with the Double-strand Specific Nuclease for FzD5 mRNA assay. Microchem J 2022. [DOI: 10.1016/j.microc.2022.108179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
4
|
Chen J, Qiud T, Mauk MG, Su Z, Fan Y, Yuan DJ, Zhou Q, Qiao Y, Bau HH, Ying J, Song J. Programmable endonuclease combined with isothermal polymerase amplification to selectively enrich for rare mutant allele fractions. CHINESE CHEM LETT 2022; 33:4126-4132. [PMID: 36091579 PMCID: PMC9454931 DOI: 10.1016/j.cclet.2021.11.065] [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] [Indexed: 11/17/2022]
Abstract
Liquid biopsy is a highly promising method for non-invasive detection of tumor-associated nucleic acid fragments in body fluids but is challenged by the low abundance of nucleic acids of clinical interest and their sequence homology with the vast background of nucleic acids from healthy cells. Recently, programmable endonucleases such as clustered regularly interspaced short palindromic repeat (CRISPR) associated protein (Cas) and prokaryotic Argonautes have been successfully used to remove background nucleic acids and enrich mutant allele fractions, enabling their detection with deep next generation sequencing (NGS). However, the enrichment level achievable with these assays is limited by futile binding events and off-target cleavage. To overcome these shortcomings, we conceived a new assay (Programmable Enzyme-Assisted Selective Exponential Amplification, PASEA) that combines the cleavage of wild type alleles with concurrent polymerase amplification. While PASEA increases the numbers of both wild type and mutant alleles, the numbers of mutant alleles increase at much greater rates, allowing PASEA to achieve an unprecedented level of selective enrichment of targeted alleles. By combining CRISPR-Cas9 based cleavage with recombinase polymerase amplification, we converted samples with 0.01% somatic mutant allele fractions (MAFs) to products with 70% MAFs in a single step within 20 min, enabling inexpensive, rapid genotyping with such as Sanger sequencers. Furthermore, PASEA's extraordinary efficiency facilitates sensitive real-time detection of somatic mutant alleles at the point of care with custom designed Exo-RPA probes. Real-time PASEA' performance was proved equivalent to clinical amplification refractory mutation system (ARMS)-PCR and NGS when testing over hundred cancer patients' samples. This strategy has the potential to reduce the cost and time of cancer screening and genotyping, and to enable targeted therapies in resource-limited settings.
Collapse
Affiliation(s)
- Junman Chen
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tian Qiud
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Michael G. Mauk
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zheng Su
- Center for Global Health, School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yaguang Fan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment, Tianjin Lung Cancer Institute, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Dennis J. Yuan
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qinghua Zhou
- Sichuan Lung Cancer Institute, Sichuan Lung Cancer Center, West China Hospital, Chengdu, Sichuan University, China
| | - Youlin Qiao
- Center for Global Health, School of Population Medicine and Public Health, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Haim H. Bau
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jianming Ying
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Jinzhao Song
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou 310022, China
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, Philadelphia, PA 19104, USA
| |
Collapse
|
5
|
Sun Y, Huang Y, Qi T, Jin Q, Jia C, Zhao J, Feng S, Liang L. Wet-Etched Microchamber Array Digital PCR Chip for SARS-CoV-2 Virus and Ultra-Early Stage Lung Cancer Quantitative Detection. ACS OMEGA 2022; 7:1819-1826. [PMID: 35036821 PMCID: PMC8751011 DOI: 10.1021/acsomega.1c05082] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 12/22/2021] [Indexed: 05/02/2023]
Abstract
We report a novel design of chamber-based digital polymerase chain reaction (cdPCR) chip structure. Using a wet etching process and silicon-glass bonding, the chamber size can be adjusted independently of the process and more feasibly in a normal lab. In addition, the structure of the chip is optimized through hydrodynamic computer simulations to eliminate dead space when the sample is injected into the chip. The samples will be distributed to each separated microchambers for an isolated reaction based on Poisson distribution. Due to the difference in expansion coefficients, isolation of the sample in the microchambers by the oil phase on top ensures homogeneity and independence of the sample in the microchambers. The prepared microarray cdPCR chip enables high-throughput and high-sensitivity quantitative measurement of the SARS-CoV-2 virus gene and the mutant lung cancer gene. We applied the chip for the detection of different concentrations of the mix containing the open reading frame 1ab (ORF1ab) gene, the most specific and conservative gene region of the SARS-CoV-2 virus. In addition to this, we also successfully detected the fluorescence of the epidermal growth factor receptor (EGFR) mutant gene in independent microchambers. At a throughput of 46 200 microchambers, solution mixtures containing both genes were successfully tested quantitatively, with a detection limit of 10 copies/μL. Importantly, the chips are individually inexpensive and easy to industrialize. In addition, the microarray can provide a unified solution for other viral sequences, cancer marker assay development, and point-of-care testing (POCT).
Collapse
Affiliation(s)
- Yimeng Sun
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaru Huang
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- School
of Life Sciences, Shanghai Normal University, Shanghai 200235, China
| | - Tong Qi
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| | - Qinghui Jin
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
- Faculty
of Electrical Engineering and Computer Science, Ningbo University, Ningbo 315211, 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
- Center
of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shilun Feng
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| | - Lijuan Liang
- State
Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem
and Information Technology, Chinese Academy
of Sciences, Shanghai 200050, China
| |
Collapse
|
6
|
Li Y, Li H, Xie Y, Chen S, Qin R, Dong H, Yu Y, Wang J, Qian X, Qin W. An Integrated Strategy for Mass Spectrometry-Based Multiomics Analysis of Single Cells. Anal Chem 2021; 93:14059-14067. [PMID: 34643370 DOI: 10.1021/acs.analchem.0c05209] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-cell-based genomics and transcriptomics analysis have revealed substantial cellular heterogeneity among seemingly identical cells. Knowledge of the cellular heterogeneity at multiomics levels is vital for a better understanding of tumor metastasis and drug resistance, stem cell differentiation, and embryonic development. However, unlike genomics and transcriptomics studies, single-cell characterization of metabolites, proteins, and post-translational modifications at the omics level remains challenging due to the lack of amplification methods and the wide diversity of these biomolecules. Therefore, new tools that are capable of investigating these unamplifiable "omes" from the same single cells are in high demand. In this work, a microwell chip was prepared and the internal surface was modified for hydrophilic interaction liquid chromatography-based tandem extraction of metabolites and proteins and subsequent protein digestion. Next, direct electrospray ionization mass spectrometry was adopted for single-cell metabolome identification, and a data-independent acquisition-mass spectrometry approach was established for simultaneous proteome profiling and phosphoproteome analysis without phosphopeptide enrichment. This integrated strategy resulted in 132 putatively annotated compounds, more than 1200 proteins, and the first large-scale phosphorylation data set from single-cell analysis. Application of this strategy in chemical perturbation studies provides a multiomics view of cellular changes, demonstrating its capability for more comprehensive investigation of cellular heterogeneity.
Collapse
Affiliation(s)
- Yuanyuan Li
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Hang Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yuping Xie
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Shuo Chen
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Ritian Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yongliang Yu
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Jianhua Wang
- Research Center for Analytical Sciences, College of Sciences, Northeastern University, Shenyang 110819, P. R. China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, P. R. China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, P. R. China
| |
Collapse
|
7
|
Ma L, Shi M, Chang Y, Liu M. Digital Counting of Biomolecules Using Engineered Functional DNA Superstructures. Anal Chem 2021; 93:8071-8076. [PMID: 34019378 DOI: 10.1021/acs.analchem.1c01435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is currently a great need for developing a simple and effective biosensing platform for the detection of single biomolecules (e.g., DNAs, RNAs, or proteins) in the biological, medical, and environmental fields. Here, we show a versatile and sensitive fluorescence counting strategy for quantifying proteins and microRNAs by employing functional DNA superstructures (denoted as 3D DNA). A 3D DNA biolabel was first engineered to become highly fluorescent and carry recognition elements for the target of interest. The presence of a target cross-links the resultant of the 3D DNA biolabel and a surface-bound capturing antibody or DNA oligonucleotide, thus forming a sandwich complex that can be easily resolved using traditional fluorescence microscopy. The broad utility of this platform is illustrated by engineering two different 3D DNA biolabels that enable the quantification of β-lactamase (one secreted bacterial hydrolase) and miR-21 (one overexpressed microRNA in cancer cells) with detection limits of 100 aM and 1 fM, respectively. We envision that the approach described herein will find useful applications in chemical biology, medical diagnostics, and biosensing.
Collapse
Affiliation(s)
- Liuchang Ma
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Meng Shi
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Yangyang Chang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| | - Meng Liu
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China
| |
Collapse
|
8
|
Renewable photoelectrochemical cytosensing platform for rapid capture and detection of circulating tumor cells. Anal Chim Acta 2021; 1142:1-9. [PMID: 33280686 DOI: 10.1016/j.aca.2020.10.049] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/16/2020] [Accepted: 10/23/2020] [Indexed: 12/17/2022]
Abstract
Determination of circulating tumor cells (CTCs) is crucial for cancer diagnosis and therapy at an early stage. However, extremely low concentration of CTCs in peripheral blood makes the detection of CTCs challenging. In this study, a reusable cytosensor was developed for rapid detection of CTCs based on excellent photoelectrochemical (PEC) characteristic of semiconductor nanoarrays. Using typical breast cancer cell, MCF-7 cell, as a target model, a PEC sensing platform was constructed with polymerized aminophenylboronic acid (APBA) layer coated CdS/ZnO nanorod arrays, exhibiting outstanding performance for the capture and detection of CTCs. In this design, the polymerized APBA provides abundant binding sites for capturing terminal sialic acid (SA) molecules in CTCs. As a result, the PEC cytosensor shows good sensitivity and specificity with concentrations ranging from 50 to 1.0 × 106 cells/mL MCF-7 cells. Moreover, the PEC cytosensor can be rapidly and effectively recovered via a short-time bias triggered cell release and subsequent repair of APBA. This study establishes a new approach to refine a PEC cytosensor for stable monitoring and provides a robust PEC electrode with high sensitivity and low cost for clinical diagnosis related to CTCs.
Collapse
|