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Multiplex protein profiling method for extracellular vesicle protein detection. Sci Rep 2021; 11:12477. [PMID: 34127763 PMCID: PMC8203679 DOI: 10.1038/s41598-021-92012-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/21/2021] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are small nanometer-sized membrane sacs secreted into biological fluids by all cells. EVs encapsulate proteins, RNAs and metabolites from its origin cell and play important roles in intercellular communication events. Over the past decade, EVs have become a new emerging source for cancer diagnostics. One of the challenges in the study of EVs and there utility as diagnostic biomarkers is the amount of EVs needed for traditional protein analysis methods. Here, we present a new immuno-PCR method that takes advantage of commercially available TotalSeq antibodies containing DNA conjugated oligos to identify immobilized protein analysts using real-time qPCR. Using this method, we demonstrate that multiple EV surface proteins can be profiled simultaneously with high sensitivity and specificity. This approach was also successfully applied to similar protocol using cell and serum samples. We further described the development of a micro-size exclusion chromatography method, where we were able to detect EV surface proteins with as little as 10 μL of human serum when combined with immuno-PCR. Overall, these results show that the immuno-PCR method results in rapid detection of multiple EV markers from small sample volumes in a single tube.
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2
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Lin JC, Wang CC, Jiang RS, Wang WY, Liu SA. Application of proximity ligation assays to identify potential plasma biomarkers in oral cavity cancer patients: A case control study. Cancer Biomark 2021; 29:17-23. [PMID: 32568177 DOI: 10.3233/cbm-191195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Practical cancer biomarkers for oral cavity cancer are currently in limited use. OBJECTIVE We aimed to investigate the differences in soluble E-cadherin between patients with oral cavity cancer and matched healthy participants via Proximity Ligation Assay (PLA). METHODS Samples were taken from both patients diagnosed with oral cavity cancer, as well as non-cancerous participants. PLA was used to detect soluble E-cadherin and Cycle threshold (Ct) values derived from qPCR in order to calculate the number of starting amplicons. RESULTS In total, 74 patients with oral cavity cancer and 55 matched non-cancerous participants were included for final analysis. The Ct value of E-cadherin was found to be lower in oral cavity cancer patients when compared with that of the matched non-cancerous participants (20.72 ± 0.39 versus 21.27 ± 0.45, P< 0.001). Using a Ct value of 20.9 as a cut-off point, the sensitivity and specificity of discriminating patients with oral cavity cancer from the healthy controls was 63.5% and 87.3%, respectively. CONCLUSION Plasma soluble E-cadherin levels were significantly higher in patients with oral cavity cancer when compared with those from the matched non-cancerous participants.
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Affiliation(s)
- Jin-Ching Lin
- Department of Radiation Oncology, Changhua Christian Hospital, Changhua, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Chen-Chi Wang
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan
| | - Rong-San Jiang
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Wen-Yi Wang
- Department of Nursing, HungKuang University, Taichung, Taiwan
| | - Shih-An Liu
- Department of Otolaryngology, Taichung Veterans General Hospital, Taichung, Taiwan.,Center for Quality Management, Taichung Veterans General Hospital, Taichung, Taiwan.,Faculty of Medicine, School of Medicine, National Yang-Ming University, Taipei, Taiwan.,Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
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3
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Sensitive determination of the human epidermal growth factor receptor 2 (HER2) by immuno-polymerase chain reaction with inductively coupled plasma-mass spectrometry detection. Anal Chim Acta 2019; 1090:39-46. [DOI: 10.1016/j.aca.2019.09.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 07/26/2019] [Accepted: 09/16/2019] [Indexed: 11/17/2022]
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4
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Tian T, Song Y, Wang J, Fu B, He Z, Xu X, Li A, Zhou X, Wang S, Zhou X. Small-Molecule-Triggered and Light-Controlled Reversible Regulation of Enzymatic Activity. J Am Chem Soc 2016; 138:955-61. [DOI: 10.1021/jacs.5b11532] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Tian Tian
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Yanyan Song
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Jiaqi Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Boshi Fu
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Zhiyong He
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xianqun Xu
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Anling Li
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Xin Zhou
- Zhongnan
Hospital, Wuhan University, Wuhan 430071, Hubei Province, China
| | - Shaoru Wang
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
| | - Xiang Zhou
- College
of Chemistry and Molecular Sciences, Institute of Advanced Studies,
Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Wuhan 430072, Hubei
Province, China
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5
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Brasino MD, Cha JN. Isothermal rolling circle amplification of virus genomes for rapid antigen detection and typing. Analyst 2016; 140:5138-44. [PMID: 26040578 DOI: 10.1039/c5an00721f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In this work, isothermal rolling circle amplification (RCA) of the multi-kilobase genome of engineered filamentous bacteriophage is used to report the presence and identification of specific protein analytes in solution. First, bacteriophages were chosen as sensing platforms because peptides or antibodies that bind medically relevant targets can be isolated through phage display or expressed as fusions to their p3 and p8 coat proteins. Second, the circular, single-stranded genome contained within the phage serves as a natural large DNA template for a RCA reaction to rapidly generate exponential amounts of double stranded DNA in a single isothermal step that can be easily detected using low-cost fluorescent nucleic acid stains. Amplifying the entire phage genome also provides high detection sensitivities. Furthermore, since the sequence of the viral DNA can be easily modified with multiple restriction enzyme sites, a simple DNA digest can be applied to detect and identify multiple antigens simultaneously. The methods developed here will lead to protein sensors that are highly scalable to produce, can be run without complex biological equipment and do not require the use of multiple antibodies or high-cost fluorescent DNA probes or nucleotides.
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Affiliation(s)
- Michael D Brasino
- Materials Science and Engineering Program, University of Colorado, Boulder, USA
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6
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Secrets of a covalent interaction for biomaterials and biotechnology: SpyTag and SpyCatcher. Curr Opin Chem Biol 2015; 29:94-9. [DOI: 10.1016/j.cbpa.2015.10.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 10/01/2015] [Indexed: 01/20/2023]
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7
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Sensitive ligand-based protein quantification using immuno-PCR: A critical review of single-probe and proximity ligation assays. Biotechniques 2015; 56:217-28. [PMID: 24919231 DOI: 10.2144/000114164] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Quantitative PCR (qPCR) of reverse-transcribed mRNA has revolutionized gene expression analyses. qPCR analysis is based on the prevalent assumption that mRNA transcript numbers provide an adequate measure of specific biomarker expression. However, taking the complexity of protein turnover into account, there is a need to correlate qPCR-derived transcriptional patterns with protein translational patterns so as to not leave behind important pathobiological details. One emerging approach in protein analysis is PCR-coupled protein quantification, often denoted as immuno-PCR (iPCR), which targets soluble proteins. Here we review recent trends and applications in iPCR assays that may bridge the gap between classical enzyme-linked immunosorbent assays and mass spectrometry methodologies in terms of sensitivity and multiplexing.
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8
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Yan Z, Gan N, Zhang H, Wang D, Qiao L, Cao Y, Li T, Hu F. A sandwich-hybridization assay for simultaneous determination of HIV and tuberculosis DNA targets based on signal amplification by quantum dots-PowerVision™ polymer coding nanotracers. Biosens Bioelectron 2015; 71:207-213. [PMID: 25911447 DOI: 10.1016/j.bios.2015.04.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/19/2015] [Accepted: 04/05/2015] [Indexed: 11/15/2022]
Abstract
A novel sandwich-hybridization assay for simultaneous electrochemical detection of multiple DNA targets related to human immune deficiency virus (HIV) and tuberculosis (TB) was developed based on the different quantum dots-PowerVision(TM) polymer nanotracers. The polymer nanotracers were respectively fabricated by immobilizing SH-labeled oligonucleotides (s-HIV or s-TB), which can partially hybrid with virus DNA (HIV or TB), on gold nanoparticles (Au NPs) and then modified with PowerVision(TM) (PV) polymer-encapsulated quantum dots (CdS or PbS) as signal tags. PV is a dendrimer enzyme linked polymer, which can immobilize abundant QDs to amplify the stripping voltammetry signals from the metal ions (Pb or Cd). The capture probes were prepared through the immobilization of SH-labeled oligonucleotides, which can complementary with HIV and TB DNA, on the magnetic Fe3O4@Au (GMPs) beads. After sandwich-hybridization, the polymer nanotracers together with HIV and TB DNA targets were simultaneously introduced onto the surface of GMPs. Then the two encoding metal ions (Cd(2+) and Pb(2+)) were used to differentiate two viruses DNA due to the different subsequent anodic stripping voltammetric peaks at -0.84 V (Cd) and -0.61 V (Pb). Because of the excellent signal amplification of the polymer nanotracers and the great specificity of DNA targets, this assay could detect targets DNA as low as 0.2 femtomolar and exhibited excellent selectivity with the dynamitic range from 0.5 fM to 500 pM. Those results demonstrated that this electrochemical coding assay has great potential in applications for screening more viruses DNA while changing the probes.
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Affiliation(s)
- Zhongdan Yan
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Ning Gan
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
| | - Huairong Zhang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - De Wang
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Li Qiao
- Faculty of Marine, Ningbo University, Ningbo 315211, PR China
| | - Yuting Cao
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Tianhua Li
- State Key Laboratory Base of Novel Functional Materials and Preparation Science, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Futao Hu
- Faculty of Marine, Ningbo University, Ningbo 315211, PR China
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Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A. Parallel barcoding of antibodies for DNA-assisted proteomics. Proteomics 2014; 14:2432-6. [DOI: 10.1002/pmic.201400215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Revised: 08/27/2014] [Accepted: 09/24/2014] [Indexed: 12/27/2022]
Affiliation(s)
- Mahya Dezfouli
- Science for Life Laboratory; Division of Gene Technology; School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Sanja Vickovic
- Science for Life Laboratory; Division of Gene Technology; School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Maria Jesus Iglesias
- Science for Life Laboratory; Affinity Proteomics; Division of Proteomics and Nanobiotechnology; School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Jochen M. Schwenk
- Science for Life Laboratory; Affinity Proteomics; Division of Proteomics and Nanobiotechnology; School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
| | - Afshin Ahmadian
- Science for Life Laboratory; Division of Gene Technology; School of Biotechnology; Royal Institute of Technology (KTH); Solna Sweden
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