1
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Cui Y, Qian H, Yin J, Xu C, Luo P, Zhang X, Yu M, Su B, Li X, Lin J. Single-molecule analysis reveals the phosphorylation of FLS2 governs its spatiotemporal dynamics and immunity. eLife 2024; 12:RP91072. [PMID: 39046447 PMCID: PMC11268883 DOI: 10.7554/elife.91072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
The Arabidopsis thaliana FLAGELLIN-SENSITIVE2 (FLS2), a typical receptor kinase, recognizes the conserved 22 amino acid sequence in the N-terminal region of flagellin (flg22) to initiate plant defense pathways, which was intensively studied in the past decades. However, the dynamic regulation of FLS2 phosphorylation at the plasma membrane after flg22 recognition needs further elucidation. Through single-particle tracking, we demonstrated that upon flg22 treatment the phosphorylation of Ser-938 in FLS2 impacts its spatiotemporal dynamics and lifetime. Following Förster resonance energy transfer-fluorescence lifetime imaging microscopy and protein proximity indexes assays revealed that flg22 treatment increased the co-localization of GFP-tagged FLS2/FLS2S938D but not FLS2S938A with AtRem1.3-mCherry, a sterol-rich lipid marker, indicating that the phosphorylation of FLS2S938 affects FLS2 sorting efficiency to AtRem1.3-associated nanodomains. Importantly, we found that the phosphorylation of Ser-938 enhanced flg22-induced FLS2 internalization and immune responses, demonstrating that the phosphorylation may activate flg22-triggered immunity through partitioning FLS2 into functional AtRem1.3-associated nanodomains, which fills the gap between the FLS2S938 phosphorylation and FLS2-mediated immunity.
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Affiliation(s)
- Yaning Cui
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Hongping Qian
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Jinhuan Yin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Changwen Xu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Pengyun Luo
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Xi Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Meng Yu
- College of Life Sciences, Hebei Agricultural UniversityBaodingChina
| | - Bodan Su
- Biotechnology Research InstituteBeijingChina
| | - Xiaojuan Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry UniversityBeijingChina
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2
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Ma Z, Xu H, Ye BC. Recent progress in quantitative technologies for the analysis of cancer-related exosome proteins. Analyst 2023; 148:4954-4966. [PMID: 37721099 DOI: 10.1039/d3an01228j] [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: 09/19/2023]
Abstract
Exosomes are a kind of extracellular vesicles, which play a significant role in intercellular communication and molecular exchange. Cancer-derived exosomes are potential and ideal biomarkers for the early diagnosis and treatment monitoring of cancers because of their abundant biological information and contribution to the interaction between cancer cells and the tumor microenvironment. However, there are a number of drawbacks, such as low sensitivity and tedious steps, in conventional detection techniques. Furthermore, exosome quantification is not enough to accurately distinguish cancer patients from healthy individuals. Therefore, developing efficient, accurate, and inexpensive exosome surface protein analysis techniques is necessary and critical. In recent years, a considerable number of researchers have presented novel detection strategies in this field. This review summarizes the recent progress in quantitative technologies for the analysis of cancer-related exosome proteins, mainly including the detection methods based on aptamers, nanomaterials, and antibodies, discusses a roadmap for future developments, and aims to offer an innovative perspective of exosome research.
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Affiliation(s)
- Zhongwen Ma
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Huiying Xu
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
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3
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Zhu R, Santat LA, Markson JS, Nandagopal N, Gregrowicz J, Elowitz MB. Reconstitution of morphogen shuttling circuits. SCIENCE ADVANCES 2023; 9:eadf9336. [PMID: 37436981 DOI: 10.1126/sciadv.adf9336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 06/08/2023] [Indexed: 07/14/2023]
Abstract
Developing tissues form spatial patterns by establishing concentration gradients of diffusible signaling proteins called morphogens. The bone morphogenetic protein (BMP) morphogen pathway uses a family of extracellular modulators to reshape signaling gradients by actively "shuttling" ligands to different locations. It has remained unclear what circuits are sufficient to enable shuttling, what other patterns they can generate, and whether shuttling is evolutionarily conserved. Here, using a synthetic, bottom-up approach, we compared the spatiotemporal dynamics of different extracellular circuits. Three proteins-Chordin, Twsg, and the BMP-1 protease-successfully displaced gradients by shuttling ligands away from the site of production. A mathematical model explained the different spatial dynamics of this and other circuits. Last, combining mammalian and Drosophila components in the same system suggests that shuttling is a conserved capability. Together, these results reveal principles through which extracellular circuits control the spatiotemporal dynamics of morphogen signaling.
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Affiliation(s)
- Ronghui Zhu
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Leah A Santat
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Joseph S Markson
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Jan Gregrowicz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Michael B Elowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
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4
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Bohrmann L, Burghardt T, Rodríguez-Rodríguez C, Herth MM, Saatchi K, Häfeli UO. Quantitative Evaluation of a Multimodal Aptamer-Targeted Long-Circulating Polymer for Tumor Targeting. ACS OMEGA 2023; 8:11003-11020. [PMID: 37008162 PMCID: PMC10061651 DOI: 10.1021/acsomega.2c07762] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
Aptamers are promising targeting agents for imaging and therapy of numerous diseases, including cancer. However, a significant shortcoming of aptamers is their poor stability and fast excretion, limiting their application in vivo. Common strategies to overcome these challenges is to chemically modify aptamers in order to increase their stability and/or to apply formulation technologies such as conjugating them to polymers or nanocarriers in order to increase their circulation half-life. This is expected to result in improved cellular uptake or retention to passively targeted nanomedicines. Herein, we report a modular conjugation strategy based on click chemistry between functionalized tetrazines and trans-cyclooctene (TCO), for the modification of high molecular weight hyperbranched polyglycerol (HPG) with sgc8 aptamer, fluorescent dyes, and 111In. Our data indicate strong affinity of sgc8 against a range of solid tumor-derived cell lines that have previously not been tested with this aptamer. Nevertheless, nonspecific uptake of scrambled ssDNA-functionalized HPG in cells highlights inherent challenges of aptamer-targeted probes that remain to be solved for clinical translation. We validate HPG-sgc8 as a nontoxic nanoprobe with high affinity against MDA-MB-468 breast and A431 lung cancer cells and show significantly increased plasma stability compared to free sgc8. In vivo quantitative SPECT/CT imaging indicates EPR-mediated tumor uptake of HPG-sgc8 and nontargeted or scrambled ssDNA-conjugated HPG but no statistically significant difference between these formulations in terms of total tumor uptake or retention. Our study emphasizes the need for stringent controls and quantification in the evaluation of aptamer-targeted probes. For this purpose, our versatile synthesis strategy provides a simple approach for the design and evaluation of long-circulating aptamer-conjugated nanoformulations.
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Affiliation(s)
- Lennart Bohrmann
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
| | - Tobias Burghardt
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | | | - Matthias M. Herth
- Department
of Drug Design and Pharmacology, Faculty of Health and Medicinal Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
- Department
of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, Blegdamsvej
9, 2100 Copenhagen, Denmark
| | - Katayoun Saatchi
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Urs O. Häfeli
- Faculty
of Pharmaceutical Sciences, University of
British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Department
of Pharmacy, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen, Denmark
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5
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Du Y, Lyu Y, Li S, Ding D, Chen J, Yang C, Sun Y, Qu F, Xiao Z, Jiang J, Tan W. Ligand Dilution Analysis Facilitates Aptamer Binding Characterization at the Single-Molecule Level. Angew Chem Int Ed Engl 2023; 62:e202215387. [PMID: 36479802 DOI: 10.1002/anie.202215387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 12/12/2022]
Abstract
Cell-specific aptamers offer a powerful tool to study membrane receptors at the single-molecule level. Most target receptors of aptamers are highly expressed on the cell surface, but difficult to analyze in situ because of dense distribution and fast velocity. Therefore, we herein propose a random sampling-based analysis strategy termed ligand dilution analysis (LDA) for easily implemented aptamer-based receptor study. Receptor density on the cell surface can be calculated based on a regression model. By using a synergistic ligand dilution design, colocalization and differentiation of aptamer and monoclonal antibody (mAb) binding on a single receptor can be realized. Once this is accomplished, precise binding site and detailed aptamer-receptor binding mode can be further determined using molecular docking and molecular dynamics simulation. The ligand dilution strategy also sets the stage for an aptamer-based dynamics analysis of two- and three-dimensional motion and fluctuation of highly expressed receptors on the live cell membrane.
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Affiliation(s)
- Yulin Du
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yifan Lyu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Shenzhen Research Institute, Hunan University, Shenzhen, Guangdong 518000, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiquan Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ding Ding
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianghuai Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Yang Sun
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fengli Qu
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Zeyu Xiao
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jianhui Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.,Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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6
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Shi Q, Wu Y, Xu Y, Bao M, Chen X, Huang K, Yang Q, Yang Y. Virus Mimetic Framework DNA as a Non-LNP Gene Carrier for Modulated Cell Endocytosis and Apoptosis. ACS NANO 2023; 17:2460-2471. [PMID: 36693051 DOI: 10.1021/acsnano.2c09772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Mimicking the size and shape of spherical viruses, we constructed a soccer-ball shaped virus-inspired DNA origami (ViDO) framework as a programmable non-LNP (lipid nanoparticle) gene carrier. The DNA framework was decorated with precisely controlled recognition molecules outside and loaded with adequate genetic molecules inside. Five variants were constructed to systematically investigate their cell uptake and modulated gene silencing efficiency. Cellular uptake was enhanced with an increasing number of aptamers, while with a median number of aptamer supply, dispersed distribution performed better than the clustered pattern. Intriguingly, the transfection efficiency was maximized using the ViDO with clustered five aptamers, which exhibited a competitive RNA silencing effect induced by Lipo2000 with low cytotoxicity. Our results revealed the effects of aptamer distribution patterns on endocytosis and transfection, thus providing a programmable platform for meticulous optimization of the gene delivery system.
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Affiliation(s)
- Qian Shi
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yuanyuan Wu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yunyun Xu
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Min Bao
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xiao Chen
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Kui Huang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Qiulan Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yang Yang
- Institute of Molecular Medicine and Shanghai Key Laboratory for Nucleic Acid Chemistry and Nanomedicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
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7
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Rollins ZA, Chan A, Shirure VS, George SC. Receptor-ligand non-equilibrium kinetics (RLNEK) 1.0: An integrated Trackmate laminar flow chamber analysis. J Immunol Methods 2022; 511:113381. [PMID: 36341963 DOI: 10.1016/j.jim.2022.113381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 10/21/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Although parallel plate flow chamber assays are widely performed, extraction of kinetic parameters is limited to specialized labs with mathematical expertise and customized video-microscopy tracking tools. The recent development of Trackmate has increased researcher accessibility to tracking particles in video-microscopy experiments; however, there is a lack of tools that analyze this tracking information. We report a software tool, compatible with Trackmate, that extracts Receptor Ligand Non-Equilibrium Kinetic (RLNEK) parameters from video-microscopy data. This software should be of particular interest to the community of researchers and scientists interrogating the target-specific binding and release of immune cells.
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Affiliation(s)
- Zachary A Rollins
- Department of Chemical Engineering, University of California, Davis, Davis, CA, USA
| | - Allison Chan
- Department of Chemical Engineering, University of California, Davis, Davis, CA, USA
| | - Venktesh S Shirure
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, USA.
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8
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Sánchez MF, Dietz MS, Müller U, Weghuber J, Gatterdam K, Wieneke R, Heilemann M, Lanzerstorfer P, Tampé R. Dynamic in Situ Confinement Triggers Ligand-Free Neuropeptide Receptor Signaling. NANO LETTERS 2022; 22:8363-8371. [PMID: 36219818 PMCID: PMC9614963 DOI: 10.1021/acs.nanolett.2c03506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 09/25/2022] [Indexed: 06/16/2023]
Abstract
Membrane receptor clustering is fundamental to cell-cell communication; however, the physiological function of receptor clustering in cell signaling remains enigmatic. Here, we developed a dynamic platform to induce cluster formation of neuropeptide Y2 hormone receptors (Y2R) in situ by a chelator nanotool. The multivalent interaction enabled a dynamic exchange of histidine-tagged Y2R within the clusters. Fast Y2R enrichment in clustered areas triggered ligand-independent signaling as determined by an increase in cytosolic calcium and cell migration. Notably, the calcium and motility response to ligand-induced activation was amplified in preclustered cells, suggesting a key role of receptor clustering in sensitizing the dose response to lower ligand concentrations. Ligand-independent versus ligand-induced signaling differed in the binding of arrestin-3 as a downstream effector, which was recruited to the clusters only in the presence of the ligand. This approach allows in situ receptor clustering, raising the possibility to explore different receptor activation modalities.
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Affiliation(s)
- M. Florencia Sánchez
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Marina S. Dietz
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Ulrike Müller
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Julian Weghuber
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
- FFoQSI
- Austrian Competence Centre for Feed and Food Quality, Safety &
Innovation, FFoQSI GmbH, Technopark 1D, 3430 Tulln, Austria
| | - Karl Gatterdam
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Ralph Wieneke
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
| | - Mike Heilemann
- Institute
of Physical and Theoretical Chemistry, Goethe
University Frankfurt, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Peter Lanzerstorfer
- School
of Engineering and Environmental Sciences, University of Applied Sciences Upper Austria, 4600 Wels, Austria
| | - Robert Tampé
- Institute
of Biochemistry, Biocenter, Goethe University
Frankfurt, Max-von-Laue-Str.
9, 60438 Frankfurt
am Main, Germany
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9
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Xie M, Guo L, Xing S, Cao S, Zhao Z, Liang K, Li J, Luo S, Zhang Y, Wang L. Cell imaging with multi-color DNA framework probes. Chem Commun (Camb) 2021; 57:11318-11321. [PMID: 34635891 DOI: 10.1039/d1cc04305f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Utilizing the programmability of the fractal DNA frameworks, multi-color probes were constructed by arranging fluorescent molecules and nucleic acid aptamers on the structure. Multiplexed cell imaging and classification was realized through pattern recognition.
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Affiliation(s)
- Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
| | - Linjie Guo
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China. .,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shu Xing
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Shuting Cao
- Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Ziwei Zhao
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China. .,Shanghai Frontier Innovation Research Institute Co., Ltd., Shanghai 201108, China
| | - Kaiyi Liang
- Radiology Department of Jiading District Central Hospital Affiliated Shanghai University of Medicine & Health Sciences, Key Laboratory of Shanghai Municipal Health Commission for Smart Image, Shanghai 201800, China
| | - Jiang Li
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China. .,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shihua Luo
- Department of Traumatology, Rui Jin Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200025, China.
| | - Yu Zhang
- Bioimaging Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, The Interdisciplinary Research Center, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China. .,Division of Physical Biology, CAS Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China.
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10
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Study Progress of Important Agricultural Heritage Systems (IAHS): A Literature Analysis. SUSTAINABILITY 2021. [DOI: 10.3390/su131910859] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Important Agricultural Heritage Systems (IAHS), as a new type of heritage, has received extensive attention from the international scientific communities. With the increase of IAHS research, reviews on it have been conducted by many scholars. However, visualized research to show future research trends of IAHS are lacking. Therefore, using metrology analysis methods, this study aims at presenting the progress of research and the general development trends of Globally Important Agricultural Heritage Systems (GIAHS) in the world from 2006 to 2020 to provide ideas for the development of countries or regions in the future. This study mapped 292 literatures from Web of Science core collections from 2006 to 2020 by CiteSpace software. The results show that research on IAHS from 2006 to 2020 experienced two stages: the fluctuating increase stage, and the steady growth stage. Author groups from China, Italy, the USA, Japan, etc., contributed many papers on IAHS. Institutions including the Chinese Academy of Sciences, the University of Florence and the University of Padua in Italy, etc., have a relatively high influence on international IAHS research. Agriculture Ecosystems & Environment is the most cited journal. Agricultural Heritage Systems, regeneration, agriculture, agroforestry, dry-stone wall, social capital, instability, and agricultural biodiversity have been hotspots in the past 15 years. The research themes mainly focus on GIAHS, tourism, livelihood assets, and direct georeferencing. Authors in different regions concern different research themes. In the future, the fields of applications and microscopic views, social sciences, applications of standardized quantitative research methods, and broadened international cooperation should be paid more attention.
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11
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Metabolic limits on classical information processing by biological cells. Biosystems 2021; 209:104513. [PMID: 34450208 DOI: 10.1016/j.biosystems.2021.104513] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/14/2021] [Accepted: 08/14/2021] [Indexed: 01/16/2023]
Abstract
Biological information processing is generally assumed to be classical. Measured cellular energy budgets of both prokaryotes and eukaryotes, however, fall orders of magnitude short of the power required to maintain classical states of protein conformation and localization at the Å, fs scales predicted by single-molecule decoherence calculations and assumed by classical molecular dynamics models. We suggest that decoherence is limited to the immediate surroundings of the cell membrane and of intercompartmental boundaries within the cell, and that bulk cellular biochemistry implements quantum information processing. Detection of Bell-inequality violations in responses to perturbation of recently-separated sister cells would provide a sensitive test of this prediction. If it is correct, modeling both intra- and intercellular communication requires quantum theory.
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12
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Bao W, Tian F, Lyu C, Liu B, Li B, Zhang L, Liu X, Li F, Li D, Gao X, Wang S, Wei W, Shi X, Li Y. Experimental and theoretical explorations of nanocarriers' multistep delivery performance for rational design and anticancer prediction. SCIENCE ADVANCES 2021; 7:7/6/eaba2458. [PMID: 33547068 PMCID: PMC7864577 DOI: 10.1126/sciadv.aba2458] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 12/17/2020] [Indexed: 06/12/2023]
Abstract
The poor understanding of the complex multistep process taken by nanocarriers during the delivery process limits the delivery efficiencies and further hinders the translation of these systems into medicine. Here, we describe a series of six self-assembled nanocarrier types with systematically altered physical properties including size, shape, and rigidity, as well as both in vitro and in vivo analyses of their performance in blood circulation, tumor penetration, cancer cell uptake, and anticancer efficacy. We also developed both data and simulation-based models for understanding the influence of physical properties, both individually and considered together, on each delivery step and overall delivery process. Thus, beyond finding that nanocarriers that are simultaneously endowed with tubular shape, short length, and low rigidity outperformed the other types, we now have a suit of theoretical models that can predict how nanocarrier properties will individually and collectively perform in the multistep delivery of anticancer therapies.
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Affiliation(s)
- Weier Bao
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Falin Tian
- Laboratory of Theoretical and Computational Nanoscience, Chinese Academy of Sciences (CAS) Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Chengliang Lyu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Bin Liu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Bin Li
- Laboratory of Theoretical and Computational Nanoscience, Chinese Academy of Sciences (CAS) Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Luyao Zhang
- Laboratory of Theoretical and Computational Nanoscience, Chinese Academy of Sciences (CAS) Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Xianwu Liu
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Feng Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Dan Li
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China
| | - Xiaoyong Gao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Shuo Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Wei Wei
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Xinghua Shi
- Laboratory of Theoretical and Computational Nanoscience, Chinese Academy of Sciences (CAS) Key Laboratory for Nanosystem and Hierarchy Fabrication, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, P. R. China.
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, P. R. China
| | - Yuan Li
- Key Laboratory of Precision Nutrition and Food Quality, Key Laboratory of Functional Dairy, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, P. R. China.
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13
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Detection of membrane receptors on per tumor cell by nonimmobilized cell capillary electrophoresis and a mathematic model. Talanta 2021; 222:121425. [PMID: 33167195 DOI: 10.1016/j.talanta.2020.121425] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 06/21/2020] [Accepted: 07/15/2020] [Indexed: 11/22/2022]
Abstract
Folate receptors (FRs) are a class of valuable therapeutic target which is highly expressed on a variety of cancers. The accurate detection of the expression of FRs in different cells is conducive to improve the accuracy of FR targeted tumor therapy. Herein, a method based on nonimmobilized cell capillary electrophoresis (NICCE) combined with a mathematic model to quantify FRs on each single tumor cell was developed. At first, we studied the interactions between FA and A549, HT-29, HepG2, and U87MG cells by NICCE respectively, and calculated the kinetic parameters (Ka, k', ka, and kd). Next, we established a mathematic model to accurately determine the number of moles of FRs on per A549, HT-29, HepG2, and U87MG cell for the first time, that were (10.44 ± 0.53) × 10-19 mol, (34.32 ± 1.33) × 10-19 mol, (337.14 ± 10.11) × 10-19 mol, and (37.31 ± 2.13) × 10-19 mol. Then, these re-sults were proved to be consistent with the results of enzyme-linked immunosorbent assay (ELISA). Therefore, this method is simple, rapid, sensitive, and without protein separation or purification, which is expected to achieve clinical detection of cell membrane receptor expression level of cell membrane receptors on a single cell, which may be greatly beneficial to further clinical diagnosis and therapy.
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14
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Mondal S, Narayan KB, Powers I, Botterbusch S, Baumgart T. Endophilin recruitment drives membrane curvature generation through coincidence detection of GPCR loop interactions and negative lipid charge. J Biol Chem 2021; 296:100140. [PMID: 33268381 PMCID: PMC7948419 DOI: 10.1074/jbc.ra120.016118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Revised: 11/25/2020] [Accepted: 12/01/2020] [Indexed: 12/23/2022] Open
Abstract
Endophilin plays key roles during endocytosis of cellular receptors, including generating membrane curvature to drive internalization. Electrostatic interactions between endophilin's BIN/Amphiphysin/Rvs domain and anionic membrane lipids have been considered the major driving force in curvature generation. However, the SH3 domain of endophilin also interacts with the proline-rich third intracellular loop (TIL) of various G-protein-coupled receptors (GPCRs), and it is unclear whether this interaction has a direct role in generating membrane curvature during endocytosis. To examine this, we designed model membranes with a membrane density of 1400 receptors per μm2 represented by a covalently conjugated TIL region from the β1-adrenergic receptor. We observed that TIL recruits endophilin to membranes composed of 95 mol% of zwitterionic lipids via the SH3 domain. More importantly, endophilin recruited via TIL tubulates vesicles and gets sorted onto highly curved membrane tubules. These observations indicate that the cellular membrane bending and curvature sensing activities of endophilin can be facilitated through detection of the TIL of activated GPCRs in addition to binding to anionic lipids. Furthermore, we show that TIL electrostatically interacts with membranes composed of anionic lipids. Therefore, anionic lipids can modulate TIL/SH3 domain binding. Overall, our findings imply that an interplay between TIL, charged membrane lipids, BAR domain, and SH3 domain could exist in the biological system and that these components may act in coordination to regulate the internalization of cellular receptors.
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Affiliation(s)
- Samsuzzoha Mondal
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Karthik B Narayan
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Imania Powers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Samuel Botterbusch
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tobias Baumgart
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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15
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Karagöz Z, Rijns L, Dankers PY, van Griensven M, Carlier A. Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks. Comput Struct Biotechnol J 2020; 19:303-314. [PMID: 33425258 PMCID: PMC7779863 DOI: 10.1016/j.csbj.2020.12.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 12/15/2020] [Accepted: 12/16/2020] [Indexed: 02/06/2023] Open
Abstract
The interactions between cells and their extracellular matrix (ECM) are critically important for homeostatic control of cell growth, proliferation, differentiation and apoptosis. Transmembrane integrin molecules facilitate the communication between ECM and the cell. Since the characterization of integrins in the late 1980s, there has been great advancement in understanding the function of integrins at different subcellular levels. However, the versatility in molecular pathways integrins are involved in, the high diversity in their interaction partners both outside and inside the cell as well as on the cell membrane and the short lifetime of events happening at the cell-ECM interface make it difficult to elucidate all the details regarding integrin function experimentally. To overcome the experimental challenges and advance the understanding of integrin biology, computational modeling tools have been used extensively. In this review, we summarize the computational models of integrin signaling while we explain the function of integrins at three main subcellular levels (outside the cell, cell membrane, cytosol). We also discuss how these computational modeling efforts can be helpful in other disciplines such as biomaterial design. As such, this review is a didactic modeling summary for biomaterial researchers interested in complementing their experimental work with computational tools or for seasoned computational scientists that would like to advance current in silico integrin models.
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Affiliation(s)
- Zeynep Karagöz
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Laura Rijns
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Patricia Y.W. Dankers
- Department of Biomedical Engineering and Institute for Complex Molecular Systems, Eindhoven University of Technology, PO Box 513, 5600 MB Eindhoven, the Netherlands
| | - Martijn van Griensven
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
| | - Aurélie Carlier
- Department of Cell Biology-Inspired Tissue Engineering, MERLN Institute for Technology-Inspired Regenerative Medicine, Maastricht University, Universiteitssingel 40, 6229 ER Maastricht, the Netherlands
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16
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Quantifying the adhesive strength between the SARS-CoV-2 S-proteins and human receptor and its effect in therapeutics. Sci Rep 2020; 10:17538. [PMID: 33067518 PMCID: PMC7568573 DOI: 10.1038/s41598-020-74189-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/21/2020] [Indexed: 12/21/2022] Open
Abstract
The binding affinity and adhesive strength between the spike (S) glycoproteins of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and the human angiotensin-converting enzyme 2 (ACE2) receptor is computed using molecular dynamics (MD) simulations. The calculations indicate that the binding affinity is [Formula: see text] [Formula: see text] with a maximum adhesive force of [Formula: see text] pN. Our analysis suggests that only 27 (13 in S-protein, 14 in ACE2) residues are active during the initial fusion process between the S-protein and ACE2 receptor. With these insights, we investigated the effect of possible therapeutics in the size and wrapping time of virus particles by reducing the binding energy. Our analysis indicates that this energy has to be reduced significantly, around 50% or more, to block SARS-CoV-2 particles with radius in the order of [Formula: see text] nm. Our study provides concise target residues and target binding energy reduction between S-proteins and receptors for the development of new therapeutics treatments for COVID-19 guided by computational design.
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Yan ZJ, Wang D, Ye Z, Fan T, Wu G, Deng L, Yang L, Li B, Liu J, Ma T, Dong C, Li ZT, Xiao L, Wang Y, Wang W, Hou JL. Artificial Aquaporin That Restores Wound Healing of Impaired Cells. J Am Chem Soc 2020; 142:15638-15643. [PMID: 32876439 DOI: 10.1021/jacs.0c00601] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Artificial aquaporins are synthetic molecules that mimic the structure and function of natural aquaporins (AQPs) in cell membranes. The development of artificial aquaporins would provide an alternative strategy for treatment of AQP-related diseases. In this report, an artificial aquaporin has been constructed from an amino-terminated tubular molecule, which operates in a unimolecular mechanism. The artificial channel can work in cell membranes with high water permeability and selectivity rivaling those of AQPs. Importantly, the channel can restore wound healing of the cells that contain function-lost AQPs.
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Affiliation(s)
- Zhao-Jun Yan
- Department of Chemistry, Fudan University, Shanghai, China
| | - Dongdong Wang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Zhongju Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, China
| | - Ting Fan
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Gang Wu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Liyun Deng
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Lu Yang
- Department of Chemistry, Western University, London, Ontario, Canada
| | - Binxiao Li
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jianwei Liu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Tonghui Ma
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Zhan-Ting Li
- Department of Chemistry, Fudan University, Shanghai, China
| | - Lehui Xiao
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition, College of Chemistry, Nankai University, Tianjin, China
| | - Yunfeng Wang
- ENT Institute and Otorhinolaryngology Department of Eye & ENT Hospital, Fudan University, Shanghai, China
| | - Wenning Wang
- Department of Chemistry, Fudan University, Shanghai, China
| | - Jun-Li Hou
- Department of Chemistry, Fudan University, Shanghai, China
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18
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Nosaz Z, Rasoulinejad S, Mousavi Gargari SL. Development of a DNA aptamer to detect Brucella abortus and Brucella melitensis through cell SELEX. IRANIAN JOURNAL OF VETERINARY RESEARCH 2020; 21:294-300. [PMID: 33584842 PMCID: PMC7871736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
BACKGROUND Brucellosis is a zoonosis, caused by Brucella spp. which are small aerobic intracellular coccobacilli, localized in the reproductive organs of host animals, causing abortion and sterility. The diagnosis of this zoonosis is based on microbiological, serological or real time-polymerase chain reaction (RT-PCR) laboratory tests. Although the common microbiological and serological based assays have advantages, they are not able to solve the diagnosis problems. AIMS To overcome some of the limitations of present techniques, in this study, we developed an aptamer through whole-cell systematic evolution of Ligands by EXponential enrichment (SELEX) procedures to detect Brucella. METHODS We used mixture of Brucella melitensis and Brucella abortus as the target. In order to prepare the single-stranded DNA (ssDNA) aptamer, the DNA library was amplified with 5´-phosphorylated reverse primer and treated with lambda exonuclease. The SELEX procedure was performed by incubating the ssDNA pool with a bacterial suspension in a binding buffer. The selected procedures were monitored by flow cytometry using FITC-labelled forward primer. Aptamers with the highest binding affinity towards the target and the lowest to other strains were selected. RESULTS Two aptamers namely B20 and B21 showed significant binding affinity toward B. melitensis and B. abortus. The dissociation constant (Kd) for aptamers B20 and B21 was 40.179 ± 3.06 pM and 184.396 ± 465 pM, respectively. CONCLUSION The isolated aptamers were able to identify B. melitensis and B. abortus with a remarkable binding efficiency and appropriated Kd in a picoMolar range and therefore can be good candidates in the development of any rapid assay test implanted on routine brucellosis diagnoses.
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Affiliation(s)
- Z. Nosaz
- MSc in Microbial Biotechnology, Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran; ,These authors contributed equally to this work
| | - S. Rasoulinejad
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany; ,These authors contributed equally to this work
| | - S. L. Mousavi Gargari
- Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran,Correspondence: S. L. Mousavi Gargari, Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran. E-mail:
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19
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Guo Q, Wu Z, Peng Y, Peng W, Huang Q, Peng M, Huang N, Hu X, Fu T, Zhao Z, Tan W. Tumor Extracellular pH-Driven Cancer-Selective Artificial Receptor-Mediated Tumor-Targeted Fluorescence Imaging. Anal Chem 2019; 91:13349-13354. [DOI: 10.1021/acs.analchem.9b03779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Qian Guo
- Key Laboratory of Phytochemical R&D of Hunan Province, and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Zhan Wu
- Key Laboratory of Phytochemical R&D of Hunan Province, and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Yongbo Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Wenyi Peng
- Key Laboratory of Phytochemical R&D of Hunan Province, and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Qin Huang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Miao Peng
- Key Laboratory of Phytochemical R&D of Hunan Province, and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Ni Huang
- Key Laboratory of Phytochemical R&D of Hunan Province, and Key Laboratory of Chemical Biology & Traditional Chinese Medicine Research (Ministry of Education of China), College of Chemistry and Chemical Engineering, Hunan Normal University, Changsha 410081, China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory for Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, and Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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20
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Qin YT, Peng H, He XW, Li WY, Zhang YK. Highly Effective Drug Delivery and Cell Imaging Using Fluorescent Double-Imprinted Nanoparticles by Targeting Recognition of the Epitope of Membrane Protein. Anal Chem 2019; 91:12696-12703. [PMID: 31532634 DOI: 10.1021/acs.analchem.9b02123] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanocarriers with both targeting ability and stable loading of drugs can more effectively deliver drugs to precise tumor sites for therapeutic effects. Accordingly, we have rationally designed fluorescent molecularly imprinted polymer nanoparticles (FMIPs), which use N-terminal epitope of P32 membrane protein as the primary template and doxorubicin (DOX) as the secondary template. The DOX imprinted cavity can stably carry the drug and the epitope-imprinted cavity allows FMIPs to actively recognize the P32-positive 4T1 cancer cells. The targeted therapeutic effect of DOX-loaded FMIPs (FMIPs@DOX) is investigated in vitro and in vivo. The FMIPs@DOX only causes apoptosis in 4T1 cancer cells compared to C8161 cells (expressing low level of P32). In addition, highly effective inhibition of 4T1 malignant breast tumors using FMIPs@DOX is achieved in the model of tumor-bearing mice. Importantly, the antitumor effect achieved by intravenous injection of FMIPs@DOX is almost identical to that by intratumoral injection. Furthermore, the FMIPs can serve as a targeted fluorescence imaging agent due to the high specificity of the epitope-imprinted cavity and the stable fluorescence of the embedded silicon nanoparticles. These results demonstrate the effectiveness of the FMIPs for active targeted drug delivery and imaging. Furthermore, the FMIPs provide a direction for drug-loaded nanocarrier.
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Affiliation(s)
- Ya-Ting Qin
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China
| | - Hui Peng
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China
| | - Xi-Wen He
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China
| | - Wen-You Li
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China.,Collaborative Innovation Center of Chemical Science and Engineering (Tianjin) , Tianjin 300071 , China
| | - Yu-Kui Zhang
- College of Chemistry, Research Center for Analytical Sciences, State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Biosensing and Molecular Recognition , Nankai University , Tianjin 300071 , China.,National Chromatographic Research and Analysis Center , Dalian Institute of Chemical Physics, Chinese Academy of Sciences , Dalian 116023 , China
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The Increased PTK7 Expression Is a Malignant Factor in Cervical Cancer. DISEASE MARKERS 2019; 2019:5380197. [PMID: 30944666 PMCID: PMC6421733 DOI: 10.1155/2019/5380197] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 10/30/2018] [Accepted: 11/13/2018] [Indexed: 12/20/2022]
Abstract
Cervical cancer is one of the most common malignant neoplasms in gynecology. Protein tyrosine kinase 7 (PTK7) with an inactive kinase domain is an important regulator of multiple Wnt pathways under normal and various pathological conditions and overexpressed in various tumors; however, the clinical and biological significance of PTK7 in cervical cancer is still unknown. In the present study, the protein expression level of PTK7 was detected in clinical cervical cancer patient samples, and the relationship between PTK7 expression and clinicopathological features was analyzed. In addition, the Kaplan-Meier method was performed to estimate the overall survival (OS) and progression-free survival (PFS) of patients to investigate the clinicopathological significance of PTK7 expression. Functional assays demonstrated that knocking down PTK7 might inhibit the ability of cancer cells to proliferate and invade or migrate, both in vivo and in vitro. Thus, PTK7 might serve as a potential target for cervical cancer.
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Wan LY, Yuan WF, Ai WB, Ai YW, Wang JJ, Chu LY, Zhang YQ, Wu JF. An exploration of aptamer internalization mechanisms and their applications in drug delivery. Expert Opin Drug Deliv 2019; 16:207-218. [PMID: 30691313 DOI: 10.1080/17425247.2019.1575808] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/25/2019] [Indexed: 12/21/2022]
Abstract
INTRODUCTION As 'chemical antibodies', aptamers have some advantages, such as lack of immunogenicity, rapid tissue penetration, cell internalization and so on. Consequently, more and more aptamers have been screened out by the systematic evolution of ligands through exponential enrichment for the desired cells or membrane receptors. On the basis of the result, researchers use aptamers to guide drug targeting to the desired cells and internalization in vivo. AREAS COVERED In this review, we explore the mechanisms of cargo- or aptamer-mediated internalization, and then briefly summarize five strategies for exploring the mechanism of aptamer internalization. Finally, we focus on four types of applications involving aptamer internalization: aptamers as drugs, aptamers as chemical drug-delivery systems, aptamer-based chimeras and aptamer-conjugated nanoparticles or block copolymer micelles. EXPERT OPINION Two aptamer-internalization mechanisms are known, namely receptor-mediated endocytosis and macropinocytosis. The latter mechanism, which is has only been verified in the internalization of nucleolin aptamer shuttles between the nucleus and cytoplasm, may be important for nuclear internalization and cargo molecule escape from the endosomal compartment. Thus, it is feasible to use some strategies to further explore the macropinocytosis internalization mechanism and then to screen for aptamers similar to the nucleolin aptamer for use with the desired cell types as a targeted delivery tool.
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Affiliation(s)
- Lin-Yan Wan
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Wen-Fang Yuan
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Wen-Bing Ai
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
| | - Yao-Wei Ai
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
| | - Jiao-Jiao Wang
- c Medical College , China Three Gorges University , Yichang , China
| | - Liang-Yin Chu
- e School of Chemical Engineering , Sichuan University , Chengdu , China
| | - Yan-Qiong Zhang
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
| | - Jiang-Feng Wu
- a The People's Hospital , China Three Gorges University , Yichang , China
- b Institute of Organ Fibrosis and Targeted Drug Delivery , China Three Gorges University , Yichang , China
- c Medical College , China Three Gorges University , Yichang , China
- d The Yiling Hospital of Yichang , Yichang , Hubei , China
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Transition metal complexes based aptamers as optical diagnostic tools for disease proteins and biomolecules. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.09.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Shen Z, Ye H, Yi X, Li Y. Membrane Wrapping Efficiency of Elastic Nanoparticles during Endocytosis: Size and Shape Matter. ACS NANO 2019; 13:215-228. [PMID: 30557506 DOI: 10.1021/acsnano.8b05340] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Using coarse-grained molecular dynamics simulations, we systematically investigate the receptor-mediated endocytosis of elastic nanoparticles (NPs) with different sizes, ranging from 25 to 100 nm, and shapes, including sphere-like, oblate-like, and prolate-like. Simulation results provide clear evidence that the membrane wrapping efficiency of NPs during endocytosis is a result of competition between receptor diffusion kinetics and thermodynamic driving force. The receptor diffusion kinetics refer to the kinetics of receptor recruitment that are affected by the contact edge length between the NP and membrane. The thermodynamic driving force represents the amount of required free energy to drive NPs into a cell. Under the volume constraint of elastic NPs, the soft spherical NPs are found to have similar contact edge lengths to rigid ones and to less efficiently be fully wrapped due to their elastic deformation. Moreover, the difference in wrapping efficiency between soft and rigid spherical NPs increases with their sizes, due to the increment of their elastic energy change. Furthermore, because of its prominent large contact edge length, the oblate ellipsoid is found to be the least sensitive geometry to the variation in NP's elasticity among the spherical, prolate, and oblate shapes during the membrane wrapping. In addition, simulation results indicate that conflicting experimental observations on the efficiency of cellular uptake of elastic NPs could be caused by their different mechanical properties. Our simulations provide a detailed mechanistic understanding about the influence of NPs' size, shape, and elasticity on their membrane wrapping efficiency, which serves as a rational guidance for the design of NP-based drug carriers.
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Affiliation(s)
- Zhiqiang Shen
- Department of Mechanical Engineering , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Huilin Ye
- Department of Mechanical Engineering , University of Connecticut , Storrs , Connecticut 06269 , United States
| | - Xin Yi
- Department of Mechanics and Engineering Science, College of Engineering, and Beijing Innovation Center for Engineering Science and Advanced Technology , Peking University , Beijing 100871 , China
| | - Ying Li
- Department of Mechanical Engineering and Institute of Materials Science , University of Connecticut , Storrs , Connecticut 06269 , United States
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Fan Y, Li L, Lu M, Si H, Tang B. In situ fluorescent profiling of living cell membrane proteins at a single-molecule level. Chem Commun (Camb) 2019; 55:4043-4046. [DOI: 10.1039/c9cc00244h] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A signal amplification method is developed for visualization analysis of membrane proteins on living cells at a single-molecule level.
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Affiliation(s)
- Yuanyuan Fan
- College of Chemistry
- Chemical Engineering and Materials Science
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
| | - Lu Li
- College of Chemistry
- Chemical Engineering and Materials Science
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
| | - Meng Lu
- College of Chemistry
- Chemical Engineering and Materials Science
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
| | - Haibin Si
- College of Chemistry
- Chemical Engineering and Materials Science
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
| | - Bo Tang
- College of Chemistry
- Chemical Engineering and Materials Science
- Key Laboratory of Molecular and Nano Probes
- Ministry of Education
- Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong
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26
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Zhou N, Su F, Guo C, He L, Jia Z, Wang M, Jia Q, Zhang Z, Lu S. Two-dimensional oriented growth of Zn-MOF-on-Zr-MOF architecture: A highly sensitive and selective platform for detecting cancer markers. Biosens Bioelectron 2019; 123:51-58. [DOI: 10.1016/j.bios.2018.09.079] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/03/2018] [Accepted: 09/21/2018] [Indexed: 11/26/2022]
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Kim DH, Park S, Kim DK, Jeong MG, Noh J, Kwon Y, Zhou K, Lee NK, Ryu SH. Direct visualization of single-molecule membrane protein interactions in living cells. PLoS Biol 2018; 16:e2006660. [PMID: 30543635 PMCID: PMC6307816 DOI: 10.1371/journal.pbio.2006660] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 12/27/2018] [Accepted: 11/23/2018] [Indexed: 12/11/2022] Open
Abstract
Interactions between membrane proteins are poorly understood despite their importance in cell signaling and drug development. Here, we present a co-immunoimmobilization assay (Co-II) enabling the direct observation of membrane protein interactions in single living cells that overcomes the limitations of currently prevalent proximity-based indirect methods. Using Co-II, we investigated the transient homodimerizations of epidermal growth factor receptor (EGFR) and beta-2 adrenergic receptor (β2-AR) in living cells, revealing the differential regulation of these receptors’ dimerizations by molecular conformations and microenvironment in a plasma membrane. Co-II should provide a simple, rapid, and robust platform for visualizing both weak and strong protein interactions in the plasma membrane of living cells. Protein–protein interactions govern cellular processes. The majority of these physical interactions previously identified are strong/permanent interactions, which typically remain unbroken even after purification. The weak/transient interactions between proteins have been implicated in the control of dynamic cellular process that maintain cellular homeostasis and trigger signaling cascades upon environmental changes. However, these interactions are poorly investigated, mainly due to the methodological limitations. Here, we have developed a co-immunoimmobilization assay called Co-II that enables the direct visualization of protein–protein interactions in the membrane of living cells at the single-molecule level. Co-II is based on the intuitive concept that if the protein of interest is immobilized, the interacting protein must be co-immobilized. The use of intrinsic protein diffusivity fundamentally overcomes the limitations of proximity-based methods. Using Co-II, we study the transient homodimerizations of EGFR and β2-AR in living cells, which have been implicated in several types of cancers and heart diseases. We show that the dimerization of these receptors is differently regulated by molecular conformations and the microenvironment in the plasma membrane.
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Affiliation(s)
- Do-Hyeon Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Soyeon Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Dong-Kyun Kim
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Min Gyu Jeong
- Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Jungeun Noh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Yonghoon Kwon
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Kai Zhou
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Nam Ki Lee
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, Pohang, Republic of Korea
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- * E-mail: (SHR); (NKL)
| | - Sung Ho Ryu
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Republic of Korea
- * E-mail: (SHR); (NKL)
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Lyu Y, Teng IT, Zhang L, Guo Y, Cai R, Zhang X, Qiu L, Tan W. Comprehensive Regression Model for Dissociation Equilibria of Cell-Specific Aptamers. Anal Chem 2018; 90:10487-10493. [PMID: 30039967 PMCID: PMC6522138 DOI: 10.1021/acs.analchem.8b02484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
A comprehensive nonlinear regression model for dissociation equilibria of cell-specific aptamers is proposed by considering the effect of receptor expression level. Benefiting from the global regression of simultaneous equations, the fitted parameters reach a very significant level, indicating the statistical validity of this updated model. According to the fitting results, we found that dissociation constants fitted using the previous model are obviously larger than the updated values, which can be explained by the effect of receptor number on curve fitting. In addition, equivalent receptor density can be estimated using the updated model, which may lead to some new judgments about reported results of cell-SELEX.
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Affiliation(s)
- Yifan Lyu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Yian Guo
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Ren Cai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Liping Qiu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, People’s Republic of China
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, People’s Republic of China
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Inter-face, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida 32611-7200, United States
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Lei Y, Qiao Z, Tang J, He X, Shi H, Ye X, Yan L, He D, Wang K. DNA nanotriangle-scaffolded activatable aptamer probe with ultralow background and robust stability for cancer theranostics. Theranostics 2018; 8:4062-4071. [PMID: 30128036 PMCID: PMC6096399 DOI: 10.7150/thno.24683] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Accepted: 06/16/2018] [Indexed: 12/23/2022] Open
Abstract
Activatable aptamers have emerged as promising molecular tools for cancer theranostics, but reported monovalent activatable aptamer probes remain problematic due to their unsatisfactory affinity and poor stability. To address this problem, we designed a novel theranostic strategy of DNA nanotriangle-scaffolded multivalent split activatable aptamer probe (NTri-SAAP), which combines advantages of programmable self-assembly, multivalent effect and target-activatable architecture. Methods: NTri-SAAP was assembled by conjugating multiple split activatable aptamer probes (SAAPs) on a planar DNA nanotriangle scaffold (NTri). Leukemia CCRF-CEM cell line was used as the model to investigate its detection, imaging and therapeutic effect both in vitro and in vivo. Binding affinity and stability were evaluated using flow cytometry and nuclease resistance assays. Results: In the free state, NTri-SAAP was stable with quenched signals and loaded doxorubicin, while upon binding to target cells, it underwent a conformation change with fluorescence activation and drug release after internalization. Compared to monovalent SAAP, NTri-SAAP displayed greatly-improved target binding affinity, ultralow nonspecific background and robust stability in harsh conditions, thus affording contrast-enhanced tumor imaging within an extended time window of 8 h. Additionally, NTri-SAAP increased doxorubicin loading capacity by ~5 times, which further realized a high anti-tumor efficacy in vivo with 81.95% inhibition but no obvious body weight loss. Conclusion: These results strongly suggest that the biocompatible NTri-SAAP strategy would provide a promising platform for precise and high-quality theranostics.
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Li W, Wang L, Wang Y, Jiang W. Binding-induced nicking site reconstruction strategy for quantitative detection of membrane protein on living cell. Talanta 2018; 189:383-388. [PMID: 30086935 DOI: 10.1016/j.talanta.2018.06.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/06/2018] [Accepted: 06/09/2018] [Indexed: 01/01/2023]
Abstract
Here, a binding-induced nicking site reconstruction strategy has been fabricated for quantitative detection of membrane protein on living cell. Taking protein tyrosine kinase-7 (PTK7) as model analyst, first, an aptamer probe was designed with an aptamer sequence, a trigger sequence and a nicking site. In the absence of PTK7, the aptamer sequence could partially hybridize with the trigger sequence, forming a stem-loop structure. And the two complementary sequences of the nicking site were separated, which could not be recognized by nicking enzyme. In the presence of PTK7, the aptamer probe and PTK7 binding caused the reconstruction of the probe, leading to the hybridization of the two separated nicking site sequences. Then, the nicking site could be identified and nicked, yielding the release of the trigger sequence. Next, the trigger sequence could initiate the homogeneous cascade amplification, producing multiple G-quadruplex structures. By inserting the N-Methyl Mesoporphyrin IX (NMM), enhanced fluorescence signal could be acquired. Through the binding-induced nicking site reconstruction, the trigger sequence could be released on the surface of living cell and became more accessible. By combining the cascade rolling circle amplification (RCA) and hybridization chain reaction (HCR), high sensitivity was achieved with a detection limit of 0.3 fM. Moreover, Quantitative assay of PTK7 on living cancer cells and normal cells were performed, suggesting that the proposed method was sensitive enough to detect changes in PTK7 expression. Thus, this strategy provided a novel and reliable method for membrane protein expression assay on living cell.
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Affiliation(s)
- Wei Li
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China
| | - Lei Wang
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China
| | - Yan Wang
- The 88th Hospital of PLA, 270100 Tai'an, PR China.
| | - Wei Jiang
- Key Laboratory of Natural Products Chemical Biological, Ministry of Education, School of Pharmacy, Shandong University, 250012 Jinan, PR China; School of Chemistry and Chemical Engineering, Shandong University, 250100 Jinan, PR China.
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Jiang Y, Shi M, Liu Y, Wan S, Cui C, Zhang L, Tan W. Aptamer/AuNP Biosensor for Colorimetric Profiling of Exosomal Proteins. Angew Chem Int Ed Engl 2017; 56:11916-11920. [PMID: 28834063 PMCID: PMC5912341 DOI: 10.1002/anie.201703807] [Citation(s) in RCA: 346] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Indexed: 12/30/2022]
Abstract
Exosomes constitute an emerging biomarker for cancer diagnosis because they carry multiple proteins that reflect the origins of parent cells. Assessing exosome surface proteins provides a powerful means of identifying a combination of biomarkers for cancer diagnosis. We report a sensor platform that profiles exosome surface proteins in minutes by the naked eye. The sensor consists of a gold nanoparticle (AuNP) complexed with a panel of aptamers. The complexation of aptamers with AuNPs protects the nanoparticles from aggregating in a high-salt solution. In the presence of exosomes, the non-specific and weaker binding between aptamers and the AuNP is broken, and the specific and stronger binding between exosome surface protein and the aptamer displaces aptamers from the AuNP surface and results in AuNP aggregation. This aggregation results in a color change and generates patterns for the identification of multiple proteins on the exosome surface.
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Affiliation(s)
- Ying Jiang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Muling Shi
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Yuan Liu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Shuo Wan
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Cheng Cui
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Liqin Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Life Sciences, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Department of Chemistry, Department of Physiology and Functional Genomics, Center for Research at Bio/nano Interface, UF Health Cancer Center, UF Genetics Institute, University of Florida, Gainesville, FL, 32611, USA
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Chen K, Georgiev TZ, Sheng W, Zheng X, Varillas JI, Zhang J, Hugh Fan Z. Tumor cell capture patterns around aptamer-immobilized microposts in microfluidic devices. BIOMICROFLUIDICS 2017; 11:054110. [PMID: 29034054 PMCID: PMC5624804 DOI: 10.1063/1.5000707] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 09/15/2017] [Indexed: 05/04/2023]
Abstract
Circulating tumor cells (CTCs) have shown potential for cancer diagnosis and prognosis. Affinity-based CTC isolation methods have been proved to be efficient for CTC detection in clinical blood samples. One of the popular choices for affinity-based CTC isolation is to immobilize capture agents onto an array of microposts in microchannels, providing high CTC capture efficiency due to enhanced interactions between tumor cells and capture agents on the microposts. However, how the cells interact with microposts under different flow conditions and what kind of capture pattern results from the interactions have not been fully investigated; a full understanding of these interactions will help to design devices and choose experimental conditions for higher CTC capture effeciency. We report our study on their interaction and cell distribution patterns around microposts under different flow conditions. Human acute lymphoblastic leukemia cells (CCRF-CEM) were used as target cancer cells in this study, while the Sgc8 aptamer that has specific binding with CCRF-CEM cells was employed as a capture agent. We investigated the effects of flow rates and micropost shapes on the cell capture efficiency and capture patterns on microposts. While a higher flow rate decreased cell capture efficiency, we found that the capture pattern around microposts also changed, with much more cells captured in the front half of a micropost than at the back half. We also found the ratio of cells captured on microposts to the cells captured by both microposts and channel walls increased as a function of the flow rate. We compared circular microposts with an elliptical shape and found that the geometry affected the capture distribution around microposts. In addition, we have developed a theoretical model to simulate the interactions between tumor cells and micropost surfaces, and the simulation results are in agreement with our experimental observation.
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Affiliation(s)
- Kangfu Chen
- Interdisciplinary Microsystems Group (IMG), Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, USA
| | - Teodor Z Georgiev
- Interdisciplinary Microsystems Group (IMG), Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, USA
| | - Weian Sheng
- Interdisciplinary Microsystems Group (IMG), Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, USA
| | - Xiangjun Zheng
- Interdisciplinary Microsystems Group (IMG), Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, USA
| | - Jose I Varillas
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, P.O. Box 116131, Gainesville, Florida 32611, USA
| | - Jinling Zhang
- Interdisciplinary Microsystems Group (IMG), Department of Mechanical and Aerospace Engineering, University of Florida, P.O. Box 116250, Gainesville, Florida 32611, USA
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Liu Z, Chen W, Han Y, Ouyang J, Chen M, Hu S, Deng L, Liu YN. A label-free sensitive method for membrane protein detection based on aptamer and AgNCs transfer. Talanta 2017; 175:470-476. [PMID: 28842019 DOI: 10.1016/j.talanta.2017.07.071] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/14/2017] [Accepted: 07/23/2017] [Indexed: 11/30/2022]
Abstract
Recently, membrane proteins have been considered as candidate cancer biomarkers and drug targets, due to their important roles in numerous physiological processes. Therefore, a facile, sensitive and quantitative detection of the membrane proteins is crucial for better understanding their roles in cancer cells and further validating their function in clinical research. We report a highly facile and sensitive detection method for membrane proteins on living cells in situ based on membrane protein-triggered release of cytosine (C)-rich single-stranded DNA (ssDNA) sequences, and the subsequent silver nanoclusters (AgNCs) transfer from polymer to C-rich ssDNA. The high-quantum yield and stable DNA-AgNCs allow the accurate detection of membrane proteins with facile operations and a common fluorescence spectrophotometer. The detection of protein tyrosine kinase-7 (PTK7), a membrane protein model, displays a response range from 30pM to 2nM with a detection limit of 12pM. The expression of PTK7 on single Hela cell and CCRF-CEM cell was calculated to be 7.5 × 10-19mol and 1.8 × 10-18mol, respectively. Given the simple and facile operation of this method, this detection platform can be applied as a universal strategy for ultrasensitive detection of membrane protein on cell in situ.
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Affiliation(s)
- Zhenjun Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Wansong Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Yajin Han
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Jiang Ouyang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Min Chen
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Shengqiang Hu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China
| | - Liu Deng
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China.
| | - You-Nian Liu
- College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, PR China.
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Effect of probe diffusion on the SOFI imaging accuracy. Sci Rep 2017; 7:44665. [PMID: 28333166 PMCID: PMC5363082 DOI: 10.1038/srep44665] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/13/2017] [Indexed: 01/19/2023] Open
Abstract
Live-cell super-resolution fluorescence imaging is becoming commonplace for exploring biological systems, though sample dynamics can affect the imaging quality. In this work we evaluate the effect of probe diffusion on super-resolution optical fluctuation imaging (SOFI), using a theoretical model and numerical simulations based on the imaging of live cells labelled with photochromic fluorescent proteins. We find that, over a range of physiological conditions, fluorophore diffusion results in a change in the amplitude of the SOFI signal. The magnitude of this change is approximately proportional to the on-time ratio of the fluorophores. However, for photochromic fluorescent proteins this effect is unlikely to present a significant distortion in practical experiments in biological systems. Due to this lack of distortions, probe diffusion strongly enhances the SOFI imaging by avoiding spatial undersampling caused by the limited labeling density.
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36
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Zhao LJ, Yu RJ, Ma W, Han HX, Tian H, Qian RC, Long YT. Sensitive detection of protein biomarkers using silver nanoparticles enhanced immunofluorescence assay. Theranostics 2017; 7:876-883. [PMID: 28382160 PMCID: PMC5381250 DOI: 10.7150/thno.17575] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023] Open
Abstract
Detection of biomarkers is extremely important for the early diagnosis of diseases. Here, we developed an easy and highly sensitive fluorescence detection system for the determination of biomarkers by combining the rapid separation of magnetic beads and silver nanoparticles labeled antibodies. An ultrasensitive silver ions fluorescence probe 3', 6'-bis (diethylamino)-2-(2-iodoethyl) spiro[isoindoline-1, 9'-xanthen]-3-one (Ag+-FP) was applied to immunoassay. A significant signal amplification was achieved as the AgNPs can be dissolved by H2O2 and generate numerous Ag+, which would turn "on" the fluorescence of Ag+-FP. Using α-fetoprotein (AFP) and C-reactive protein (CRP) as target analytes, good linear responses were obtained from 0.1 to 10 ng mL-1 and the limits of detection (LOD) were as low as 70 pg·mL-1 and 30 pg·mL-1, respectively. In addition, the developed system was further evaluated for the detection of real samples including 30 positive serum specimens obtained from hepatocarcinoma patients and 20 negative serum samples, and performs as well as the commercial electrochemiluminescence immunoassay (ECLI) method with less cost and more convenience. Thus, the designed detection system can be used as a promising platform for the detection of a variety of biomarkers and served as a powerful tool in clinical diagnosis.
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Affiliation(s)
- Li-Jun Zhao
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
| | - Ru-Jia Yu
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
| | - Wei Ma
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
| | - Huan-Xing Han
- Translational Medicine Center, Changzheng Hospital, the Second Military Medical University, P. R. China
| | - He Tian
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
| | - Ruo-Can Qian
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
| | - Yi-Tao Long
- Key Laboratory for Advanced Materials and Department of Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, P. R. China
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Yi X, Gao H. Kinetics of receptor-mediated endocytosis of elastic nanoparticles. NANOSCALE 2017; 9:454-463. [PMID: 27934990 DOI: 10.1039/c6nr07179a] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
It is now widely recognized that mechanical properties play critical roles in the cell uptake of nanomaterials. Here we conduct a theoretical study on the kinetics of receptor-mediated endocytosis of elastic nanoparticles that is limited by receptor diffusion, specifically focusing on how the uptake rate depends on the nanoparticle stiffness and size, membrane tension and binding strength between membrane receptors and ligands grafted on the nanoparticle surface. It is shown that, while soft nanoparticles are energetically less prone to full wrapping than stiff ones, the wrapping of the former is kinetically faster than that of the latter. Spherical and cylindrical elastic nanoparticles show dramatic differences in the effect of stiffness on the uptake rate. Additional theoretical analysis is performed to investigate the role of the stochastic receptor-ligand binding in the endocytosis of elastic nanoparticles. The relation between the uptake efficiency and uptake proneness is discussed. This study provides new insight into the elasticity effects on cell uptake and may serve as a design guideline for the controlled endocytosis and diagnostics delivery.
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Affiliation(s)
- Xin Yi
- School of Engineering, Brown University, Providence, Rhode Island 02912, USA.
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Alfavian H, Mousavi Gargari SL, Rasoulinejad S, Medhat A. Development of a DNA aptamer that binds specifically to group A Streptococcus serotype M3. Can J Microbiol 2016; 63:160-168. [PMID: 28121169 DOI: 10.1139/cjm-2016-0495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories. Therefore, development of a new M-typing technique is needed. Aptamers with the ability to detect their target with a high degree of accuracy and specificity can be ideal candidates for specific M-typing of Streptococcus pyogenes. In this study DNA aptamers with a high binding affinity towards S. pyogenes serotype M3 were selected through 12 iterative rounds of the Systematic Evolution of Ligands by EXponential (SELEX) enrichment procedure using live cells as a target. We monitored the progress of the SELEX procedure by flow cytometry analysis. Of several aptamer sequences analyzed, 12L18A showed the highest binding efficiency towards S. pyogenes type M3, with an apparent dissociation constant (Kd) of 7.47 ± 1.72 pmol/L being the lowest. Therefore the isolated aptamer can be used in any tool, such as a biosensor, for the detection of S. pyogenes and can be used in the development of a novel M-typing system.
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Affiliation(s)
- Hanif Alfavian
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | | | - Samaneh Rasoulinejad
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Arvin Medhat
- b GENEXIR Biopharma, a knowledge-based company at Pasteur Institute of Iran Health Technology Park, Tehran, Iran
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Lin S, He B, Yang C, Leung CH, Mergny JL, Ma DL. Luminescence switch-on assay of interferon-gamma using a G-quadruplex-selective iridium(III) complex. Chem Commun (Camb) 2016; 51:16033-6. [PMID: 26399215 DOI: 10.1039/c5cc06655g] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In this study, we synthesized a series of 9 luminescent iridium(III) complexes and studied their ability to function as luminescent probes for G-quadruplex DNA. The iridium(III) complex 8 [Ir(pbtz)2(dtbpy)]PF6 (where pbtz = 2-phenylbenzo[d]thiazole; dtbpy = 4,4'-di-tert-butyl-2,2'-bipyridine) showed high selectivity for G-quadruplex DNA over single-stranded and double-stranded DNA, and was subsequently utilized for the development of a label-free oligonucleotide-based assay for interferon-gamma (IFN-γ), an important biomarker for a range of immune and infectious diseases, in aqueous solution. We further demonstrated that this assay could monitor IFN-γ levels even in the presence of cellular debris. This assay represents the first G-quadruplex-based assay for IFN-γ detection described in the literature.
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Affiliation(s)
- Sheng Lin
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Bingyong He
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China.
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China.
| | - Jean-Louis Mergny
- University of Bordeaux, ARNA laboratory, Bordeaux, France. and INSERM, U869, IECB, Pessac, France
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. and Partner State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China
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40
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Koschut D, Richert L, Pace G, Niemann HH, Mély Y, Orian-Rousseau V. Live cell imaging shows hepatocyte growth factor-induced Met dimerization. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1863:1552-8. [PMID: 27094128 DOI: 10.1016/j.bbamcr.2016.04.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 04/01/2016] [Accepted: 04/15/2016] [Indexed: 12/24/2022]
Abstract
The canonical model of receptor tyrosine kinase (RTK) activation assumes that ligand-induced dimerization of inactive receptor monomers is a prerequisite for autophosphorylation. For several RTK families, recent results of fluorescence microscopy provided evidence for preformed receptor dimers that may or may not require ligand binding for kinase activity. Here we report, for the first time, the application of advanced quantitative fluorescence microscopy techniques to study changes in the oligomerization state of the RTK Met in response to stimulation by its endogenous ligand hepatocyte growth factor (HGF). We used inducible C-terminal fusions between Met and enhanced green fluorescent protein (EGFP) or red fluorescent protein (RFP) in combination with fluorescence resonance energy transfer (FRET)-based fluorescence-lifetime imaging microscopy (FLIM) and fluorescence correlation spectroscopy (FCS). A small fraction of HGF-independent Met dimers appeared to be present in cells even at low receptor density. At high receptor density, both the fraction of Met dimers and the level of Met autophosphorylation increased in the absence of HGF. Stimulation with HGF at low receptor density significantly increased the fraction of Met dimers on live cells. We found no indications of Met oligomers larger than dimers. Our findings thus confirm a model of Met activation through HGF-induced dimerization and at the same time they support previous reports of Met dimers in unstimulated cells. The tools established in this work will be useful to further characterize the mechanism of Met activation and to define the contribution of co-receptors.
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Affiliation(s)
- David Koschut
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Postfach 3640, 76021 Karlsruhe, Germany
| | - Ludovic Richert
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie 74 route du Rhin, 67401 Illkirch, France
| | - Giuseppina Pace
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Postfach 3640, 76021 Karlsruhe, Germany
| | - Hartmut H Niemann
- Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany
| | - Yves Mély
- UMR 7213 CNRS, Laboratoire de Biophotonique et Pharmacologie, Faculté de Pharmacie 74 route du Rhin, 67401 Illkirch, France
| | - Véronique Orian-Rousseau
- Karlsruhe Institute of Technology (KIT), Institute of Toxicology and Genetics (ITG), Postfach 3640, 76021 Karlsruhe, Germany.
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41
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Lyu Y, Chen G, Shangguan D, Zhang L, Wan S, Wu Y, Zhang H, Duan L, Liu C, You M, Wang J, Tan W. Generating Cell Targeting Aptamers for Nanotheranostics Using Cell-SELEX. Am J Cancer Res 2016; 6:1440-52. [PMID: 27375791 PMCID: PMC4924511 DOI: 10.7150/thno.15666] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2016] [Accepted: 05/12/2016] [Indexed: 12/21/2022] Open
Abstract
Detecting and understanding changes in cell conditions on the molecular level is of great importance for the accurate diagnosis and timely therapy of diseases. Cell-based SELEX (Systematic Evolution of Ligands by EXponential enrichment), a foundational technology used to generate highly-specific, cell-targeting aptamers, has been increasingly employed in studies of molecular medicine, including biomarker discovery and early diagnosis/targeting therapy of cancer. In this review, we begin with a mechanical description of the cell-SELEX process, covering aptamer selection, identification and identification, and aptamer characterization; following this introduction is a comprehensive discussion of the potential for aptamers as targeting moieties in the construction of various nanotheranostics. Challenges and prospects for cell-SELEX and aptamer-based nanotheranostic are also discussed.
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42
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De Michele C, De Los Rios P, Foffi G, Piazza F. Simulation and Theory of Antibody Binding to Crowded Antigen-Covered Surfaces. PLoS Comput Biol 2016; 12:e1004752. [PMID: 26967624 PMCID: PMC4788199 DOI: 10.1371/journal.pcbi.1004752] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 01/12/2016] [Indexed: 01/08/2023] Open
Abstract
In this paper we introduce a fully flexible coarse-grained model of immunoglobulin G (IgG) antibodies parametrized directly on cryo-EM data and simulate the binding dynamics of many IgGs to antigens adsorbed on a surface at increasing densities. Moreover, we work out a theoretical model that allows to explain all the features observed in the simulations. Our combined computational and theoretical framework is in excellent agreement with surface-plasmon resonance data and allows us to establish a number of important results. (i) Internal flexibility is key to maximize bivalent binding, flexible IgGs being able to explore the surface with their second arm in search for an available hapten. This is made clear by the strongly reduced ability to bind with both arms displayed by artificial IgGs designed to rigidly keep a prescribed shape. (ii) The large size of IgGs is instrumental to keep neighboring molecules at a certain distance (surface repulsion), which essentially makes antigens within reach of the second Fab always unoccupied on average. (iii) One needs to account independently for the thermodynamic and geometric factors that regulate the binding equilibrium. The key geometrical parameters, besides excluded-volume repulsion, describe the screening of free haptens by neighboring bound antibodies. We prove that the thermodynamic parameters govern the low-antigen-concentration regime, while the surface screening and repulsion only affect the binding at high hapten densities. Importantly, we prove that screening effects are concealed in relative measures, such as the fraction of bivalently bound antibodies. Overall, our model provides a valuable, accurate theoretical paradigm beyond existing frameworks to interpret experimental profiles of antibodies binding to multi-valent surfaces of different sorts in many contexts. Antibodies are the main working horses of the human immune system. Remarkably, no matter the size or the shape of the pathological intruders, these extremely flexible three-lobe molecules are able to form a complex, thus eliciting an immune response. What makes antibodies so effective? To answer this and other questions, we have developed a simplified computational scheme to simulate the dynamics of many antibodies interacting with each other and with antigens. Coarse-grained models are a great opportunity, as they give access to a true multi-scale approach to biologically relevant problems. In this work, our innovative method allowed us to simulate the binding process of many antibodies to surface-adsorbed antigens. This led us to elucidate and quantify many important physical aspects of their biological function in agreement with experiments, such as the role of their flexibility and crowding effects at the hapten-covered surface, which were shown to finely regulate the avidity.
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Affiliation(s)
| | - Paolo De Los Rios
- Institute of Theoretical Physics, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Giuseppe Foffi
- Laboratoire de Physique des Solides (LPS), UMR8502, Université Paris sud, Orsay, France
| | - Francesco Piazza
- Université d'Orléans, Centre de Biophysique Moléculaire, CNRS-UPR4301, Orléans, France
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43
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Fan D, Wu C, Wang K, Gu X, Liu Y, Wang E. A polydopamine nanosphere based highly sensitive and selective aptamer cytosensor with enzyme amplification. Chem Commun (Camb) 2015; 52:406-9. [PMID: 26526224 DOI: 10.1039/c5cc06754e] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With CCRF-CEM as the model cell, a highly sensitive and selective cytosensor was developed by taking advantage of polydopamine nanospheres for the first time. The strategies of aptamer/membrane protein recognition and Exonuclease III assisted cycle amplification were used for improving selectivity and sensitivity. The detection of limit reached was as low as 15 cells per mL.
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Affiliation(s)
- Daoqing Fan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, P. R. China.
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44
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Bamrungsap S, Treetong A, Apiwat C, Wuttikhun T, Dharakul T. SERS-fluorescence dual mode nanotags for cervical cancer detection using aptamers conjugated to gold-silver nanorods. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1639-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Lin S, Gao W, Tian Z, Yang C, Lu L, Mergny JL, Leung CH, Ma DL. Luminescence switch-on detection of protein tyrosine kinase-7 using a G-quadruplex-selective probe. Chem Sci 2015; 6:4284-4290. [PMID: 29218197 PMCID: PMC5707507 DOI: 10.1039/c5sc01320h] [Citation(s) in RCA: 154] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 05/17/2015] [Indexed: 12/22/2022] Open
Abstract
A series of luminescent iridium(iii) complexes were synthesised and evaluated for their ability to act as luminescent G-quadruplex-selective probes. The iridium(iii) complex 9 [Ir(pbi)2(5,5-dmbpy)]PF6 (where pbi = 2-phenyl-1H-benzo[d]imidazole; 5,5-dmbpy = 5,5'-dimethyl-2,2'-bipyridine) exhibited high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA, and was employed to construct a G-quadruplex-based assay for protein tyrosine kinase-7 (PTK7) in aqueous solution. PTK7 is an important biomarker for a range of leukemias and solid tumors. In the presence of PTK7, the specific binding of the sgc8 aptamer sequence triggers a structural transition and releases the G-quadruplex-forming sequence. The formation of the nascent G-quadruplex structure is then detected by the G-quadruplex-selective iridium(iii) complex with an enhanced luminescent response. Moreover, the application of the assay for detecting PTK7 in cellular debris and membrane protein extract was demonstrated. To our knowledge, this is the first G-quadruplex-based assay for PTK7.
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Affiliation(s)
- Sheng Lin
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Wei Gao
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Zeru Tian
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Lihua Lu
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
| | - Jean-Louis Mergny
- University of Bordeaux , ARNA Laboratory , Bordeaux , France .
- INSERM , U869 , IECB , Pessac , France
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine , Institute of Chinese Medical Sciences , University of Macau , Macao , China .
| | - Dik-Lung Ma
- Department of Chemistry , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China .
- Partner State Key Laboratory of Environmental and Biological Analysis , Hong Kong Baptist University , Kowloon Tong , Hong Kong , China
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46
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Wang YM, Wu Z, Liu SJ, Chu X. Structure-Switching Aptamer Triggering Hybridization Chain Reaction on the Cell Surface for Activatable Theranostics. Anal Chem 2015; 87:6470-4. [PMID: 26044187 DOI: 10.1021/acs.analchem.5b01634] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The ability to probe low-abundance biomolecules or transport a high-load drug in target cells is essential for biology and theranostics. We develop a novel activatable theranostic approach by using a structure-switching aptamer triggered hybridization chain reaction (HCR) on the cell surface, which for the first time creates an aptamer platform enabling real-time activation and amplification for fluorescence imaging and targeting therapy. The aptamer probe is designed not to initiate HCR in its free state but trigger HCR on binding to the target cell via structure switching. The HCR not only amplifies fluorescence signals from a fluorescence-quenched probe for activatable tumor imaging but also accumulates high-load prodrugs from a drug-labeled probe and induces its uptake and conversion into cisplatin in cells for selective tumor therapy. An in vitro assay shows that this approach affords efficient signal amplification for fluorescence detection of target protein tyrosine kinase-7 (PTK7) with a detection limit of 1 pM. Live cell studies reveal that it provides high-contrast fluorescence imaging and highly sensitive detection of tumor cells, while renders high-efficiency drug delivery into tumor cells via an endocytosis pathway. The results imply the potential of the developed approach as a promising platform for early stage diagnosis and precise therapy of tumors.
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Affiliation(s)
- Yu-Min Wang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Zhan Wu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Si-Jia Liu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, P. R. China
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47
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Xiong X, Lv Y, Chen T, Zhang X, Wang K, Tan W. Nucleic acid aptamers for living cell analysis. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:405-426. [PMID: 24896309 DOI: 10.1146/annurev-anchem-071213-015944] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as "chemical antibodies," have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.
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Affiliation(s)
- Xiangling Xiong
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
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48
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Li L, Wang Q, Feng J, Tong L, Tang B. Highly sensitive and homogeneous detection of membrane protein on a single living cell by aptamer and nicking enzyme assisted signal amplification based on microfluidic droplets. Anal Chem 2014; 86:5101-7. [PMID: 24779994 DOI: 10.1021/ac500881p] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Membrane proteins play vital roles in numerous physiological functions. Recently, they have been considered as candidate biomarkers for cancer and recognized as major drug targets. So, accurate, sensitive, and high-throughput quantitative detection of the membrane proteins is crucial for better understanding their roles in cancer cells and further validating their function in clinical research. Here, we report a highly sensitive and homogeneous detection of membrane protein on single living cells by aptamer and nicking enzyme assisted fluorescence signal amplification in microfluidic droplets. The homogeneous reaction based on the membrane protein-triggered conformation alteration of hairpin probe can improve the detection accuracy with elimination of several washing and separation steps. The microfluidic system provides a high-throughput platform for the detection of a single cell, and the highly monodisperse droplet can function as an independent microreactor for the aptamer and nicking enzyme assisted fluorescence signal amplification, coordinating with the small volume of the confined space (a droplet), increased reaction rate, and highly sensitive detection of membrane protein on single cell can be reached.
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Affiliation(s)
- Lu Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Normal University , Jinan 250014, P. R. China
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49
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Recent applications of fluorescence correlation spectroscopy in live systems. FEBS Lett 2014; 588:3571-84. [PMID: 24726724 DOI: 10.1016/j.febslet.2014.03.056] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Revised: 03/29/2014] [Accepted: 03/31/2014] [Indexed: 11/20/2022]
Abstract
Fluorescence correlation spectroscopy (FCS) is a widely used technique in biophysics and has helped address many questions in the life sciences. It provides important advantages compared to other fluorescence and biophysical methods. Its single molecule sensitivity allows measuring proteins within biological samples at physiological concentrations without the need of overexpression. It provides quantitative data on concentrations, diffusion coefficients, molecular transport and interactions even in live organisms. And its reliance on simple fluorescence intensity and its fluctuations makes it widely applicable. In this review we focus on applications of FCS in live samples, with an emphasis on work in the last 5 years, in the hope to provide an overview of the present capabilities of FCS to address biologically relevant questions.
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50
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Huang C, Zhang Y, Yuan H, Gao H, Zhang S. Role of nanoparticle geometry in endocytosis: laying down to stand up. NANO LETTERS 2013; 13:4546-50. [PMID: 23972158 DOI: 10.1021/nl402628n] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nanoparticles (NPs) hold great promises for targeted disease diagnosis and therapy. Despite considerable progress in biomimetic design of NP-bioconjugates, the roles of NP size and shape in endocytosis are still not fully understood. Using an efficient coarse-grained molecular dynamics (CGMD) model, we simulate receptor-mediated endocytosis of NPs of various sizes and shapes. Our simulations demonstrate that both NP size and shape modulate the kinetics of endocytosis. For spherical NPs, there exists an optimal size at which endocytosis takes the shortest time. For a spherocylindrical NP with the initial upright docking position on the membrane plane, endocytosis proceeds through a laying-down-then-standing-up sequence. A free energy analysis reveals that NP size primarily determines whether endocytosis can complete, while NP shape breaks the symmetry of curvature energy landscape and hence dictates the endocytic pathway and the angle of entry. The findings shed light on the rational design of NP-based diagnostic and therapeutic agents with improved cellular targeting.
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Affiliation(s)
- Changjin Huang
- Department of Engineering Science and Mechanics, The Pennsylvania State University , University Park, Pennsylvania 16802, United States
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