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Ko T, Fumoto S, Kurosaki T, Nakashima M, Miyamoto H, Sasaki H, Nishida K. Interaction of γ-Polyglutamic Acid/Polyethyleneimine/Plasmid DNA Ternary Complexes with Serum Components Plays a Crucial Role in Transfection in Mice. Pharmaceutics 2024; 16:522. [PMID: 38675183 PMCID: PMC11053868 DOI: 10.3390/pharmaceutics16040522] [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: 02/21/2024] [Revised: 03/20/2024] [Accepted: 03/30/2024] [Indexed: 04/28/2024] Open
Abstract
Typical examples of non-viral vectors are binary complexes of plasmid DNA with cationic polymers such as polyethyleneimine (PEI). However, problems such as cytotoxicity and hemagglutination, owing to their positively charged surfaces, hinder their in vivo use. Coating binary complexes with anionic polymers, such as γ-polyglutamic acid (γ-PGA), can prevent cytotoxicity and hemagglutination. However, the role of interactions between these complexes and serum components in in vivo gene transfer remains unclear. In this study, we analyzed the contribution of serum components to in vivo gene transfer using PEI/plasmid DNA binary complexes and γ-PGA/PEI/plasmid DNA ternary complexes. In binary complexes, heat-labile components in the serum greatly contribute to the hepatic and splenic gene expression of the luciferase gene. In contrast, serum albumin and salts affected the hepatic and splenic gene expression in the ternary complexes. Changes in physicochemical characteristics, such as increased particle size and decreased absolute values of ζ-potential, might be involved in the enhanced gene expression. These findings would contribute to a better understanding of in vivo non-viral gene transfer using polymers, such as PEI and γ-PGA.
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Affiliation(s)
- Tomotaka Ko
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Shintaro Fumoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Tomoaki Kurosaki
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Moe Nakashima
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Hirotaka Miyamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Hitoshi Sasaki
- Institute of Tropical Medicine, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
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2
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Hu D, Fumoto S, Yoshikawa N, Peng J, Miyamoto H, Tanaka M, Nishida K. Diffusion coefficient of cationic liposomes during lipoplex formation determines transfection efficiency in HepG2 cells. Int J Pharm 2023; 637:122881. [PMID: 36963641 DOI: 10.1016/j.ijpharm.2023.122881] [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: 12/02/2022] [Revised: 02/21/2023] [Accepted: 03/19/2023] [Indexed: 03/26/2023]
Abstract
Cationic lipid-based lipoplexes are well-known for gene delivery. To determine the relationship between physicochemical characteristics and transfection efficiency, cationic liposomes of different sizes were prepared and incubated with plasmid DNA at different temperatures to form lipoplexes. We found that the liposome diffusion coefficient during lipoplex formation strongly correlated with the physicochemical characteristics of lipoplexes, accessibility of plasmid DNA in lipoplexes, and logarithm of gene expression per metabolic activity. Clathrin-mediated endocytosis was the major route for lipoplexes comprising 100 nm-liposomes, as reported previously. As liposome size increased, the major route shifted to lipid raft-mediated endocytosis. In addition, macropinocytosis was observed for all liposome sizes. The role of reactive oxygen species might depend on liposome size and endocytosis. Information from this study would be useful for understanding cationic lipoplex-mediated transfection.
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Affiliation(s)
- Die Hu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Shintaro Fumoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan.
| | - Naoki Yoshikawa
- Department of Pharmacy, University of Miyazaki Hospital, 5200 Kihara, Kiyotake-Cho, Miyazaki 889-1692, Japan
| | - Jianqing Peng
- The High Efficacy Application of Natural Medicinal Resources Engineering Center of Guizhou Province, School of Pharmaceutical Sciences, Guizhou Medical University, University Town, Guian New District, Guiyang, 550025, China
| | - Hirotaka Miyamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki 852-8501, Japan
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3
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Zambo B, Morlet B, Negroni L, Trave G, Gogl G. Native holdup (nHU) to measure binding affinities from cell extracts. SCIENCE ADVANCES 2022; 8:eade3828. [PMID: 36542723 PMCID: PMC9770967 DOI: 10.1126/sciadv.ade3828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Characterizing macromolecular interactions is essential for understanding cellular processes, yet most methods currently used to detect protein interactions from cells are qualitative. Here, we introduce the native holdup (nHU) approach to estimate equilibrium binding constants of protein interactions directly from cell extracts. Compared to other pull-down-based assays, nHU requires less sample preparation and can be coupled to any analytical methods as readouts, such as Western blotting or mass spectrometry. We use nHU to explore interactions of SNX27, a cargo adaptor of the retromer complex and find good agreement between in vitro affinities and those measured directly from cell extracts using nHU. We discuss the strengths and limitations of nHU and provide simple protocols that can be implemented in most laboratories.
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Affiliation(s)
- Boglarka Zambo
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
| | - Gilles Trave
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
| | - Gergo Gogl
- Équipe Labellisée Ligue 2015, Département de Biologie Structurale Intégrative, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258/CNRS UMR 7104/Université de Strasbourg, 1 rue Laurent Fries, BP 10142, Illkirch F-67404, France
- Corresponding author. (G.T.); (G.G.)
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4
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Elhabashy H, Merino F, Alva V, Kohlbacher O, Lupas AN. Exploring protein-protein interactions at the proteome level. Structure 2022; 30:462-475. [DOI: 10.1016/j.str.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/26/2021] [Accepted: 02/02/2022] [Indexed: 02/08/2023]
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5
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A Quantitative Systems Approach to Define Novel Effects of Tumour p53 Mutations on Binding Oncoprotein MDM2. Int J Mol Sci 2021; 23:ijms23010053. [PMID: 35008477 PMCID: PMC8744954 DOI: 10.3390/ijms23010053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/13/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022] Open
Abstract
Understanding transient protein interactions biochemically at the proteome scale remains a long-standing challenge. Current tools developed to study protein interactions in high-throughput measure stable protein complexes and provide binary readouts; they do not elucidate dynamic and weak protein interactions in a proteome. The majority of protein interactions are transient and cover a wide range of affinities. Nucleic acid programmable protein arrays (NAPPA) are self-assembling protein microarrays produced by freshly translating full-length proteins in situ on the array surface. Herein, we have coupled NAPPA to surface plasmon resonance imaging (SPRi) to produce a novel label-free platform that measures many protein interactions in real-time allowing the determination of the KDs and rate constants. The developed novel NAPPA-SPRi technique showed excellent ability to study protein-protein interactions of clinical mutants of p53 with its regulator MDM2. Furthermore, this method was employed to identify mutant p53 proteins insensitive to the drug nutlin-3, currently in clinical practice, which usually disrupts the p53-MDM2 interactions. Thus, significant differences in the interactions were observed for p53 mutants on the DNA binding domain (Arg-273-Cys, Arg-273-His, Arg-248-Glu, Arg-280-Lys), on the structural domain (His-179-Tyr, Cys-176-Phe), on hydrophobic moieties in the DNA binding domain (Arg-280-Thr, Pro-151-Ser, Cys-176-Phe) and hot spot mutants (Gly-245-Cys, Arg-273-Leu, Arg-248-Glu, Arg-248-Gly), which signifies the importance of point mutations on the MDM2 interaction and nutlin3 effect, even in molecular locations related to other protein activities.
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6
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Gao H, Wang J, Liu J, Ye S, Meng X, Song S, Wang C, Yu X, Zhu L, Wang H, Lei S, Yang Y. Peptoid Nanosheet-Based Sensing System for the Diagnosis and Surveillance of Amnestic Mild Cognitive Impairment and Alzheimer's Disease. ACS Chem Neurosci 2021; 12:4257-4264. [PMID: 34726371 DOI: 10.1021/acschemneuro.1c00613] [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] [Indexed: 02/08/2023] Open
Abstract
Alzheimer's disease (AD) is one of the most common neurodegenerative diseases characterized by progressive cognitive decline. Early diagnosis and dynamic monitoring are essential to the treatment and care of AD but challenging. Here we develop a noninvasive, blood-based AD detection method based on surface plasmonic resonance imaging (SPRi) technique. The functionalized sensing SPRi chips were constructed with self-assembled loop-displaying peptoid nanosheets to improve the detection sensitivity of plasma amyloid β42 (Aβ42). We analyze the plasma from 30 clinically diagnosed AD patients, 29 amnestic cognitive impairment (aMCI) patients, and 30 control individuals and demonstrate that this sensing system can significantly distinguish the three groups with high sensitivity and specificity. In the follow-up studies of the aMCI patients, we find that decrease in the binding signals in the patients correlates with the disease progression into AD whereas the almost unchanged signals correlate with stable disease remaining at aMCI status. These results show the capability of the peptoid-nanosheet-based SRPi sensing system for the early diagnosis and dynamic monitoring of AD.
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Affiliation(s)
- Houqian Gao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
| | - Jiali Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, School of Science & Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China
| | - Jingyi Liu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Siyuan Ye
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
- Department of Chemistry, Tsinghua University, Beijing 100084, P. R. China
| | - Xue Meng
- Beijing Key Laboratory of Translational Medicine for the Diagnosis and Treatment of Dementia, Peking University Sixth Hospital (Institute of Mental Health), NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders, Beijing 100190, China
| | - Shuya Song
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Xin Yu
- Beijing Key Laboratory of Translational Medicine for the Diagnosis and Treatment of Dementia, Peking University Sixth Hospital (Institute of Mental Health), NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders, Beijing 100190, China
| | - Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Huali Wang
- Beijing Key Laboratory of Translational Medicine for the Diagnosis and Treatment of Dementia, Peking University Sixth Hospital (Institute of Mental Health), NHC Key Laboratory of Mental Health, National Clinical Research Center for Mental Disorders, Beijing 100190, China
| | - Shengbin Lei
- Tianjin Key Laboratory of Molecular Optoelectronic Science, Department of Chemistry, School of Science & Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin 300072, P. R. China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
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7
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Yoshikawa N, Fumoto S, Yoshikawa K, Hu D, Okami K, Kato R, Nakashima M, Miyamoto H, Nishida K. Interaction of Lipoplex with Albumin Enhances Gene Expression in Hepatitis Mice. Pharmaceutics 2020; 12:E341. [PMID: 32290201 PMCID: PMC7238045 DOI: 10.3390/pharmaceutics12040341] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/04/2020] [Accepted: 04/09/2020] [Indexed: 12/14/2022] Open
Abstract
Understanding the in vivo fate of lipoplex, which is composed of cationic liposomes and DNA, is an important issue toward gene therapy. In disease conditions, the fate of lipoplex might change compared with the normal condition. Here, we examined the contribution of interaction with serum components to in vivo transfection using lipoplex in hepatitis mice. Prior to administration, lipoplex was incubated with serum or albumin. In the liver, the interaction with albumin enhanced gene expression in hepatitis mice, while in the lung, the interaction with serum or albumin enhanced it. In normal mice, the interaction with albumin did not enhance hepatic and pulmonary gene expression. Furthermore, hepatic and pulmonary gene expression levels of albumin-interacted lipoplex were correlated with serum transaminases in hepatitis mice. The albumin interaction increased the hepatic accumulation of lipoplex and serum tumor necrosis factor-α level. We suggest that the interaction with albumin enhanced the inflammation level after the administration of lipoplex in hepatitis mice. Consequently, the enhancement of the inflammation level might enhance the gene expression level. Information obtained in the current study will be valuable toward future clinical application of the lipoplex.
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Affiliation(s)
- Naoki Yoshikawa
- Department of Pharmacy, University of Miyazaki Hospital, 5200 Kihara, Kiyotake-cho, Miyazaki 889-1692, Japan
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Shintaro Fumoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Keiko Yoshikawa
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Die Hu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Kazuya Okami
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Riku Kato
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Mikiro Nakashima
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Hirotaka Miyamoto
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto, Nagasaki-shi, Nagasaki 852-8501, Japan
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8
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Yang M, Moroz P, Jin Z, Budkina DS, Sundrani N, Porotnikov D, Cassidy J, Sugiyama Y, Tarnovsky AN, Mattoussi H, Zamkov M. Delayed Photoluminescence in Metal-Conjugated Fluorophores. J Am Chem Soc 2019; 141:11286-11297. [DOI: 10.1021/jacs.9b04697] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - Zhicheng Jin
- Department of Chemistry, Biochemistry, Florida State University, Tallahassee, Florida 32303, United States
| | | | | | | | | | - Yuya Sugiyama
- Asahi-Kasei Corporation, Healthcare R&D Center, 2-1 Samejima, Fuji City, Shizuoka 416-8501 Japan
| | | | - Hedi Mattoussi
- Department of Chemistry, Biochemistry, Florida State University, Tallahassee, Florida 32303, United States
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9
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Wang Z, Huang X, Cheng Z. Automatic Spot Identification Method for High Throughput Surface Plasmon Resonance Imaging Analysis. BIOSENSORS 2018; 8:E85. [PMID: 30217054 PMCID: PMC6163621 DOI: 10.3390/bios8030085] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 09/10/2018] [Indexed: 12/23/2022]
Abstract
An automatic spot identification method is developed for high throughput surface plasmon resonance imaging (SPRi) analysis. As a combination of video accessing, image enhancement, image processing and parallel processing techniques, the method can identify the spots in SPRi images of the microarray from SPRi video data. In demonstrations of the method, SPRi video data of different protein microarrays were processed by the method. Results show that our method can locate spots in the microarray accurately regardless of the microarray pattern, spot-background contrast, light nonuniformity and spotting defects, but also can provide address information of the spots.
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Affiliation(s)
- Zhiyou Wang
- School of Electronic and Communication, Changsha University, Changsha 410003, China.
| | - Xiaoqing Huang
- School of Electronic and Communication, Changsha University, Changsha 410003, China.
| | - Zhiqiang Cheng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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10
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Fathi F, Rezabakhsh A, Rahbarghazi R, Rashidi MR. Early-stage detection of VE-cadherin during endothelial differentiation of human mesenchymal stem cells using SPR biosensor. Biosens Bioelectron 2017; 96:358-366. [DOI: 10.1016/j.bios.2017.05.018] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 05/03/2017] [Accepted: 05/09/2017] [Indexed: 02/08/2023]
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11
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Zhu L, Zhao Z, Cheng P, He Z, Cheng Z, Peng J, Wang H, Wang C, Yang Y, Hu Z. Antibody-Mimetic Peptoid Nanosheet for Label-Free Serum-Based Diagnosis of Alzheimer's Disease. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2017; 29:1700057. [PMID: 28605073 DOI: 10.1002/adma.201700057] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Revised: 04/28/2017] [Indexed: 06/07/2023]
Abstract
Alzheimer's disease (AD) is the most common form of dementia characterized by progressive cognitive decline. Current diagnosis of AD is based on symptoms, neuropsychological tests, and neuroimaging, and is usually evident years after the pathological process. Early assessment at the preclinical or prodromal stage is in a great demand since treatment after the onset can hardly stop or reverse the disease progress. However, early diagnosis of AD is challenging due to the lack of reliable noninvasive approaches. Here, an antibody-mimetic self-assembling peptoid nanosheet containing surface-exposed Aβ42-recognizing loops is constructed, and a label-free sensor for the detection of AD serum is developed. The loop-displaying peptoid nanosheet is demonstrated to have high affinity to serum Aβ42, and to be able to identify AD sera with high sensitivity. The dense distribution of molecular recognition loops on the robust peptoid nanosheet scaffold not only mimics the architecture of antibodies, but also reduces the nonspecific binding in detecting multicomponent samples. This antibody-mimetic 2D material holds great potential toward the blood-based diagnosis of AD, and meanwhile provides novel insights into the antibody alternative engineering and the universal application in biological and chemical sensors.
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Affiliation(s)
- Ling Zhu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zijian Zhao
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Peng Cheng
- State Key Laboratory of Tribology, Department of Mechanical Engineering, Tsinghua University, Beijing, 100084, China
| | - Zhaohui He
- Department of Neurosurgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400016, China
| | - Zhiqiang Cheng
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Jiaxi Peng
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Huayi Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Chen Wang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Yanlian Yang
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory of Standardization and Measurement for Nanotechnology, CAS Key Laboratory of Biological Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, China
- Sino-Danish Colloge, University of Chinese Academy of Sciences, Beijing, 100049, China
- Yangtze River Delta Academy of Nanotechnology and Industry Development Research, Zhejiang Province, Jiaxing, 314000, China
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12
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Gao Y, Li Y, Zhang C, Zhao M, Deng C, Lan Q, Liu Z, Su N, Wang J, Xu F, Xu Y, Ping L, Chang L, Gao H, Wu J, Xue Y, Deng Z, Peng J, Xu P. Enhanced Purification of Ubiquitinated Proteins by Engineered Tandem Hybrid Ubiquitin-binding Domains (ThUBDs). Mol Cell Proteomics 2016; 15:1381-96. [PMID: 27037361 DOI: 10.1074/mcp.o115.051839] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Indexed: 11/06/2022] Open
Abstract
Ubiquitination is one of the most common post-translational modifications, regulating protein stability and function. However, the proteome-wide profiling of ubiquitinated proteins remains challenging due to their low abundance in cells. In this study, we systematically evaluated the affinity of ubiquitin-binding domains (UBDs) to different types of ubiquitin chains. By selecting UBDs with high affinity and evaluating various UBD combinations with different lengths and types, we constructed two artificial tandem hybrid UBDs (ThUBDs), including four UBDs made of DSK2p-derived ubiquitin-associated (UBA) and ubiquilin 2-derived UBA (ThUDQ2) and of DSK2p-derived UBA and RABGEF1-derived A20-ZnF (ThUDA20). ThUBD binds to ubiquitinated proteins, with markedly higher affinity than naturally occurring UBDs. Furthermore, it displays almost unbiased high affinity to all seven lysine-linked chains. Using ThUBD-based profiling with mass spectrometry, we identified 1092 and 7487 putative ubiquitinated proteins from yeast and mammalian cells, respectively, of which 362 and 1125 proteins had ubiquitin-modified sites. These results demonstrate that ThUBD is a refined and promising approach for enriching the ubiquitinated proteome while circumventing the need to overexpress tagged ubiquitin variants and use antibodies to recognize ubiquitin remnants, thus providing a readily accessible tool for the protein ubiquitination research community.
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Affiliation(s)
- Yuan Gao
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Yanchang Li
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Chengpu Zhang
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Mingzhi Zhao
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Chen Deng
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Qiuyan Lan
- the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zexian Liu
- the ‖Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; and
| | - Na Su
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Jingwei Wang
- the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Feng Xu
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Yongru Xu
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Lingyan Ping
- the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Lei Chang
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Huiying Gao
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China
| | - Junzhu Wu
- the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yu Xue
- the ‖Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China; and
| | - Zixin Deng
- the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Junmin Peng
- the **Departments of Structural Biology and Developmental Neurobiology, St. Jude Proteomics Facility, St. Jude Children's Research Hospital, Memphis, Tennessee 38105
| | - Ping Xu
- From the ‡State Key Laboratory of Proteomics, National Engineering Research Center for Protein Drugs, Beijing Proteome Research Center, National Center for Protein Sciences Beijing, Beijing Institute of Radiation Medicine, Beijing 102206,China; the ¶School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China;
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13
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Wang W, Fang Q, Hu Z. High-Throughput Peptide Screening on a Bimodal Imprinting Chip Through MS-SPRi Integration. Methods Mol Biol 2016; 1352:111-25. [PMID: 26490471 DOI: 10.1007/978-1-4939-3037-1_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Screening of high affinity and high specificity peptide probes towards various targets is important in the biomedical field while traditional peptide screening procedure is manual and tedious. Herein, a bimodal imprinting microarray system to embrace the whole peptide screening process is presented. Surface Plasmon Resonance imaging (SPRi) and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS) are combined for both quantitative and qualitative identification of the peptide. The method provides a solution for high efficiency peptide screening.
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Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, No.11. Beiyitiao Zhongguancun, Beijing, 100190, China.
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14
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Zhou Y, Liu Z, Rothschild KJ, Lim MJ. Proteome-wide drug screening using mass spectrometric imaging of bead-arrays. Sci Rep 2016; 6:26125. [PMID: 27194112 PMCID: PMC4872124 DOI: 10.1038/srep26125] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 04/27/2016] [Indexed: 12/17/2022] Open
Abstract
A fundamental challenge in the drug discovery process is to develop compounds with high efficacy and minimal side-effects. We describe a new approach to proteome-wide drug screening for detection of on- and off-target binding which combines the advantages of mass spectrometry with microarray technology. The method involves matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) of agarose micro-beads randomly arrayed at high-density in custom micro-well plates. Each bead carries a unique protein target and a corresponding photocleavable mass-tag for coding (PC-Mass-Tag). Compounds bound to specific protein beads and a photo-released coding PC-Mass-Tag are detected simultaneously using MALDI-MSI. As an initial demonstration of this approach, two kinase-targeted drugs, Dasatinib and Brigatinib (AP26113), were simultaneously screened against a model 50-member kinase-bead library. A MALDI-MSI scan performed at the equivalent density of 495,000 beads in the footprint of a microscope slide yielded 100% sensitivity for detecting known strong interactions with no false positives.
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Affiliation(s)
- Ying Zhou
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Ziying Liu
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
| | - Kenneth J Rothschild
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States.,Molecular Biophysics Laboratory, Department of Physics and Photonics Center, Boston University, Boston, MA 02215, United States
| | - Mark J Lim
- AmberGen, Inc., 313 Pleasant Street, Watertown, MA 02472, United States
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15
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Zhou L, Wang K, Li Q, Nice EC, Zhang H, Huang C. Clinical proteomics-driven precision medicine for targeted cancer therapy: current overview and future perspectives. Expert Rev Proteomics 2016; 13:367-81. [PMID: 26923776 DOI: 10.1586/14789450.2016.1159959] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cancer is a common disease that is a leading cause of death worldwide. Currently, early detection and novel therapeutic strategies are urgently needed for more effective management of cancer. Importantly, protein profiling using clinical proteomic strategies, with spectacular sensitivity and precision, offer excellent promise for the identification of potential biomarkers that would direct the development of targeted therapeutic anticancer drugs for precision medicine. In particular, clinical sample sources, including tumor tissues and body fluids (blood, feces, urine and saliva), have been widely investigated using modern high-throughput mass spectrometry-based proteomic approaches combined with bioinformatic analysis, to pursue the possibilities of precision medicine for targeted cancer therapy. Discussed in this review are the current advantages and limitations of clinical proteomics, the available strategies of clinical proteomics for the management of precision medicine, as well as the challenges and future perspectives of clinical proteomics-driven precision medicine for targeted cancer therapy.
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Affiliation(s)
- Li Zhou
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Kui Wang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China
| | - Qifu Li
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Edouard C Nice
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
| | - Canhua Huang
- a State Key Laboratory of Biotherapy and Cancer Center, West China Hospital , Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu , P.R. China.,b Department of Neurology , The Affiliated Hospital of Hainan Medical College , Haikou , Hainan , P.R. China
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16
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Liu XC, Gao JM, Liu S, Liu L, Wang JR, Qu XJ, Cai B, Wang SL. Targeting apoptosis is the major battle field for killing cancers. World J Transl Med 2015; 4:69-77. [DOI: 10.5528/wjtm.v4.i3.69] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 04/27/2015] [Accepted: 08/31/2015] [Indexed: 02/05/2023] Open
Abstract
Targeting apoptosis is one of the major strategies for cancer therapy. Essentially, most of the conventional cancer therapeutic drugs that are in the clinical use induce apoptosis and in part necrosis of malignant cells and therefore prevent cancer progression and metastasis. Although these cytotoxic anticancer drugs are important weapons for killing cancers, their toxic side effects limited their application. The molecularly targeted therapeutics that are based on the deeper understanding of the defects in the apoptotic signaling in cancers are emerging and have shown promising anticancer activity in selectively killing cancers but not normal cells. The examples of molecular targets that are under exploration for cancer therapy include the cell surface receptors such as TNFR family death receptors, the intrinsic Bcl-2 family members and some other intracellular molecules like p53, MDM2, IAP, and Smac. The advance in the high-throughput bio-technologies has greatly accelerated the progress of cancer drug discovery.
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17
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Bejhed RS, Tian B, Eriksson K, Brucas R, Oscarsson S, Strömberg M, Svedlindh P, Gunnarsson K. Magnetophoretic Transport Line System for Rapid On-Chip Attomole Protein Detection. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10296-10302. [PMID: 26309059 DOI: 10.1021/acs.langmuir.5b01947] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A lab-on-a-chip traveling wave magnetophoresis approach for sensitive and rapid protein detection is reported. In this method, a chip-based magnetic microarray comprising lines of micrometer-sized thin film magnetic elements was used to control the movement of magnetic beads (MBs). The MBs and the chip were functionalized, forming a sandwich-type assay. The MBs were transported across a detection area, and the presence of target molecules resulted in the immobilization of MBs within this area. Target quantification was accomplished by MB counting in the detection area using an optical microscope. In order to demonstrate the versatility of the microarray, biotinylated antiavidin was selected as the target protein. In this case, avidin-functionalized MBs and an avidin-functionalized detection area were used. With a total assay time of 1 to 1.5 h (depending on the labeling approach used), a limit of detection in the attomole range was achieved. Compared to on-chip surface plasmon resonance biodetection systems, our method has a larger dynamic range and is about a factor of 500 times more sensitive. Furthermore, our MB transportation system can operate in any chip-based biosensor platform, thereby significantly improving traditional biosensors.
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Affiliation(s)
- Rebecca S Bejhed
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Bo Tian
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Kristofer Eriksson
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Rimantas Brucas
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Sven Oscarsson
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Mattias Strömberg
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Peter Svedlindh
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
| | - Klas Gunnarsson
- Department of Engineering Sciences, Division of Solid State Physics, The Ångström Laboratory, Uppsala University , Box 534, SE-751 21 Uppsala, Sweden
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18
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Label-free detection microarray for novel peptide ligands screening base on MS–SPRi combination. Talanta 2015; 134:705-711. [DOI: 10.1016/j.talanta.2014.12.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/07/2014] [Accepted: 12/11/2014] [Indexed: 12/30/2022]
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19
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Cheng Z, Wang Z, Gillespie DE, Lausted C, Zheng Z, Yang M, Zhu J. Plain silver surface plasmon resonance for microarray application. Anal Chem 2015; 87:1466-9. [PMID: 25583410 DOI: 10.1021/ac504110t] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The application scope of surface plasmon resonance (SPR) and SPR imaging (SPRi) is rapidly growing, and tools such as high-performance and low-cost slides could enable more rapid growth of the field. We describe herein a novel silver slide, addressing the inherent instability of plain silver structure by improving adhesion between the glass substrate and the silver layer with a thin buffer layer of gold. Covered by a self-assembled monolayer (SAM) only, SPR characteristics of the slide remain steady for more than 3 months under regular storage. In a bioassay, the slide substantiates the predicted nearly 100% sensitivity improvement over gold slides and exhibits exceptional performance stability as determined by sensitivity and resolution measurements during the extended 40,000 s multicycle experiment. We demonstrate the suitability of this new slide for large-area SPRi, describing analysis results from a 1 296-ligand protein microarray. We predict this slide structure will provide a stable, high-sensitivity solution for high-throughput SPRi applications and other surface analysis platforms.
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Affiliation(s)
- Zhiqiang Cheng
- National Center for NanoScience and Technology , Beijing 100190, People's Republic of China
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20
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Tyagi D, Perez JB, Nand A, Zhiqiang C, Wang P, Na J, Zhu J. Detection of embryonic stem cell lysate biomarkers by surface plasmon resonance with reduced nonspecific adsorption. Anal Biochem 2014; 471:29-37. [PMID: 25447493 DOI: 10.1016/j.ab.2014.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/29/2014] [Accepted: 11/01/2014] [Indexed: 12/11/2022]
Abstract
Surface plasmon resonance imaging (SPRi) has emerged as a versatile biosensor to detect a wide range of biomolecular interactions with divergent potential applications. However, the use of this advanced-level technology for stem cell lysate study is still not much explored. Cell lysates are significant biological analytes used for disease diagnostics and proteomic studies, but their complex nature limits their use as an analyte for SPRi biosensors. Here, we review the problems associated with the use of SPRi for stem cell lysate study and examine the role of surface chemistry, running buffer, and blocking solution in order to minimize nonspecific adsorption (NSA). We detect the expression of Oct4, Sox2, Nanog, Rex1, and Lin28 biomarkers present in mouse embryonic stem cell (mESC) lysate against their corresponding antibodies immobilized on the sensor surface with reduced NSA. The current study shows that the conjunction of SPRi and microarray can be used as a label-free, high-throughput, and rapid technique for detection of biomarkers and their relative abundance in stem cell lysate study.
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Affiliation(s)
- Deependra Tyagi
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Javier Batista Perez
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Amita Nand
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Zhiqiang
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Peizhe Wang
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jie Na
- Centre for Stem Cell Biology and Regenerative Medicine, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jingsong Zhu
- National Center for Nanoscience and Technology, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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21
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Zhu L, Wang K, Cui J, Liu H, Bu X, Ma H, Wang W, Gong H, Lausted C, Hood L, Yang G, Hu Z. Label-free quantitative detection of tumor-derived exosomes through surface plasmon resonance imaging. Anal Chem 2014; 86:8857-64. [PMID: 25090139 PMCID: PMC4151789 DOI: 10.1021/ac5023056] [Citation(s) in RCA: 181] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Exosomes
are endosome-derived membrane vesicles carrying proteins
and nucleic acids that are involved in cellular functions such as
intercellular communication, protein and RNA secretion, and antigen
presentation. Therefore, exosomes serve as potential biomarkers for
many diseases including cancer. Because exosomes are difficult to
enrich or purify from biofluids, quantification of exosomes is tedious
and inaccurate. Here, we present a real-time, label-free, and quantitative
method to detect and characterize tumor-derived exosomes without enrichment
or purification. Utilizing surface plasmon resonance imaging (SPRi)
in combination with antibody microarrays specific to the extracellular
domains of exosome membrane proteins, exosomes in tumor cell culture
medium can be quantitatively detected. We found a positive correlation
between the metastatic potential of tumor cell lines and exosome secretion.
This method provides an easy, efficient, and novel way to detect exosome
secretion and thus an avenue toward the diagnosis and prognosis prediction
of cancer.
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Affiliation(s)
- Ling Zhu
- National Center for Nanoscience and Technology , No. 11, Beiyitiao Zhongguancun, Beijing 100190, P. R. China
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22
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Wang W, Li M, Wei Z, Wang Z, Bu X, Lai W, Yang S, Gong H, Zheng H, Wang Y, Liu Y, Li Q, Fang Q, Hu Z. Bimodal Imprint Chips for Peptide Screening: Integration of High-Throughput Sequencing by MS and Affinity Analyses by Surface Plasmon Resonance Imaging. Anal Chem 2014; 86:3703-7. [DOI: 10.1021/ac500465e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Weizhi Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Menglin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Zewen Wei
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zihua Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiangli Bu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Wenjia Lai
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Shu Yang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - He Gong
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Hui Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Yuqiao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Ying Liu
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
| | - Qin Li
- Department
of Biomedical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Qiaojun Fang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Zhiyuan Hu
- CAS Key Laboratory for Biomedical Effects of Nanomaterials & Nanosafety, National Center for Nanoscience and Technology of China, Beijing 100190, China
- Beijing
Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing 102206, China
- Institute for Systems Biology, 401 Terry Avenue N, Seattle, Washington 98109, United States
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23
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Hu Z, Lausted C, Yoo H, Yan X, Brightman A, Chen J, Wang W, Bu X, Hood L. Quantitative liver-specific protein fingerprint in blood: a signature for hepatotoxicity. Am J Cancer Res 2014; 4:215-28. [PMID: 24465277 PMCID: PMC3900804 DOI: 10.7150/thno.7868] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 12/04/2013] [Indexed: 02/06/2023] Open
Abstract
We discuss here a new approach to detecting hepatotoxicity by employing concentration changes of liver-specific blood proteins during disease progression. These proteins are capable of assessing the behaviors of their cognate liver biological networks for toxicity or disease perturbations. Blood biomarkers are highly desirable diagnostics as blood is easily accessible and baths virtually all organs. Fifteen liver-specific blood proteins were identified as markers of acetaminophen (APAP)-induced hepatotoxicity using three proteomic technologies: label-free antibody microarrays, quantitative immunoblotting, and targeted iTRAQ mass spectrometry. Liver-specific blood proteins produced a toxicity signature of eleven elevated and four attenuated blood protein levels. These blood protein perturbations begin to provide a systems view of key mechanistic features of APAP-induced liver injury relating to glutathione and S-adenosyl-L-methionine (SAMe) depletion, mitochondrial dysfunction, and liver responses to the stress. Two markers, elevated membrane-bound catechol-O-methyltransferase (MB-COMT) and attenuated retinol binding protein 4 (RBP4), report hepatic injury significantly earlier than the current gold standard liver biomarker, alanine transaminase (ALT). These biomarkers were perturbed prior to onset of irreversible liver injury. Ideal markers should be applicable for both rodent model studies and human clinical trials. Five of these mouse liver-specific blood markers had human orthologs that were also found to be responsive to human hepatotoxicity. This panel of liver-specific proteins has the potential to effectively identify the early toxicity onset, the nature and extent of liver injury and report on some of the APAP-perturbed liver networks.
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24
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Chandra H, Reddy PJ, Srivastava S. Protein microarrays and novel detection platforms. Expert Rev Proteomics 2014; 8:61-79. [DOI: 10.1586/epr.10.99] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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25
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Stoevesandt O, Taussig MJ. Affinity proteomics: the role of specific binding reagents in human proteome analysis. Expert Rev Proteomics 2014; 9:401-14. [DOI: 10.1586/epr.12.34] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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26
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Sung J, Kim PJ, Ma S, Funk CC, Magis AT, Wang Y, Hood L, Geman D, Price ND. Multi-study integration of brain cancer transcriptomes reveals organ-level molecular signatures. PLoS Comput Biol 2013; 9:e1003148. [PMID: 23935471 PMCID: PMC3723500 DOI: 10.1371/journal.pcbi.1003148] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 06/05/2013] [Indexed: 12/23/2022] Open
Abstract
We utilized abundant transcriptomic data for the primary classes of brain cancers to study the feasibility of separating all of these diseases simultaneously based on molecular data alone. These signatures were based on a new method reported herein – Identification of Structured Signatures and Classifiers (ISSAC) – that resulted in a brain cancer marker panel of 44 unique genes. Many of these genes have established relevance to the brain cancers examined herein, with others having known roles in cancer biology. Analyses on large-scale data from multiple sources must deal with significant challenges associated with heterogeneity between different published studies, for it was observed that the variation among individual studies often had a larger effect on the transcriptome than did phenotype differences, as is typical. For this reason, we restricted ourselves to studying only cases where we had at least two independent studies performed for each phenotype, and also reprocessed all the raw data from the studies using a unified pre-processing pipeline. We found that learning signatures across multiple datasets greatly enhanced reproducibility and accuracy in predictive performance on truly independent validation sets, even when keeping the size of the training set the same. This was most likely due to the meta-signature encompassing more of the heterogeneity across different sources and conditions, while amplifying signal from the repeated global characteristics of the phenotype. When molecular signatures of brain cancers were constructed from all currently available microarray data, 90% phenotype prediction accuracy, or the accuracy of identifying a particular brain cancer from the background of all phenotypes, was found. Looking forward, we discuss our approach in the context of the eventual development of organ-specific molecular signatures from peripheral fluids such as the blood. From a multi-study, integrated transcriptomic dataset, we identified a marker panel for differentiating major human brain cancers at the gene-expression level. The ISSAC molecular signatures for brain cancers, composed of 44 unique genes, are based on comparing expression levels of pairs of genes, and phenotype prediction follows a diagnostic hierarchy. We found that sufficient dataset integration across multiple studies greatly enhanced diagnostic performance on truly independent validation sets, whereas signatures learned from only one dataset typically led to high error rate. Molecular signatures of brain cancers, when obtained using all currently available gene-expression data, achieved 90% phenotype prediction accuracy. Thus, our integrative approach holds significant promise for developing organ-level, comprehensive, molecular signatures of disease.
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Affiliation(s)
- Jaeyun Sung
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, United States of America
| | - Pan-Jun Kim
- Asia Pacific Center for Theoretical Physics, Pohang, Gyeongbuk, Republic of Korea
- Department of Physics, POSTECH, Pohang, Gyeongbuk, Republic of Korea
| | - Shuyi Ma
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, United States of America
| | - Cory C. Funk
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Andrew T. Magis
- Institute for Systems Biology, Seattle, Washington, United States of America
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Yuliang Wang
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Chemical and Biomolecular Engineering, University of Illinois, Urbana, Illinois, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Donald Geman
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Nathan D. Price
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail:
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27
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28
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Stigter E, de Jong G, van Bennekom W. Coupling surface-plasmon resonance and mass spectrometry to quantify and to identify ligands. Trends Analyt Chem 2013. [DOI: 10.1016/j.trac.2012.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ouellet E, Lund L, Lagally ET. Multiplexed surface plasmon resonance imaging for protein biomarker analysis. Methods Mol Biol 2013; 949:473-90. [PMID: 23329461 DOI: 10.1007/978-1-62703-134-9_30] [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: 02/16/2023]
Abstract
The reliable detection of ligand and analyte binding is of significant importance for the field of medical diagnostics. Recent advances in proteomics and the rapid expansion in the number of identified protein biomarkers enhance the need for reliable techniques for their identification in complex samples. Surface plasmon resonance imaging (SPRi) provides label-free detection of this binding process in real-time. This chapter details the fabrication of an SPR imaging instrument and its use in analyzing molecular binding interactions with the use of a high-density microfluidic SPRi chip, capable of multiplexed analysis as well as various immobilization chemistries. Controlled recovery of bound biomarkers is demonstrated to enable their identification using mass spectrometry. Finally, activated leukocyte cell adhesion molecule (ALCAM), a protein biomarker associated with a variety of cancers, is identified from human crude cell lysates using the microfluidic surface plasmon resonance imaging (SPRi) instrument.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
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Fang Y. Ligand-receptor interaction platforms and their applications for drug discovery. Expert Opin Drug Discov 2012; 7:969-88. [PMID: 22860803 DOI: 10.1517/17460441.2012.715631] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
INTRODUCTION The study of drug-target interactions is essential for the understanding of biological processes and for the efforts to develop new therapeutic molecules. Increased ligand-binding assays have coincided with the advances in reagents, detection and instrumentation technologies, the expansion in therapeutic targets of interest, and the increasingly recognized importance of biochemical aspects of drug-target interactions in determining the clinical performance of drug molecules. Nowadays, ligand-binding assays can determine every aspect of many drug-target interactions. AREAS COVERED Given that ligand-target interactions are very diverse, the author has decided to focus on the binding of small molecules to protein targets. This article first reviews the key biochemical aspects of drug-target interactions, and then discusses the detection principles of various ligand-binding techniques in the context of their primary applications for drug discovery and development. EXPERT OPINION Equilibrium-binding affinity should not be used as a solo indicator for the in vivo pharmacology of drugs. The clinical relevance of drug-binding kinetics demands high throughput kinetics early in drug discovery. The dependence of ligand binding and function on the conformation of targets necessitates solution-based and whole cell-based ligand-binding assays. The increasing need to examine ligand binding at the proteome level, driven by the clinical importance of the polypharmacology of ligands, has started to make the structure-based in silico binding screen an indispensable technique for drug discovery and development. Integration of different ligand-binding assays is important to improve the efficiency of the drug discovery and development process.
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Affiliation(s)
- Ye Fang
- Biochemical Technologies, Science and Technology Division, Corning, Inc., Corning, NY 14831, USA.
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Nand A, Gautam A, Pérez JB, Merino A, Zhu J. Emerging technology of in situ cell free expression protein microarrays. Protein Cell 2012; 3:84-8. [PMID: 22426976 DOI: 10.1007/s13238-012-2012-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Recently, in situ protein microarrays have been developed for large scale analysis and high throughput studies of proteins. In situ protein microarrays produce proteins directly on the solid surface from pre-arrayed DNA or RNA. The advances in in situ protein microarrays are exemplified by the ease of cDNA cloning and cell free protein expression. These technologies can evaluate, validate and monitor protein in a cost effective manner and address the issue of a high quality protein supply to use in the array. Here we review the importance of recently employed methods: PISA (protein in situ array), DAPA (DNA array to protein array), NAPPA (nucleic acid programmable protein array) and TUSTER microarrays and the role of these methods in proteomics.
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Affiliation(s)
- Amita Nand
- National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
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Whole blood screening of antibodies using label-free nanoparticle biophotonic array platform. Biosens Bioelectron 2012; 36:1-5. [PMID: 22591657 DOI: 10.1016/j.bios.2012.04.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2012] [Accepted: 04/12/2012] [Indexed: 01/15/2023]
Abstract
A gold nanoparticle, localised plasmon array biosensor using light scattering has been employed in the detection of allergen-specific antibodies in whole blood and sera. The array sensor was functionalized with four different allergens, cat dander (Fel d1), dust mite (Der p1), peanut allergen (Ara h1) and dog dander (Can f1) and immuno-kinetic assay was performed to detect their respective anti-allergen IgG antibodies. Specific positive responses to antibodies at a concentration of 25 nM were observed for Fel d1, Der p1, and Ara h1 allergens, while the Can f1 channel served as a reference control. The sensitivity was further enhanced using a secondary anti-IgG detection antibodies to give a limit of detection of 2 nM. The results indicate the potential for nanoparticle scattering multiplexed arrays to screen unprepared blood samples at point-of-care for assays of complex samples such as the whole blood.
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Yoshikawa N, Sakamoto K, Mizuno S, Sakaguchi J, Miyamoto H, Mine T, Sasaki H, Fumoto S, Nishida K. Multiple components in serum contribute to hepatic transgene expression by lipoplex in mice. J Gene Med 2012; 13:632-43. [PMID: 22002583 DOI: 10.1002/jgm.1618] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Interaction of cationic liposome/plasmid DNA complex (lipoplex) with serum was not a limiting factor for in vivo transfection. After intraportal injection of lipoplex, hepatic transgene expression was enhanced by interaction with serum in mice. In the present study, we analyzed the mechanism of enhanced hepatic transgene expression of lipoplex by interaction with serum components. METHODS Lipoplexes were incubated with several serum components for 5 min at 37 ° C before administration. Transfection efficiency of lipoplexes was measured 6 h after intraportal injection of lipoplex in mice. RESULTS Depletion of divalent cation from serum decreased hepatic transgene expression. The addition of calcium ion to divalent cation-depleted serum restored transgene expression. Heat-inactivated serum and bovine serum albumin diminished the enhancing effect of serum on hepatic transgene expression. On the other hand, removal of anionic proteins from serum using an anion-exchanging column was critical for the enhancing effect of serum on transgene expression. Among the serum components tested, fibronectin and complement component C3 enhanced hepatic transgene expression. CONCLUSIONS Hepatic transgene expression by lipoplex was enhanced by interaction with multiple components in serum. Interaction of lipoplex with serum could be an important factor for successful in vivo gene transfer. Hence, the information obtained in the present study is valuable for the future development of effective gene carriers.
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Affiliation(s)
- Naoki Yoshikawa
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan
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34
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Proteomic technologies for the study of osteosarcoma. Sarcoma 2012; 2012:169416. [PMID: 22550414 PMCID: PMC3329661 DOI: 10.1155/2012/169416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/04/2011] [Indexed: 02/07/2023] Open
Abstract
Osteosarcoma is the most common primary bone cancer of children and is established during stages of rapid bone growth. The disease is a consequence of immature osteoblast differentiation, which gives way to a rapidly synthesized incompletely mineralized and disorganized bone matrix. The mechanism of osteosarcoma tumorogenesis is poorly understood, and few proteomic studies have been used to interrogate the disease thus far. Accordingly, these studies have identified proteins that have been known to be associated with other malignancies, rather than being osteosarcoma specific. In this paper, we focus on the growing list of available state-of-the-art proteomic technologies and their specific application to the discovery of novel osteosarcoma diagnostic and therapeutic targets. The current signaling markers/pathways associated with primary and metastatic osteosarcoma that have been identified by early-stage proteomic technologies thus far are also described.
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35
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Askin SP, Schaeffer PM. A universal immuno-PCR platform for comparative and ultrasensitive quantification of dual affinity-tagged proteins in complex matrices. Analyst 2012; 137:5193-6. [DOI: 10.1039/c2an35857c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Reddy PJ, Sadhu S, Ray S, Srivastava S. Cancer biomarker detection by surface plasmon resonance biosensors. Clin Lab Med 2011; 32:47-72. [PMID: 22340843 DOI: 10.1016/j.cll.2011.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Panga Jaipal Reddy
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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37
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Zhang GJ, Luo ZHH, Huang MJ, Ang JJ, Kang TG, Ji H. An integrated chip for rapid, sensitive, and multiplexed detection of cardiac biomarkers from fingerprick blood. Biosens Bioelectron 2011; 28:459-63. [DOI: 10.1016/j.bios.2011.07.007] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 06/24/2011] [Accepted: 07/06/2011] [Indexed: 10/18/2022]
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38
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Gaster RS, Hall DA, Wang SX. Autoassembly protein arrays for analyzing antibody cross-reactivity. NANO LETTERS 2011; 11:2579-83. [PMID: 20804215 PMCID: PMC3136110 DOI: 10.1021/nl1026056] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 08/17/2010] [Indexed: 05/22/2023]
Abstract
We report an autoassembly protein array capable of rapidly screening for aberrant antibody-antigen binding events. Our technique combines magnetic nanoparticle technology with proximity-based, magnetically responsive nanosensors for rapid (under 15 min) and high-density screening of antibody cross-reactivity at sensitivities down to 50 fM in a homogeneous assay. This method will enable the identification of the precise cause of aberrant or cross-reactive binding events in an easy-to-use, rapid, and high-throughput manner.
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Affiliation(s)
- Richard S. Gaster
- Department of Bioengineering, Medical Scientist Training Program, School of Medicine, Department of Electrical Engineering, Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Drew A. Hall
- Department of Bioengineering, Medical Scientist Training Program, School of Medicine, Department of Electrical Engineering, Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
| | - Shan X. Wang
- Department of Bioengineering, Medical Scientist Training Program, School of Medicine, Department of Electrical Engineering, Department of Materials Science and Engineering, Stanford University, Stanford, California 94305, United States
- E-mail: . Phone: 650-723-8671. Fax: 650-736-1984. Address: Geballe Laboratory for Advanced Materials, McCullough Building, Room 351, 476 Lomita Mall, Stanford University, Stanford, CA 94305-4045
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Abstract
Surface plasmon resonance (SPR) is a label-free detection method by which molecular interactions may be analyzed on a surface. Binding data are collected in real time, allowing the determination of interaction kinetics. SPR imaging (SPRi), the focus of this review, improves upon the efficiency of SPR by facilitating analysis of multiple interactions simultaneously. Here we summarize the principles of SPRi, provide examples of how SPRi arrays can be fabricated, and illustrate the utility of SPRi through example applications from the fields of proteomics, genomics and bioengineering.
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40
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Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011; 11:2139-61. [PMID: 21548090 DOI: 10.1002/pmic.201000460] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 02/28/2011] [Accepted: 03/07/2011] [Indexed: 01/22/2023]
Abstract
Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high-abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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41
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Gaster RS, Xu L, Han SJ, Wilson RJ, Hall DA, Osterfeld SJ, Yu H, Wang SX. Quantification of protein interactions and solution transport using high-density GMR sensor arrays. NATURE NANOTECHNOLOGY 2011; 6:314-20. [PMID: 21478869 PMCID: PMC3089684 DOI: 10.1038/nnano.2011.45] [Citation(s) in RCA: 145] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/08/2011] [Indexed: 05/19/2023]
Abstract
Monitoring the kinetics of protein interactions on a high-density sensor array is vital to drug development and proteomic analysis. Label-free kinetic assays based on surface plasmon resonance are the current gold standard, but they have poor detection limits, suffer from non-specific binding, and are not amenable to high-throughput analyses. Here, we show that magnetically responsive nanosensors that have been scaled to over 100,000 sensors per cm² can be used to measure the binding kinetics of various proteins with high spatial and temporal resolution. We present an analytical model that describes the binding of magnetically labelled antibodies to proteins that are immobilized on the sensor surface. This model is able to quantify the kinetics of antibody-antigen binding at sensitivities as low as 20 zeptomoles of solute.
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Affiliation(s)
- Richard S. Gaster
- Department of Bioengineering, Stanford University, CA 94305, USA
- Medical Scientist Training Program, School of Medicine, Stanford University, CA 94305, USA
| | - Liang Xu
- Department of Materials Science and Engineering, Stanford University, CA 94305, USA
| | - Shu-Jen Han
- IBM T.J. Watson Research Center, Yorktown Heights, NY 10598
| | - Robert J. Wilson
- Department of Materials Science and Engineering, Stanford University, CA 94305, USA
| | - Drew A. Hall
- Department of Electrical Engineering, Stanford University, CA 94305, USA
| | | | - Heng Yu
- MagArray Inc., Sunnyvale, CA 94089
| | - Shan X. Wang
- Department of Materials Science and Engineering, Stanford University, CA 94305, USA
- Department of Electrical Engineering, Stanford University, CA 94305, USA
- Correspondence and requests for materials should be addressed to: Shan X. Wang (), Stanford Center for Magnetic Nanotechnology, Phone: 650-723-8671, Mail address: Geballe Laboratory for Advanced Materials, McCullough Building, Room 351, 476 Lomita Mall, Stanford University, Stanford, CA 94305-4045
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42
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Piliarik M, Bocková M, Homola J. Surface plasmon resonance biosensor for parallelized detection of protein biomarkers in diluted blood plasma. Biosens Bioelectron 2011; 26:1656-61. [PMID: 20864329 DOI: 10.1016/j.bios.2010.08.063] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 08/02/2010] [Accepted: 08/20/2010] [Indexed: 11/29/2022]
Abstract
Surface plasmon resonance (SPR) biosensor for high-throughput screening of protein biomarkers in diluted blood plasma is reported. The biosensor combines a high-resolution SPR imaging sensor and a high-density protein array with low-fouling background. The SPR imaging sensor utilizes polarization contrast and advanced referencing and provides a total of 120 sensing areas (each 200 μm×150 μm). Antibodies are immobilized on the sensing areas via hybridization of antibody-oligonucleotide conjugates to thiolated complementary oligonucleotides microspotted on the sensor surface (DNA-directed immobilization). A low-fouling background is achieved by covalent immobilization of bovine serum albumin to carboxyl-terminated thiols filling the areas among the thiolated oligonucleotides and outside the sensing areas. The biosensor was evaluated for detection of protein biomarkers relevant to cancer diagnostics--human chorionic gonadotropin (hCG) and activated leukocyte cell adhesion molecule (ALCAM) both in buffer and in 10% blood plasma. Limits of detection as low as 45 ng/mL (ALCAM) and 100 ng/mL (hCG) were achieved in blood plasma samples.
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Affiliation(s)
- Marek Piliarik
- Institute of Photonics and Electronics AS CR v.v.i., Chaberská 57, CZ-18251 Prague 8, Czech Republic
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43
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44
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Abstract
Sensors based on surface plasmon resonance have demonstrated, over the last 2 decades, to be an effective method of studying biomolecular interactions without the need for labeling. Recently, it has been adapted to high-throughput use for imaging microarray binding in real time. This provides a promising platform - a label-free protein microarray system - for the study of disease. In this example, antibody microarrays are used to efficiently profile the secretion of proteins from a cell line exposed to varying concentrations of a toxic compound.
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45
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Linman MJ, Abbas A, Cheng Q. Interface design and multiplexed analysis with surface plasmon resonance (SPR) spectroscopy and SPR imaging. Analyst 2010; 135:2759-67. [PMID: 20830330 PMCID: PMC7365140 DOI: 10.1039/c0an00466a] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Ever since the advent of surface plasmon resonance (SPR) and SPR imaging (SPRi) in the early 1990s, their use in biomolecular interaction analysis (BIA) has expanded phenomenally. An important research area in SPR sensor development is the design of novel and effective interfaces that allow for the probing of a variety of chemical and biological interactions in a highly selective and sensitive manner. A well-designed and robust interface is a necessity to obtain both accurate and pertinent biological information. This review covers the recent research efforts in this area with a specific focus towards biointerfaces, new materials for SPR biosensing, and novel array designs for SPR imaging. Perspectives on the challenges ahead and next steps for SPR technology are discussed.
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Affiliation(s)
- Matthew J. Linman
- Department of Chemistry, University of California, Riverside, California 92521
| | - Abdennour Abbas
- Department of Chemistry, University of California, Riverside, California 92521
| | - Quan Cheng
- Department of Chemistry, University of California, Riverside, California 92521
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Ray S, Mehta G, Srivastava S. Label-free detection techniques for protein microarrays: prospects, merits and challenges. Proteomics 2010; 10:731-48. [PMID: 19953541 PMCID: PMC7167936 DOI: 10.1002/pmic.200900458] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays, on which thousands of discrete proteins are printed, provide a valuable platform for functional analysis of the proteome. They have been widely used for biomarker discovery and to study protein–protein interactions. The accomplishments of DNA microarray technology, which had enabled massive parallel studies of gene expression, sparked great interest for the development of protein microarrays to achieve similar success at the protein level. Protein microarray detection techniques are often classified as being label‐based and label‐free. Most of the microarray applications have employed labelled detection such as fluorescent, chemiluminescent and radioactive labelling. These labelling strategies have synthetic challenges, multiple label issues and may exhibit interference with the binding site. Therefore, development of sensitive, reliable, high‐throughput, label‐free detection techniques are now attracting significant attention. Label‐free detection techniques monitor biomolecular interactions and simplify the bioassays by eliminating the need for secondary reactants. Moreover, they provide quantitative information for the binding kinetics. In this article, we will review several label‐free techniques, which offer promising applications for the protein microarrays, and discuss their prospects, merits and challenges.
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Affiliation(s)
- Sandipan Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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47
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Liu X, Wen F, Yang J, Chen L, Wei YQ. A review of current applications of mass spectrometry for neuroproteomics in epilepsy. MASS SPECTROMETRY REVIEWS 2010; 29:197-246. [PMID: 19598206 DOI: 10.1002/mas.20243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The brain is unquestionably the most fascinating organ, and the hippocampus is crucial in memory storage and retrieval and plays an important role in stress response. In temporal lobe epilepsy (TLE), the seizure origin typically involves the hippocampal formation. Despite tremendous progress, current knowledge falls short of being able to explain its function. An emerging approach toward an improved understanding of the complex molecular mechanisms that underlie functions of the brain and hippocampus is neuroproteomics. Mass spectrometry has been widely used to analyze biological samples, and has evolved into an indispensable tool for proteomics research. In this review, we present a general overview of the application of mass spectrometry in proteomics, summarize neuroproteomics and systems biology-based discovery of protein biomarkers for epilepsy, discuss the methodology needed to explore the epileptic hippocampus proteome, and also focus on applications of ingenuity pathway analysis (IPA) in disease research. This neuroproteomics survey presents a framework for large-scale protein research in epilepsy that can be applied for immediate epileptic biomarker discovery and the far-reaching systems biology understanding of the protein regulatory networks. Ultimately, knowledge attained through neuroproteomics could lead to clinical diagnostics and therapeutics to lessen the burden of epilepsy on society.
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Affiliation(s)
- Xinyu Liu
- National Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, China
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48
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Edelman LB, Chandrasekaran S, Price ND. Systems biology of embryogenesis. Reprod Fertil Dev 2010; 22:98-105. [PMID: 20003850 DOI: 10.1071/rd09215] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The development of a complete organism from a single cell involves extraordinarily complex orchestration of biological processes that vary intricately across space and time. Systems biology seeks to describe how all elements of a biological system interact in order to understand, model and ultimately predict aspects of emergent biological processes. Embryogenesis represents an extraordinary opportunity (and challenge) for the application of systems biology. Systems approaches have already been used successfully to study various aspects of development, from complex intracellular networks to four-dimensional models of organogenesis. Going forward, great advancements and discoveries can be expected from systems approaches applied to embryogenesis and developmental biology.
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Affiliation(s)
- Lucas B Edelman
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801, USA
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49
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Molecular imaging and targeted therapies. Biochem Pharmacol 2010; 80:731-8. [PMID: 20399197 DOI: 10.1016/j.bcp.2010.04.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Revised: 04/07/2010] [Accepted: 04/07/2010] [Indexed: 12/31/2022]
Abstract
Targeted therapeutic and imaging agents are becoming more prevalent, and are used to treat increasingly smaller segments of the patient population. This has lead to dramatic increases in the costs for clinical trials. Biomarkers have great potential to reduce the numbers of patients needed to test novel targeted agents by predicting or identifying non-response early-on and thus enriching the clinical trial population with patients more likely to respond. Biomarkers are characteristics that are objectively measured and evaluated as indicators of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention. Biomarkers can be used to predict response to specific therapies, predict response regardless of therapy, or to monitor response once a therapy has begun. In terms of drug development, predictive biomarkers have the greatest impact, as they can be used as inclusion criteria for patient segmentation. Prognostic markers are used routinely in clinical practice but do not provide direction for the use of targeted therapies. Imaging biomarkers have distinct advantages over those that require a biopsy sample in that they are "non-invasive" and can be monitored longitudinally at multiple time points in the same patient. This review will examine the role of functional and molecular imaging in predicting response to specific therapies; will explore the advantages and disadvantages of targeting intracellular or extracellular markers; and will discuss the attributes of useful targets and methods for target identification and validation.
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50
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Ouellet E, Lausted C, Lin T, Yang CWT, Hood L, Lagally ET. Parallel microfluidic surface plasmon resonance imaging arrays. LAB ON A CHIP 2010; 10:581-8. [PMID: 20162233 DOI: 10.1039/b920589f] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Surface plasmon resonance imaging (SPRi) is a label-free technique used for the quantitation of binding affinities and concentrations for a wide variety of target molecules. Although SPRi is capable of determining binding constants for multiple ligands in parallel, current commercial instruments are limited to a single analyte stream on multiple ligand spots. Measurement of binding kinetics requires the serial introduction of different analyte concentrations; such repeated experiments are conducted manually and are therefore time-intensive. To address these challenges, we have developed an integrated microfluidic array using soft lithography techniques for high-throughput SPRi-based detection and determination of binding affinities of antibodies against protein targets. The device consists of 264 element-addressable chambers isolated by microvalves. The resulting 700 pL chamber volumes, combined with a serial dilution network for simultaneous interrogation of up to six different analyte concentrations, allow for further speeding detection times. To test for device performance, human alpha-thrombin was immobilized on the sensor surface and anti-human alpha-thrombin IgG was injected across the surface at different concentrations. The equilibrium dissociation constant was determined to be 5.0 +/- 1.9 nM, which agrees well with values reported in the literature. The interrogation of multiple ligands to multiple analytes in a single device was also investigated and samples were recovered with no cross-contamination. Since each chamber can be addressed independently, this array is capable of interrogating binding events from up to 264 different immobilized ligands against multiple analytes in a single experiment. The development of high-throughput protein analytic measurements is a critical technology for systems approaches to biology and medicine.
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Affiliation(s)
- Eric Ouellet
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada V6T 1Z4
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