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Bhattacharyya P, Christopherson RI, Skarratt KK, Fuller SJ. Method for B Cell Receptor Enrichment in Malignant B Cells. Cancers (Basel) 2024; 16:2341. [PMID: 39001403 PMCID: PMC11240526 DOI: 10.3390/cancers16132341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 06/17/2024] [Accepted: 06/25/2024] [Indexed: 07/16/2024] Open
Abstract
B cells are central to the adaptive immune response and provide long-lasting immunity after infection. B cell activation is mediated by the surface membrane-bound B cell receptor (BCR) following recognition of a specific antigen. The BCR has been challenging to analyse using mass spectrometry (MS) due to the difficulty of isolating and enriching this membrane-bound protein complex. There are approximately 120,000 BCRs on the B cell surface; however, depending on the B cell activation state, there may be hundreds-of-millions to billions of proteins in a B cell. Consequently, advanced proteomic techniques such as MS workflows that use purified proteins to yield structural and protein-interaction information have not been published for the BCR complex. This paper describes a method for enriching the BCR complex that is MS-compatible. The method involves a Protein G pull down on agarose beads using an intermediary antibody to each of the BCR complex subcomponents (CD79a, CD79b, and membrane immunoglobulin). The enrichment process is shown to pull down the entire BCR complex and has the advantage of being readily compatible with further proteomic study including MS analysis. Using intermediary antibodies has the potential to enrich all isotypes of the BCR, unlike previous methods described in the literature that use protein G-coated beads to directly pull down the membrane IgG (mIgG) but cannot be used for other mIg isotypes.
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Affiliation(s)
- Puja Bhattacharyya
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Blacktown Hospital, Blacktown Rd., Blacktown, NSW 2148, Australia
| | | | - Kristen K. Skarratt
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
| | - Stephen J. Fuller
- Sydney Medical School Nepean, Faculty of Medicine and Health, The University of Sydney, Penrith, NSW 2750, Australia; (P.B.); (K.K.S.)
- Nepean Hospital, Derby Str., Kingswood, NSW 2747, Australia
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2
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Li C, Xiao J, Wu S, Liu L, Zeng X, Zhao Q, Zhang Z. Clinical application of serum-based proteomics technology in human tumor research. Anal Biochem 2023; 663:115031. [PMID: 36580994 DOI: 10.1016/j.ab.2022.115031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/27/2022]
Abstract
The rapid development of proteomics technology in the past decades has led to further human understanding of tumor research, and in some ways, the technology plays a very important supporting role in the early detection of tumors. Human serum has been shown to contain a variety of proteins closely related to life activities, and the dynamic change in proteins can often reflect the physiological and pathological conditions of the body. Serum has the advantage of easy extraction, so the application of proteomics technology in serum has become a hot spot and frontier area for the study of malignant tumors. However, there are still many difficulties in the standardized use of proteomic technologies, which inevitably limit the clinical application of proteomic technologies due to the heterogeneity of human proteins leading to incomplete whole proteome populations, in addition to most serum protein markers being now not highly specific in aiding the early detection of tumors. Nevertheless, further development of proteomics technologies will greatly increase our understanding of tumor biology and help discover more new tumor biomarkers with specificity that will enable medical technology.
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Affiliation(s)
- Chen Li
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Juan Xiao
- Department of Otorhinolaryngology, The Second Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Shihua Wu
- Department of Pathology, The Second Hospital of Shaoyang College, Hunan, Shaoyang, 422000, Hunan Province, China
| | - Lu Liu
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China
| | - Xuemei Zeng
- Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China
| | - Qiang Zhao
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China.
| | - Zhiwei Zhang
- Department of Pathology, The First Affiliated Hospital of University of South China, Hunan, Hengyang, 421001, Hunan Province, China; Cancer Research Institute of Hengyang Medical College, University of South China, Key Laboratory of Cancer Cellular and Molecular Pathology in Hunan Province, Hunan, Hengyang, 421001, China.
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3
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Dutta S, Smith MD. Detection of Protein-Protein Interactions Utilizing the Split-Ubiquitin Membrane-Based Yeast Two-Hybrid System. Methods Mol Biol 2023; 2690:37-57. [PMID: 37450135 DOI: 10.1007/978-1-0716-3327-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Identifying the interactors of a protein is a key step in understanding its possible cellular function(s). Among the various methods that can be used to study protein-protein interactions (PPIs), the yeast two-hybrid (Y2H) assay is one of the most standardized, sensitive, and cost-effective in vivo methods available. The most commonly used GAL4-based Y2H system utilizes the yeast transcription factor GAL4 to detect interactions between soluble proteins. By virtue of involving a transcription factor, the protein-protein interactions occur in the nucleus. The split-ubiquitin Y2H system offers an alternative to the traditional GAL4-based Y2H system and takes advantage of the reconstitution of split-ubiquitin in the cytosol to identify interactions between two proteins. Moreover, new membranous and soluble interacting partner(s) can be identified by screening a target protein against proteins produced from a cDNA library using this system.
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Affiliation(s)
- Siddhartha Dutta
- Department of Microbiology and Biotechnology, Sister Nivedita University, Kolkata, West Bengal, India
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, ON, Canada.
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4
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Yan J, Zhao C, Ma Y, Yang W. Covalently Attaching Hollow Silica Nanoparticles on a COC Surface for the Fabrication of a Three-Dimensional Protein Microarray. Biomacromolecules 2022; 23:2614-2623. [PMID: 35603741 DOI: 10.1021/acs.biomac.2c00354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compared to traditional two-dimensional (2D) biochips, three-dimensional (3D) biochips exhibit the advantages of higher probe density and detection sensitivity due to their designable surface microstructure as well as enlarged surface area. In the study, we proposed an approach to prepare a 3D protein chip by deposition of a monolayer of functionalized hollow silica nanoparticles (HSNs) on an activated cyclic olefin copolymer (COC) substrate. First, the COC substrate was chemically modified through the photografting technique to tether poly[3-(trimethoxysilyl) propyl methacrylate] (PTMSPMA) brushes on it. Then, a monolayer of HSNs was deposited on the modified COC and covalently attached via a condensation reaction between the hydrolyzed pendant siloxane groups of PTMSPMA and the Si-OH groups of HSNs. The roughness of the COC substrate significantly increased to 50.3 nm after depositing a monolayer of HSNs (ranging from 100 to 700 nm), while it only caused a negligible reduction in the light transmittance of COC. The HSN-modified COC was further functionalized with epoxide groups by a silane coupling agent for binding proteins. Immunoglobulin G could be effectively immobilized on this substrate with the highest immobilization efficiency of 75.2% and a maximum immobilization density of 1.236 μg/cm2, while the highest immobilization efficiency on a 2D epoxide group-modified glass slide was only 57.4%. Moreover, immunoassay results confirmed a competitive limit of detection (LOD) (1.06 ng/mL) and a linear detection range (1-100 ng/mL) of the 3D protein chip. This facile and effective approach for fabricating nanoparticle-based 3D protein microarrays has great potential in the field of biorelated detection.
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Zhou E, Song N, Xiao Q, Farooq Z, Jia Z, Wen J, Dai C, Ma C, Tu J, Shen J, Fu T, Yi B. Construction of transgenic detection system of Brassica napus L. based on single nucleotide polymorphism chip. 3 Biotech 2022; 12:11. [PMID: 34966634 PMCID: PMC8655060 DOI: 10.1007/s13205-021-03062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 11/09/2021] [Indexed: 01/03/2023] Open
Abstract
Brassica napus L. is a vital oil crop in China. As auxiliary tools for rapeseed breeding, transgenic technologies play a considerable role in heterosis, variety improvement, and pest resistance. Research on transgenic detection technologies is of great significance for the introduction, supervision, and development of transgenic rapeseed in China. However, the transgenic detection methods currently in use are complex and time-consuming, with low output. A single nucleotide polymorphism (SNP) chip can effectively overcome such limitations. In the present study, we collected 40 transgenic elements and designed 291 probes. The probe sequences were submitted to Illumina Company, and the Infinium chip technology was used to prepare SNP chips. In the present Brassica napus transgenic detection experiment, 84 high-quality probes of 17 transgenic elements were preliminarily screened, and genotyping effect was optimised for the probe signal value. Ultimately, a transgenic detection system for B. napus was developed. The developed system has the advantages of simple operation, minimal technical errors, and stable detection outcomes. A transgenic detection sensitivity test revealed that the probe designed could accurately detect 1% of transgenic samples and had high detection sensitivity. In addition, in repeatability tests, the CaMV35S promoter coefficient of variation was approximately 3.58%. Therefore, the SNP chip had suitable repeatability in transgene detection. The SNP chip developed could be used to construct transgenic detection systems for B. napus. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03062-6.
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Affiliation(s)
- Enqiang Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Nuan Song
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Qing Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zunaira Farooq
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Zhibo Jia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jing Wen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Cheng Dai
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Chaozhi Ma
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Tingdong Fu
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
| | - Bin Yi
- National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan, 430000 China
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Fomitcheva-Khartchenko A, Rapsomaniki MA, Sobottka B, Schraml P, Kaigala GV. Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity. PLoS One 2021; 16:e0259332. [PMID: 34797831 PMCID: PMC8604290 DOI: 10.1371/journal.pone.0259332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
A new workflow for protein-based tumor heterogeneity probing in tissues is here presented. Tumor heterogeneity is believed to be key for therapy failure and differences in prognosis in cancer patients. Comprehending tumor heterogeneity, especially at the protein level, is critical for tracking tumor evolution, and showing the presence of different phenotypical variants and their location with respect to tissue architecture. Although a variety of techniques is available for quantifying protein expression, the heterogeneity observed in the tissue is rarely addressed. The proposed method is validated in breast cancer fresh-frozen tissues derived from five patients. Protein expression is quantified on the tissue regions of interest (ROI) with a resolution of up to 100 μm in diameter. High heterogeneity values across the analyzed patients in proteins such as cytokeratin 7, β-actin and epidermal growth factor receptor (EGFR) using a Shannon entropy analysis are observed. Additionally, ROIs are clustered according to their expression levels, showing their location in the tissue section, and highlighting that similar phenotypical variants are not always located in neighboring regions. Interestingly, a patient with a phenotype related to increased aggressiveness of the tumor presents a unique protein expression pattern. In summary, a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level is presented.
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Affiliation(s)
| | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
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Antibody Printing Technologies. Methods Mol Biol 2020. [PMID: 33237416 DOI: 10.1007/978-1-0716-1064-0_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Antibody microarrays are routinely employed in the lab and in the clinic for studying protein expression, protein-protein, and protein-drug interactions. The microarray format reduces the size scale at which biological and biochemical interactions occur, leading to large reductions in reagent consumption and handling times while increasing overall experimental throughput. Specifically, antibody microarrays, as a platform, offer a number of different advantages over traditional techniques in the areas of drug discovery and diagnostics. While a number of different techniques and approaches have been developed for creating micro and nanoscale antibody arrays, issues relating to sensitivity, cost, and reproducibility persist. The aim of this review is to highlight current state-of the-art techniques and approaches for creating antibody arrays by providing latest accounts of the field while discussing potential future directions.
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8
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Yoo CH, Yu JK, Seong Y, Choi JK. Microarrays Incorporating Gold Grid Patterns for Protein Quantification. ACS OMEGA 2020; 5:16664-16669. [PMID: 32685833 PMCID: PMC7364605 DOI: 10.1021/acsomega.0c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Protein microarrays are miniaturized two-dimensional arrays, incorporating thousands of immobilized proteins, typically printed in minute amounts on functionalized solid substrates, which can be analyzed in a high-throughput fashion. Irreproducibility of the printing techniques adopted, resulting in inconsistently and nonuniformly deposited microscopic spots, nonuniform signal intensities from the printed microspots, and significantly high background noise are some of the critical issues that affect protein analysis using traditional protein microarrays. To overcome such issues, in this study, we introduced a novel gold grid pattern-based protein microarray. The grid patterns incorporated in our microarray are equivalent to the spots used for protein analysis in conventional protein microarrays. We utilized the signal intensities from the grid patterns acting as spots for quantifying the protein concentration levels. To demonstrate the utility of our novel design concept, we quantified as low as 66.7 ng/mL of bovine serum albumin using our gold grid pattern-based protein microarray. Our grid pattern-based design concept for protein quantification overcame the signal nonuniformity issues and ensured that the dominance of any distorted signal from a single spot did not affect the overall protein quantification results as encountered in conventional protein microarrays.
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Affiliation(s)
- Chang-Hyuk Yoo
- Division
of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | | | - Yeju Seong
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | - Jun-Kyu Choi
- Small
Machines Company, Ltd., Daejeon 34012, Korea
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9
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Feng F, Ataca ST, Ran M, Wang Y, Breen M, Kepler TB. Gain-Scanning for Protein Microarray Assays. J Proteome Res 2020; 19:2664-2675. [PMID: 31928020 DOI: 10.1021/acs.jproteome.9b00892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Protein microarrays consist of known proteins spotted onto solid substrates and are used to perform highly multivariate assessments of protein-binding interactions. Human protein arrays are routinely applied to pathogen detection, immune response biomarker profiling, and antibody specificity profiling. Here, we describe and demonstrate a new data processing procedure, gain-scan, in which data were acquired under multiple photomultiplier tube (PMT) settings, followed by data fitting with a power function model to estimate the incident light signals of the array spots. Data acquisition under multiple PMT settings solves the difficulty of determining the single optimal PMT gain setting and allows us to maximize the detection of low-intensity signals while avoiding the saturation of high-intensity ones at the same time. The gain-scan data acquisition and fitting also significantly lower the variances over the detectable range of signals and improve the linear data normalization. The performance of the proposed procedure was verified by analyzing the profiling data of both the human polyclonal serum samples and the monoclonal antibody samples with both technical replicates and biological replicates. We showed that the multigain power function was an appropriate model for describing data acquired under multiple PMT settings. The gain-scan fitting alone or in combination with the linear normalization could effectively reduce the technical variability of the array data and lead to better sample separability and more sensitive differential analysis.
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Affiliation(s)
- Feng Feng
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States
| | - Sila Toksoz Ataca
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States
| | - Mingxuan Ran
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States
| | - Yumei Wang
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States
| | - Michael Breen
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States
| | - Thomas B Kepler
- Department of Microbiology, Boston University School of Medicine, 700 Albany Street, Boston, Massachusetts 02118, United States.,Department of Mathematics & Statistics, Boston University, Boston, Massachusetts 02118, United States
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10
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Qi Y, Wang Y, Chen C, Zhao C, Ma Y, Yang W. Facile Surface Functionalization of Cyclic Olefin Copolymer Film with Anhydride Groups for Protein Microarray Fabrication. ACS APPLIED BIO MATERIALS 2020; 3:3203-3209. [PMID: 35025362 DOI: 10.1021/acsabm.0c00200] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Immobilization of protein at high efficiency is a challenge for fabricating polymer-based protein chips. Here, a simple but effective approach was developed to fabricate a cyclic olefin copolymer (COC)-based protein microarray with a high immobilization density. In this strategy, poly(maleic anhydride-co-vinyl acetate) (poly(MAH-co-VAc)) brushes were facilely attached on the COC surface via UV-induced graft copolymerization. The introduction of poly(MAH-co-VAc) brushes resulted in an obvious increase in the surface roughness of COC. The functionalized COC showed little reduction in transparency compared with pristine COC, indicating that the photografting treatment did not alter its optical property. The graft density of the anhydride groups on the modified COC could be tuned from 0.46 to 3.2 μmol/cm2. The immobilization efficiency of immunoglobulin G (IgG) on functionalized COC reached 88% due to the high reactivity between anhydride groups and amine groups of IgGs. An immunoassay experiment demonstrated that the microarray showed high sensitivity to the target analyte.
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11
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Sanchis A, Salvador JP, Marco MP. Multiplexed immunochemical techniques for the detection of pollutants in aquatic environments. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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12
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Label-free Microarray-based Binding Affinity Constant Measurement with Modified Fluidic Arrangement. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2102-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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13
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PTMA, a new identified autoantigen for oral submucous fibrosis, regulates oral submucous fibroblast proliferation and extracellular matrix. Oncotarget 2017; 8:74806-74819. [PMID: 29088825 PMCID: PMC5650380 DOI: 10.18632/oncotarget.20419] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/20/2017] [Indexed: 01/30/2023] Open
Abstract
Oral submucous fibrosis (OSF) is a chronic, insidious disease. The presence of autoantibodies in sera of OSF patients is the most characteristic and direct evidence of OSF being an autoimmune disease. To identify the specific autoantigens which could contribute to antibody production, the Human Proteome Microarrays composed of 19000 full-length unique proteins were employed. 45 proteins correlated with OSF were identified. To validate these results, we used ELISA to validate 28 OSF-associated autoantigens in extended samples. 8 autoantigens were positive in OSF serum with high frequency compared to the healthy controls. Moreover, the mRNA expression of 8 candidates was up-regulated in OSF oral submucous tissues; among them, the protein level of PTMA, the one with the highest positive frequency, was also increased. Through searching the Bioinformatics Public Database and performing the Spearman’s rank correlation analysis, we observed that PTMA was positively correlated with fibrosis-related TGFβ1 and SMAD4, the downstream gene of TGFβ1. In TGFβ1-induced fibrosis model of primary human oral submucous fibroblast, PTMA knockdown reversed TGFβ1-induced fibrosis process through inhibiting the cell viability and proliferation of fibroblast, reducing the protein levels of PTMA, Collagen I, α-SMA and MMP9 and increasing the protein levels of SMAD4. In contrast, PTMA overexpression enhanced TGFβ1-induced fibrosis process. Taken together, PTMA is involved in TGFβ1-induced fibrosis in the primary human submucous fibroblast by regulating the expression of ECM-related markers and the downstream genes of TGFβ1. In conclusion, PTMA presents an essential autoantigen during OSF process; targeting PTMA might be a promising strategy for OSF treatment.
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Sjöberg R, Mattsson C, Andersson E, Hellström C, Uhlen M, Schwenk JM, Ayoglu B, Nilsson P. Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling. N Biotechnol 2016; 33:582-92. [DOI: 10.1016/j.nbt.2015.09.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 09/15/2015] [Accepted: 09/15/2015] [Indexed: 12/01/2022]
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15
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An overview of innovations and industrial solutions in Protein Microarray Technology. Proteomics 2016; 16:1297-308. [DOI: 10.1002/pmic.201500429] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 03/02/2016] [Accepted: 03/03/2016] [Indexed: 01/12/2023]
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16
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Paul J, Sahaf B, Perloff S, Schoenrock K, Wu F, Nakasone H, Coller J, Miklos D. High-throughput allogeneic antibody detection using protein microarrays. J Immunol Methods 2016; 432:57-64. [PMID: 26902899 DOI: 10.1016/j.jim.2016.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Revised: 02/04/2016] [Accepted: 02/08/2016] [Indexed: 01/26/2023]
Abstract
Enzyme-linked immunosorbent assays (ELISAs) have traditionally been used to detect alloantibodies in patient plasma samples post hematopoietic cell transplantation (HCT); however, protein microarrays have the potential to be multiplexed, more sensitive, and higher throughput than ELISAs. Here, we describe the development of a novel and sensitive microarray method for detection of allogeneic antibodies against minor histocompatibility antigens encoded on the Y chromosome, called HY antigens. Six microarray surfaces were tested for their ability to bind recombinant protein and peptide HY antigens. Significant allogeneic immune responses were determined in male patients with female donors by considering normal male donor responses as baseline. HY microarray results were also compared with our previous ELISA results. Our overall goal was to maximize antibody detection for both recombinant protein and peptide epitopes. For detection of HY antigens, the Epoxy (Schott) protein microarray surface was both most sensitive and reliable and has become the standard surface in our microarray platform.
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Affiliation(s)
- Jed Paul
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
| | - Bita Sahaf
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
| | - Spenser Perloff
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
| | - Kelsi Schoenrock
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States
| | - Fang Wu
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
| | - Hideki Nakasone
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
| | - John Coller
- Stanford Functional Genomics Facility, Stanford University School of Medicine, 269 West Campus Dr., CCSR #0120, Stanford, CA 94305, United States.
| | - David Miklos
- Division of Blood and Marrow Transplantation, Stanford University School of Medicine, 269 West Campus Dr., CCSR #2205, Stanford, CA 94305, United States.
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Latef AAHA, Jan S, Abd‐Allah EF, Rashid B, John R, Ahmad P. Soybean under abiotic stress. PLANT‐ENVIRONMENT INTERACTION 2016:28-42. [DOI: 10.1002/9781119081005.ch2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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18
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Gebretsadik G, Menon MKC. Proteomics and Its Applications in Diagnosis of Auto Immune Diseases. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/oji.2016.61003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Walsh G. Proteins and Proteomics. Proteins 2015. [DOI: 10.1002/9781119117599.ch1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Ursu A, Waldmann H. Hide and seek: Identification and confirmation of small molecule protein targets. Bioorg Med Chem Lett 2015; 25:3079-86. [PMID: 26115575 DOI: 10.1016/j.bmcl.2015.06.023] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/14/2022]
Abstract
Target identification and confirmation for small molecules is often the rate limiting step in drug discovery. A robust method to identify proteins addressed by small molecules is affinity chromatography using chemical probes. These usually consist of the compound of interest equipped with a linker molecule and a proper tag. Recently, methods emerged that allow the identification of protein targets without prior functionalization of the small molecule of interest. The digest offers an update on the newest developments in the area of target identification with special focus on confirmation techniques.
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Affiliation(s)
- Andrei Ursu
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany; Chemical Biology, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 6, 44221 Dortmund, Germany.
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21
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Schumacher S, Muekusch S, Seitz H. Up-to-Date Applications of Microarrays and Their Way to Commercialization. MICROARRAYS (BASEL, SWITZERLAND) 2015; 4:196-213. [PMID: 27600220 PMCID: PMC4996390 DOI: 10.3390/microarrays4020196] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/01/2015] [Accepted: 04/14/2015] [Indexed: 12/12/2022]
Abstract
This review addresses up-to-date applications of Protein Microarrays. Protein Microarrays play a significant role in basic research as well as in clinical applications and are applicable in a lot of fields, e.g., DNA, proteins and small molecules. Additionally they are on the way to enter clinics in routine diagnostics. Protein Microarrays can be powerful tools to improve healthcare. An overview of basic characteristics to mediate essential knowledge of this technique is given. To reach this goal, some challenges still have to be addressed. A few applications of Protein Microarrays in a medical context are shown. Finally, an outlook, where the potential of Protein Microarrays is depicted and speculations how the future of Protein Microarrays will look like are made.
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Affiliation(s)
- Sarah Schumacher
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Sandra Muekusch
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
| | - Harald Seitz
- Branch Bioanalytics and Bioprocesses, Fraunhofer Institute for Cell Therapy and Immunology, Am Muehlenberg 13, 14476 Potsdam, Germany.
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22
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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23
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Karimi P, Shahrokni A, Ranjbar MRN. Implementation of proteomics for cancer research: past, present, and future. Asian Pac J Cancer Prev 2015; 15:2433-8. [PMID: 24761843 DOI: 10.7314/apjcp.2014.15.6.2433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Cancer is the leading cause of the death, accounts for about 13% of all annual deaths worldwide. Many different fields of science are collaborating together studying cancer to improve our knowledge of this lethal disease, and find better solutions for diagnosis and treatment. Proteomics is one of the most recent and rapidly growing areas in molecular biology that helps understanding cancer from an omics data analysis point of view. The human proteome project was officially initiated in 2008. Proteomics enables the scientists to interrogate a variety of biospecimens for their protein contents and measure the concentrations of these proteins. Current necessary equipment and technologies for cancer proteomics are mass spectrometry, protein microarrays, nanotechnology and bioinformatics. In this paper, we provide a brief review on proteomics and its application in cancer research. After a brief introduction including its definition, we summarize the history of major previous work conducted by researchers, followed by an overview on the role of proteomics in cancer studies. We also provide a list of different utilities in cancer proteomics and investigate their advantages and shortcomings from theoretical and practical angles. Finally, we explore some of the main challenges and conclude the paper with future directions in this field.
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Affiliation(s)
- Parisa Karimi
- Johns Hopkins Bloomberg School of Public Health, Baltimore, USA E-mail :
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24
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Reuterswärd P, Gantelius J, Andersson Svahn H. An 8 minute colorimetric paper-based reverse phase vertical flow serum microarray for screening of hyper IgE syndrome. Analyst 2015; 140:7327-34. [DOI: 10.1039/c5an01013f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A reverse phase serum array with the capacity of simultaneous detection in 113 samples was developed and optimized for a vertical flow 8-minute colorimetric assay detecting IgE.
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Affiliation(s)
- Philippa Reuterswärd
- Division of Proteomics and Nanobiotechnology
- Science for Life Laboratory
- KTH Royal Institute of Technology
- Sweden
| | - Jesper Gantelius
- Division of Proteomics and Nanobiotechnology
- Science for Life Laboratory
- KTH Royal Institute of Technology
- Sweden
| | - Helene Andersson Svahn
- Division of Proteomics and Nanobiotechnology
- Science for Life Laboratory
- KTH Royal Institute of Technology
- Sweden
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25
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Brödel AK, Wüstenhagen DA, Kubick S. Cell-free protein synthesis systems derived from cultured mammalian cells. Methods Mol Biol 2015; 1261:129-40. [PMID: 25502197 DOI: 10.1007/978-1-4939-2230-7_7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present a technology for the production of target proteins using novel cell-free systems derived from cultured human K562 cells and Chinese hamster ovary (CHO) cells. The protocol includes the cultivation of cells, the preparation of translationally active lysates, and the cell-free synthesis of desired proteins. An efficient expression vector based on the internal ribosome entry site (IRES) from the intergenic region (IGR) of the cricket paralysis virus (CrPV) was constructed for both systems. The coupled batch-based platforms enable the synthesis of a broad range of target proteins such as cytosolic proteins, secreted proteins, membrane proteins embedded into endogenous microsomes, and glycoproteins. The glycosylation of erythropoietin demonstrates the successful performance of posttranslational modifications in the novel cell-free systems. Protein yields of approximately 20 μg/ml (K562-based cell-free system) and 50 μg/ml (CHO-based cell-free system) of active firefly luciferase are obtained in the coupled transcription-translation systems within 3 h. As a result, both cell-free protein synthesis systems serve as powerful tools for high-throughput proteomics.
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Affiliation(s)
- Andreas K Brödel
- Department of Cell-free Bioproduction, Fraunhofer Institute for Cell Therapy and Immunology (IZI), Branch Bioanalytics and Bioprocesses Potsdam-Golm (IZI-BB), Am Mühlenberg 13, 14476, Potsdam, Germany
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26
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Kirschning A, Walter JG, Stahl F, Schax E, Scheper T, Aliuos P, Zeilinger C. Molecular Survival Strategies of Organisms: HSP and Small Molecules for Diagnostics and Drug Development. HEAT SHOCK PROTEINS 2015. [DOI: 10.1007/978-3-319-17211-8_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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27
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He S, Zhang Y, Wang P, Xu X, Zhu K, Pan W, Liu W, Cai K, Sun J, Zhang W, Jiang X. Multiplexed microfluidic blotting of proteins and nucleic acids by parallel, serpentine microchannels. LAB ON A CHIP 2015; 15:105-12. [PMID: 25342223 DOI: 10.1039/c4lc00901k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A high-throughput, high-efficiency and straightforward microfluidic blotting method for analyzing proteins and nucleic acids.
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28
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Jang E, Kim M, Koh WG. Ag@SiO2-entrapped hydrogel microarray: a new platform for a metal-enhanced fluorescence-based protein assay. Analyst 2015; 140:3375-83. [DOI: 10.1039/c5an00251f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We developed a novel silver-based metal-enhanced fluorescence (MEF) biosensing platform that consisted of poly(ethylene glycol)(PEG) hydrogel microstructures entrapping silica-coated silver nanoparticles (Ag@SiO2).
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Affiliation(s)
- Eunji Jang
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul 120-749
- South Korea
| | - Minsu Kim
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul 120-749
- South Korea
| | - Won-Gun Koh
- Department of Chemical and Biomolecular Engineering
- Yonsei University
- Seoul 120-749
- South Korea
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29
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Abstract
Proteomics and biochemical profiling have emerged as exciting and powerful tools in clinical biomarker research. In the field of transplantation, proteomics aims not only at developing noninvasive means for immune monitoring but also to gain mechanistic insights into the pathophysiology of the alloimmune response and hence defining new therapeutic targets. This chapter provides an overview of proteomic biomarker-driven approaches and its underlying concepts and discusses the advantages, clinical implications, challenges, and limitations of this novel modality as it relates to solid organ transplantation.
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Affiliation(s)
- Katrin Kienzl-Wagner
- Center of Operative Medicine, Department of Visceral, Transplant and Thoracic Surgery, Innsbruck Medical University, Innsbruck, Austria
| | - Gerald Brandacher
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
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30
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Lian Q, Cao H, Wang F. The Cost-Efficiency Realization in the Escherichia coli-Based Cell-Free Protein Synthesis Systems. Appl Biochem Biotechnol 2014; 174:2351-67. [DOI: 10.1007/s12010-014-1143-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 08/06/2014] [Indexed: 01/08/2023]
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31
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Salter H, Holland R. Biomarkers: refining diagnosis and expediting drug development - reality, aspiration and the role of open innovation. J Intern Med 2014; 276:215-28. [PMID: 24605903 DOI: 10.1111/joim.12234] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In the last decade, there have been intensive efforts to invent, qualify and use novel biomarkers as a means to improve success rates in drug discovery and development. The biomarkers field is maturing and this article considers whether these research efforts have brought about the expected benefits. The characteristics of a clinically useful biomarker are described and the impact this area of research has had is evaluated by reviewing a few, key examples of emerging biomarkers. There is evidence that the impact has been genuine and is increasing in both the drug and the diagnostic discovery and development processes. Beneficial impact on patient health outcomes seems relatively limited thus far, with the greatest impact in oncology (again, both in terms of novel drugs and in terms of more refined diagnoses and therefore more individualized treatment). However, the momentum of research would indicate that patient benefits are likely to increase substantially and to broaden across multiple therapeutic areas. Even though this research was originally driven by a desire to improve the drug discovery and development process, and was therefore funded with this aim in mind, it seems likely that the largest impact may actually come from more refined diagnosis. Refined diagnosis will facilitate both better allocation of healthcare resources and the use of treatment regimens which are optimized for the individual patient. This article also briefly reviews emerging technological approaches and how they relate to the challenges inherent in biomarker discovery and validation, and discusses the role of public/private partnerships in innovative biomarker research.
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Affiliation(s)
- H Salter
- AstraZeneca Translational Science Centre, Science for Life Laboratory, Solna, Sweden; Department of Clinical Neuroscience, Karolinska Institutet, Solna, Sweden
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32
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Kilb N, Burger J, Roth G. Protein microarray generation by in situ protein expression from template DNA. Eng Life Sci 2014. [DOI: 10.1002/elsc.201300052] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Normann Kilb
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
| | - Jürgen Burger
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- Laboratory for MEMS Applications, Department of Microsystems Engineering—IMTEK University of Freiburg Freiburg Germany
| | - Günter Roth
- Laboratory for Microarray Copying, Centre for Biological Systems Analysis (ZBSA) University of Freiburg Freiburg Germany
- BIOSS—Centre for Biological Signalling Studies University of Freiburg Freiburg Germany
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33
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Wang H, Zhang Q, Fang X. Transcriptomics and proteomics in stem cell research. Front Med 2014; 8:433-44. [PMID: 24972645 DOI: 10.1007/s11684-014-0336-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Accepted: 03/14/2014] [Indexed: 12/20/2022]
Abstract
Stem cells are capable of self-renewal and differentiation, and the processes regulating these events are among the most comprehensively investigated topics in life sciences. In particular, the molecular mechanisms of the self-renewal, proliferation, and differentiation of stem cells have been extensively examined. Multi-omics integrative analysis, such as transcriptomics combined with proteomics, is one of the most promising approaches to the systemic investigation of stem cell biology. We reviewed the available information on stem cells by examining published results using transcriptomic and proteomic characterization of the different stem cell processes. Comprehensive understanding of these important processes can only be achieved using a systemic methodology, and employing such method will strengthen the study on stem cell biology and promote the clinical applications of stem cells.
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Affiliation(s)
- Hai Wang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100101, China
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34
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Taussig MJ, Schmidt R, Cook EA, Stoevesandt O. Development of proteome-wide binding reagents for research and diagnostics. Proteomics Clin Appl 2014; 7:756-66. [PMID: 24178846 DOI: 10.1002/prca.201300060] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 09/09/2013] [Accepted: 09/10/2013] [Indexed: 01/11/2023]
Abstract
Alongside MS, antibodies and other specific protein-binding molecules have a special place in proteomics as affinity reagents in a toolbox of applications for determining protein location, quantitative distribution and function (affinity proteomics). The realisation that the range of research antibodies available, while apparently vast is nevertheless still very incomplete and frequently of uncertain quality, has stimulated projects with an objective of raising comprehensive, proteome-wide sets of protein binders. With progress in automation and throughput, a remarkable number of recent publications refer to the practical possibility of selecting binders to every protein encoded in the genome. Here we review the requirements of a pipeline of production of protein binders for the human proteome, including target prioritisation, antigen design, 'next generation' methods, databases and the approaches taken by ongoing projects in Europe and the USA. While the task of generating affinity reagents for all human proteins is complex and demanding, the benefits of well-characterised and quality-controlled pan-proteome binder resources for biomedical research, industry and life sciences in general would be enormous and justify the effort. Given the technical, personnel and financial resources needed to fulfil this aim, expansion of current efforts may best be addressed through large-scale international collaboration.
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Affiliation(s)
- Michael J Taussig
- Protein Technology Group, The Babraham Institute, Cambridge, UK; Cambridge Protein Arrays Ltd, Babraham Research Campus, Cambridge, UK
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35
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Dutta S, Teresinski HJ, Smith MD. A split-ubiquitin yeast two-hybrid screen to examine the substrate specificity of atToc159 and atToc132, two Arabidopsis chloroplast preprotein import receptors. PLoS One 2014; 9:e95026. [PMID: 24736607 PMCID: PMC3988174 DOI: 10.1371/journal.pone.0095026] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/22/2014] [Indexed: 11/18/2022] Open
Abstract
Post-translational import of nucleus-encoded chloroplast pre-proteins is critical for chloroplast biogenesis, and the Toc159 family of proteins serve as receptors for the process. Toc159 shares with other members of the family (e.g. Toc132), homologous GTPase (G−) and Membrane (M−) domains, but a highly dissimilar N-terminal acidic (A−) domain. Although there is good evidence that atToc159 and atToc132 from Arabidopsis mediate the initial sorting step, preferentially recognizing photosynthetic and non-photosynthetic preproteins, respectively, relatively few chloroplast preproteins have been assigned as substrates for particular members of the Toc159 family, which has limited the proof for the hypothesis. The current study expands the number of known preprotein substrates for members of the Arabidopsis Toc159 receptor family using a split-ubiquitin membrane-based yeast two-hybrid system using the atToc159 G-domain (Toc159G), atToc132 G-domain (Toc132G) and atToc132 A- plus G-domains (Toc132AG) as baits. cDNA library screening with all three baits followed by pairwise interaction assays involving the 81 chloroplast preproteins identified show that although G-domains of the Toc159 family are sufficient for preprotein recognition, they alone do not confer specificity for preprotein subclasses. The presence of the A-domain fused to atToc132G (Toc132AG) not only positively influences its specificity for non-photosynthetic preproteins, but also negatively regulates the ability of this receptor to interact with a subset of photosynthetic preproteins. Our study not only substantiates the fact that atToc132 can serve as a receptor by directly binding to chloroplast preproteins but also proposes the existence of subsets of preproteins with different but overlapping affinities for more than one member of the Toc159 receptor family.
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Affiliation(s)
- Siddhartha Dutta
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Howard J Teresinski
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
| | - Matthew D Smith
- Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
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Ma J, Hart GW. O-GlcNAc profiling: from proteins to proteomes. Clin Proteomics 2014; 11:8. [PMID: 24593906 PMCID: PMC4015695 DOI: 10.1186/1559-0275-11-8] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 02/01/2014] [Indexed: 11/16/2022] Open
Abstract
O-linked β-D-N-acetylglucosamine (O-GlcNAc) modification (O-GlcNAcylation) onto serine and threonine residues of proteins is an important post-translational modification (PTM), which is involved in many crucial biological processes including transcription, translation, proteasomal degradation, and signal transduction. Aberrant protein O-GlcNAcylation is directly linked to the pathological progression of chronic diseases including diabetes, cancer, and neurodegenerative disorders. Identification, site mapping, and quantification of O-GlcNAc proteins are a prerequisite to decipher their functions. In this review, we mainly focus on technological developments regarding O-GlcNAc protein profiling. Specifically, on one hand, we show how these techniques are being used for the comprehensive characterization of certain targeted proteins in which biologists are most interested. On the other hand, we present several newly developed approaches for O-GlcNAcomic profiling as well as how they provide us with a systems perspective to crosstalk amongst different PTMs and complicated biological events. Promising technical trends are also highlighted to evoke more efforts by diverse laboratories, which would further expand our understanding of the physiological and pathological roles of protein O-GlcNAcylation in chronic diseases.
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Affiliation(s)
| | - Gerald W Hart
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, 725 North Wolfe Street, Baltimore, MD 21205-2185, USA.
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37
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Buchegger P, Preininger C. Four assay designs and on-chip calibration: gadgets for a sepsis protein array. Anal Chem 2014; 86:3174-80. [PMID: 24552299 DOI: 10.1021/ac5000784] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A protein microarray for the early stage diagnosis of sepsis that allows the simultaneous detection of C-reactive protein (CRP) (2-200 μg/mL), procalcitonin (PCT) (0.2-50 ng/mL), and interleukin 6 (IL-6) (2-2000 pg/mL) has been developed. To enable the parallel detection of the differently abundant analytes, the low binding affinity between CRP and phosphocholine is exploited in a "low-sensitive" sandwich assay for CRP. The calibration is integrated directly on the chip resulting in a "one patient-one array" format, to provide a user-friendly and rapid diagnostic tool. Four different assay designs are introduced: (I) the classical assay that works with biotin-streptavidin chemistry, (II) the rapid assay that is performed in a single detection step, and two ultrasensitive assay designs accomplished either by (III) an enzymatic or (IV) an antibody mediated amplification resulting in high density labeling. The assay designs were evaluated by the repetitive measurement of low, medium, and high concentration levels of commercially available certified control sera. The precision was similar across all assay designs (coefficient of variation (CV), CVintra: 8-14%; CVinter: 18-34%), while the sensitivity (limits of detection (LODs)) increased by 1 order of magnitude for the ultrasensitive assays (III, IV) and the accuracy was analyte dependent but best for the classical (I) and the antibody amplified (IV) assays.
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Affiliation(s)
- Patricia Buchegger
- Austrian Institute of Technology , Department of Health & Environment, Bioresources, Konrad Lorenz Straße 24, 3430 Tulln, Austria
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38
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Lim MJ, Liu Z, Braunschweiger KI, Awad A, Rothschild KJ. Correlated matrix-assisted laser desorption/ionization mass spectrometry and fluorescent imaging of photocleavable peptide-coded random bead-arrays. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:49-62. [PMID: 24285390 PMCID: PMC3894740 DOI: 10.1002/rcm.6754] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 09/27/2013] [Accepted: 09/29/2013] [Indexed: 05/13/2023]
Abstract
RATIONALE Rapidly performing global proteomic screens is an important goal in the post-genomic era. Correlated matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) and fluorescent imaging of photocleavable peptide-coded random bead-arrays was evaluated as a critical step in a new method for proteomic screening that combines many of the advantages of MS with fluorescence-based microarrays. METHODS Small peptide-coded model bead libraries containing up to 20 different bead species were constructed by attaching peptides to 30-34 µm diameter glass, agarose or TentaGel® beads using photocleavable biotin or a custom-designed photocleavable linker. The peptide-coded bead libraries were randomly arrayed into custom gold-coated micro-well plates with 45 µm diameter wells and subjected to fluorescence and MALDI mass spectrometric imaging (MALDI-MSI). RESULTS Photocleavable mass-tags from individual beads in these libraries were spatially localized as ~65 µm spots using MALDI-MSI with high sensitivity and mass resolution. Fluorescently tagged beads were identified and correlated with their matching photocleavable mass-tags by comparing the fluorescence and MALDI-MS images of the same bead-array. Post-translational modification of the peptide Kemptide was also detected on individual beads in a photocleavable peptide-coded bead-array by MALDI-MSI alone, after exposure of the beads to protein kinase A (PKA). CONCLUSIONS Correlated MALDI-MS and fluorescent imaging of photocleavable peptide-coded random bead-arrays can provide a basis for performing global proteomic screening.
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Affiliation(s)
- Mark J Lim
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
- * Correspondence to: M. J. Lim, AmberGen, Incorporated, 313 Pleasant Street, Watertown, MA 02472, USA., E-mail:
| | - Ziying Liu
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
| | | | - Amany Awad
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
| | - Kenneth J Rothschild
- AmberGen, Incorporated313 Pleasant Street, Watertown, MA, 02472, USA
- Molecular Biophysics Laboratory, Department of Physics and Photonics Center, Boston UniversityBoston, MA, 02215, USA
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GuhaThakurta D, Sheikh NA, Meagher TC, Letarte S, Trager JB. Applications of systems biology in cancer immunotherapy: from target discovery to biomarkers of clinical outcome. Expert Rev Clin Pharmacol 2014; 6:387-401. [DOI: 10.1586/17512433.2013.811814] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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40
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Liu R, Wang K, Yuan K, Wei Y, Huang C. Integrative oncoproteomics strategies for anticancer drug discovery. Expert Rev Proteomics 2014; 7:411-29. [DOI: 10.1586/epr.10.14] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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Ongaro M, Ugo P. Sensor Arrays: Arrays of Micro- and Nanoelectrodes. ENVIRONMENTAL ANALYSIS BY ELECTROCHEMICAL SENSORS AND BIOSENSORS 2014. [DOI: 10.1007/978-1-4939-0676-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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44
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Cancer proteomics. Mol Oncol 2013. [DOI: 10.1017/cbo9781139046947.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Spera R, Festa F, Bragazzi NL, Pechkova E, LaBaer J, Nicolini C. Conductometric Monitoring of Protein–Protein Interactions. J Proteome Res 2013; 12:5535-47. [DOI: 10.1021/pr400445v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rosanna Spera
- Laboratories
of Biophysics and Nanobiotechnology, Department of Experimental Medicine, University of Genova, Via Pastore 3, 16132, Genova, Italy
| | - Fernanda Festa
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Nicola L. Bragazzi
- Laboratories
of Biophysics and Nanobiotechnology, Department of Experimental Medicine, University of Genova, Via Pastore 3, 16132, Genova, Italy
| | - Eugenia Pechkova
- Nanoworld Institute, Fondazione EL.B.A. Nicolini, Largo Redaelli 7, 24020, Pradalunga, Bergamo, Italy
- Laboratories
of Biophysics and Nanobiotechnology, Department of Experimental Medicine, University of Genova, Via Pastore 3, 16132, Genova, Italy
| | - Joshua LaBaer
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
| | - Claudio Nicolini
- Nanoworld Institute, Fondazione EL.B.A. Nicolini, Largo Redaelli 7, 24020, Pradalunga, Bergamo, Italy
- Laboratories
of Biophysics and Nanobiotechnology, Department of Experimental Medicine, University of Genova, Via Pastore 3, 16132, Genova, Italy
- Virginia
G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, United States
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Lee JR, Magee DM, Gaster RS, LaBaer J, Wang SX. Emerging protein array technologies for proteomics. Expert Rev Proteomics 2013; 10:65-75. [PMID: 23414360 DOI: 10.1586/epr.12.67] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Numerous efforts have been made to understand fundamental biology of diseases based on gene expression. However, the relationship between gene expression and onset of disease often remains obscure. The great advances in protein microarrays allow us to investigate this unclear question through protein profiles, which are regarded as more reliable than gene expressions to serve as the harbinger of disease onset or as the biomarker of disease treatment monitoring. The authors review two relatively new platforms of protein arrays, along with an introduction to the common basis of protein array technologies. Immobilization of proteins on the surface of arrays and neutralizing reactive areas after the immobilization are key practical issues in the field of protein array. One of the emerging protein array technologies is the magneto-nanosensor array, where giant magnetoresistive sensors are used to quantitatively measure the analytes of interest, which are labeled with magnetic nanoparticles. Similar to giant magnetoresistive sensors, several different ways of utilizing magnetic properties for biomolecular detection have been developed and are reviewed here. Another emerging protein array technology is nucleic acid programmable protein arrays, which have thousands of protein features directly expressed by nucleic acids on the array surface. The authors anticipate that these two emerging protein array platforms can be combined to produce synergistic benefits and open new applications in proteomics and clinical diagnostics.
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Affiliation(s)
- Jung-Rok Lee
- Department of Mechanical Engineering, Stanford University, 476 Lomita Mall, Room 208, Stanford, CA 94305, USA
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Rajan NK, Duan X, Reed MA. Performance limitations for nanowire/nanoribbon biosensors. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2013; 5:629-45. [PMID: 23897672 DOI: 10.1002/wnan.1235] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Accepted: 05/12/2013] [Indexed: 01/30/2023]
Abstract
Field-effect transistor-based biosensors (bioFETs) have shown great promise in the field of fast, ultra-sensitive, label-free detection of biomolecules. Reliability and accuracy, when trying to measure small concentrations, is of paramount importance for the translation of these research devices into the clinical setting. Our knowledge and experience with these sensors has reached a stage where we are able to identify three main aspects of bioFET sensing that currently limit their applications. By considering the intrinsic device noise as a limitation to the smallest measurable signal, we show how various parameters, processing steps and surface modifications, affect the limit of detection. We also introduce the signal-to-noise ratio of bioFETs as a universal performance metric, which allows us to gain better insight into the design of more sensitive devices. Another aspect that places a limit on the performance of bioFETs is screening by the electrolyte environment, which reduces the signal that could be potentially measured. Alternative functionalization and detection schemes that could enable the use of these charge-based sensors in physiological conditions are highlighted. Finally, the binding kinetics of the receptor-analyte system are considered, both in the context of extracting information about molecular interactions using the bioFET sensor platform and as a fundamental limitation to the number of molecules that bind to the sensor surface at steady-state conditions and to the signal that is generated. Some strategies to overcome these limitations are also proposed. Taken together, these performance-limiting issues, if solved, would bring bioFET sensors closer to clinical applications.
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Affiliation(s)
- Nitin K Rajan
- Department of Applied Physics, Yale University, New Haven, CT, USA
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48
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Detection of Target Proteins by Fluorescence Anisotropy. J Fluoresc 2013; 23:881-8. [DOI: 10.1007/s10895-013-1194-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 02/24/2013] [Indexed: 01/28/2023]
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49
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Schmidt R, Cook EA, Kastelic D, Taussig MJ, Stoevesandt O. Optimised 'on demand' protein arraying from DNA by cell free expression with the 'DNA to Protein Array' (DAPA) technology. J Proteomics 2013; 88:141-8. [PMID: 23454659 DOI: 10.1016/j.jprot.2013.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/28/2013] [Accepted: 02/04/2013] [Indexed: 12/16/2022]
Abstract
UNLABELLED We have previously described a protein arraying process based on cell free expression from DNA template arrays (DNA Array to Protein Array, DAPA). Here, we have investigated the influence of different array support coatings (Ni-NTA, Epoxy, 3D-Epoxy and Polyethylene glycol methacrylate (PEGMA)). Their optimal combination yields an increased amount of detected protein and an optimised spot morphology on the resulting protein array compared to the previously published protocol. The specificity of protein capture was improved using a tag-specific capture antibody on a protein repellent surface coating. The conditions for protein expression were optimised to yield the maximum amount of protein or the best detection results using specific monoclonal antibodies or a scaffold binder against the expressed targets. The optimised DAPA system was able to increase by threefold the expression of a representative model protein while conserving recognition by a specific antibody. The amount of expressed protein in DAPA was comparable to those of classically spotted protein arrays. Reaction conditions can be tailored to suit the application of interest. BIOLOGICAL SIGNIFICANCE DAPA represents a cost effective, easy and convenient way of producing protein arrays on demand. The reported work is expected to facilitate the application of DAPA for personalized medicine and screening purposes.
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Affiliation(s)
- Ronny Schmidt
- Protein Technology Group, Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge CB22 3AT, UK.
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SHA S, YIN Y, GAO XL, HUANG ZR, YU T, ZHENG XD. A New Method of Immobilizing Antibody Probes on Immunochips Based on DNA Hybridization. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60627-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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