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Yuan Y, Hu R, Chen S, Zhang X, Liu Z, Zhou G. CKG-IMC: An inductive matrix completion method enhanced by CKG and GNN for Alzheimer's disease compound-protein interactions prediction. Comput Biol Med 2024; 177:108612. [PMID: 38838556 DOI: 10.1016/j.compbiomed.2024.108612] [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: 12/05/2023] [Revised: 04/17/2024] [Accepted: 05/11/2024] [Indexed: 06/07/2024]
Abstract
Alzheimer's disease (AD) is one of the most prevalent chronic neurodegenerative disorders globally, with a rapidly growing population of AD patients and currently no effective therapeutic interventions available. Consequently, the development of therapeutic anti-AD drugs and the identification of AD targets represent one of the most urgent tasks. In this study, in addition to considering known drugs and targets, we explore compound-protein interactions (CPIs) between compounds and proteins relevant to AD. We propose a deep learning model called CKG-IMC to predict Alzheimer's disease compound-protein interaction relationships. CKG-IMC comprises three modules: a collaborative knowledge graph (CKG), a principal neighborhood aggregation graph neural network (PNA), and an inductive matrix completion (IMC). The collaborative knowledge graph is used to learn semantic associations between entities, PNA is employed to extract structural features of the relationship network, and IMC is utilized for CPIs prediction. Compared with a total of 16 baseline models based on similarities, knowledge graphs, and graph neural networks, our model achieves state-of-the-art performance in experiments of 10-fold cross-validation and independent test. Furthermore, we use CKG-IMC to predict compounds interacting with two confirmed AD targets, 42-amino-acid β-amyloid (Aβ42) protein and microtubule-associated protein tau (tau protein), as well as proteins interacting with five FDA-approved anti-AD drugs. The results indicate that the majority of predictions are supported by literature, and molecular docking experiments demonstrate a strong affinity between the predicted compounds and targets.
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Affiliation(s)
- Yongna Yuan
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China.
| | - Rizhen Hu
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Siming Chen
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Xiaopeng Zhang
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
| | - Zhenyu Liu
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China; School of Cyberspace Security, Gansu University of Political Science and Law, Anning West Road, Lanzhou, 730070, Gansu, China
| | - Gonghai Zhou
- School of Information Science & Engineering, Lanzhou University, South Tianshui Road, Lanzhou, 730000, Gansu, China
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2
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Jang W, Song EL, Mun SJ, Bong KW. Efficient isolation of encoded microparticles in a degassed micromold for highly sensitive and multiplex immunoassay with signal amplification. Biosens Bioelectron 2024; 261:116465. [PMID: 38850735 DOI: 10.1016/j.bios.2024.116465] [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: 03/12/2024] [Revised: 05/29/2024] [Accepted: 06/02/2024] [Indexed: 06/10/2024]
Abstract
Multiplex detection of low-abundance protein biomarkers in biofluids can contribute to diverse biomedical fields such as early diagnosis and precision medicine. However, conventional techniques such as digital ELISA, microarray, and hydrogel-based assay still face limitations in terms of efficient protein detection due to issues with multiplexing capability, sensitivity, or complicated assay procedures. In this study, we present the degassed micromold-based particle isolation technique for highly sensitive and multiplex immunoassay with enzymatic signal amplification. Using degassing treatment of nanoporous polydimethylsiloxane (PDMS) micromold, the encoded particles are isolated in the mold within 5 min absorbing trapped air bubbles into the mold by air suction capability. Through 10 min of signal amplification in the isolated spaces by fluorogenic substrate and horseradish peroxidase labeled in the particle, the assay signal is amplified with one order of magnitude compared to that of the standard hydrogel-based assay. Using the signal amplification assay, vascular endothelial growth factor (VEGF) and chorionic gonadotropin beta (CG beta), the preeclampsia-related protein biomarkers, are quantitatively detected with a limit of detection (LoD) of 249 fg/mL and 476 fg/mL in phosphate buffer saline. The multiplex immunoassay is conducted to validate negligible non-specific detection signals and robust recovery rates in the multiplex assay. Finally, the VEGF and CG beta in real urine samples are simultaneously and quantitatively detected by the developed assay. Given the high sensitivity, multiplexing capability, and process simplicity, the presented particle isolation-based signal amplification assay holds significant potential in biomedical and proteomic fields.
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Affiliation(s)
- Wookyoung Jang
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - E Loomee Song
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Seok Joon Mun
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Ki Wan Bong
- Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea.
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3
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Fan T, Li C, Liu X, Xu H, Li W, Wang M, Mei X, Li D. Development of practical techniques for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. ANAL SCI 2023; 39:1839-1856. [PMID: 37517003 DOI: 10.1007/s44211-023-00396-4] [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: 04/14/2023] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Countless individuals have fallen victim to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have generated antibodies, reducing the risk of secondary infection in the short term. However, with the emergence of mutated strains, the probability of subsequent infections remains high. Consequently, the demand for simple and accessible methods for distinguishing between different variants is soaring. Although monitoring viral gene sequencing is an effective approach for differentiating between various types of SARS-CoV-2 variants, it may not be easily accessible to the general public. In this article, we provide an overview of the reported techniques that use combined approaches and adaptable testing methods that use editable recognition receptors for simultaneous detection and distinction of current and emerging SARS-CoV-2 variants. These techniques employ straightforward detection strategies, including tests capable of simultaneously identifying and differentiating between different variants. Furthermore, we recommend advancing the development of uncomplicated protocols for distinguishing between current and emerging variants. Additionally, we propose further development of facile protocols for the differentiation of existing and emerging variants.
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Affiliation(s)
- Tuocen Fan
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Chengjie Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xinlei Liu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Hongda Xu
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Wenhao Li
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Minghao Wang
- Jinzhou Medical University, Jinzhou, 121000, China
| | - Xifan Mei
- Jinzhou Medical University, Jinzhou, 121000, China.
| | - Dan Li
- Jinzhou Medical University, Jinzhou, 121000, China.
- College of Pharmacy, Jinzhou Medical University, Jinzhou, 121000, China.
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4
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Jović M, Prim D, Righini O, Tagan D, Stäuble M, Pignat M, Gallay S, Geiser M, Pfeifer ME. A novel point-of-care diagnostic prototype system for the simultaneous electrochemiluminescent sensing of multiple traumatic brain injury biomarkers. SENSORS & DIAGNOSTICS 2023; 2:964-975. [PMID: 37465008 PMCID: PMC10351028 DOI: 10.1039/d3sd00090g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/29/2023] [Indexed: 07/20/2023]
Abstract
Traumatic brain injuries (TBI) are typically acquired when a sudden violent event causes damage to the brain tissue. A high percentage (70-85%) of all TBI patients are suffering from mild TBI (mTBI), which is often difficult to detect and diagnose with standard imaging tools (MRI, CT scan) due to the absence of significant lesions and specific symptoms. Recent studies suggest that a screening test based on the measurement of a protein biomarker panel directly from a patient's blood can facilitate mTBI diagnosis. Herein, we report a novel prototype system designed as a precursor of a future hand-held point-of-care (POC) diagnostic device for the simultaneous multi-biomarker sensing, employing a microarray-type spatially resolved electrochemiluminescence immunoassay (SR-ECLIA). The small tabletop prototype consists of a screen-printed electrode compartment to conduct multi-analyte ECL sandwich assays, a potentiostat module and a light collection module, all integrated into a compact 3D-printed housing (18.2 × 16.5 × 5.0 cm), as well as an sCMOS detector. Based on this design concept, further miniaturization, system integration, performance optimization and clinical evaluation shall pave the way towards the development of a portable instrument for use at the site of accident and healthcare. To demonstrate the system's feasibility, current performance and efficiency, the simultaneous detection of three mTBI biomarkers (GFAP, h-FABP, S100β) in 50% serum was achieved in the upper pg mL-1 range. The proposed device is amenable to the detection of other biomarker panels and thus could open new medical diagnostic avenues for sensitive multi-analyte measurements with low-volume biological sample requirements.
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Affiliation(s)
- Milica Jović
- Diagnostic Systems Research Group, Institute of Life Technologies, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 19 1950 Sion Switzerland
| | - Denis Prim
- Diagnostic Systems Research Group, Institute of Life Technologies, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 19 1950 Sion Switzerland
| | - Ophélie Righini
- Diagnostic Systems Research Group, Institute of Life Technologies, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 19 1950 Sion Switzerland
| | - David Tagan
- Institute of Systems Engineering, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 23 1950 Sion Switzerland
| | - Mélanie Stäuble
- Diagnostic Systems Research Group, Institute of Life Technologies, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 19 1950 Sion Switzerland
| | - Marc Pignat
- Institute of Systems Engineering, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 23 1950 Sion Switzerland
| | - Steve Gallay
- Institute of Systems Engineering, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 23 1950 Sion Switzerland
| | | | - Marc E Pfeifer
- Diagnostic Systems Research Group, Institute of Life Technologies, School of Engineering, University of Applied Sciences and Arts Western Switzerland (HES-SO Valais-Wallis) Rue de l'Industrie 19 1950 Sion Switzerland
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5
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Juanes-Velasco P, Arias-Hidalgo C, Landeira-Viñuela A, Nuño-Soriano A, Fuentes-Vacas M, Góngora R, Hernández ÁP, Fuentes M. Functional proteomics based on protein microarray technology for biomedical research. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 138:49-65. [PMID: 38220432 DOI: 10.1016/bs.apcsb.2023.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
This chapter traces a route through Proteomics from its origins to the present day. The different proteomics applications are discussed with a focus on microarray technology. Analytical microarrays, functional microarrays and reverse phase microarrays and their different applications are discussed. Several studies are mentioned where the great versatility of this approach is shown. Finally, the advantages and future challenges of microarray technology are outlined.
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Affiliation(s)
- Pablo Juanes-Velasco
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Carlota Arias-Hidalgo
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Alicia Landeira-Viñuela
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ana Nuño-Soriano
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Marina Fuentes-Vacas
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Rafa Góngora
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain
| | - Ángela-Patricia Hernández
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Department of Pharmaceutical Sciences: Organic Chemistry, Faculty of Pharmacy, University of Salamanca, CIETUS, IBSAL, Salamanca, Spain
| | - Manuel Fuentes
- Department of Medicine and General Cytometry Service-Nucleus, CIBERONC, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain; Proteomics Unit, Cancer Research Centre (IBMCC/CSIC/USAL/IBSAL), Salamanca, Spain.
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6
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Comparison of blocking reagents for antibody microarray-based immunoassays on glass and paper membrane substrates. Anal Bioanal Chem 2023; 415:1967-1977. [PMID: 36829042 DOI: 10.1007/s00216-023-04614-w] [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: 01/17/2023] [Revised: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 02/26/2023]
Abstract
Background noise due to nonspecific binding of biomolecules on the assay substrates is one of the most common challenges that limits the sensitivity of microarray-based immunoassays. Background signal intensity usually increases when complex biological fluids are used because they have a combination of molecules and vesicles that can adsorb onto substrate surfaces. Blocking strategies coupled with surface chemistries can reduce such nonspecific binding and improve assay sensitivity. In this paper, we conducted a systematic optimization of blocking strategies on a variety of commonly used substrates for protein measurement in complex biofluids. Four blocking strategies (BSA, non-fat milk, PEG, and a protein-free solution) coupled with four surface chemistries (3-glycidoxypropyltrimethoxysilane (GPS), poly-L-lysine (PLL), aminoalkylsilane (AAS), and nitrocellulose (NC)) were studied for their effect on background, microspot, and net signal intensities. We have also explored the effect that these blocking strategies have when proteins in complex samples (plasma, serum, cell culture media, and EV lysate) are measured. Irregular spot morphology could affect signal extraction using automated software. We found that the microspots with the best morphology were the ones printed on GPS glass surfaces for all immunoassays. On NC membrane, the protein-based blocking strategies yielded the highest net fluorescent intensity with the antigen contained in PBS, plasma, serum, and serum-free cell culture media. Differently, with EV lysate samples, Pierce™ protein-free blocker yielded the best net signal intensity on both GPS and NC surfaces. The choice of blocking strategies highly depends on the substrate. Moreover, the findings discovered in this study are not limited to microarray-based immunoassays but can provide insights for other assay formats.
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7
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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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8
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Thornton EL, Paterson SM, Gidden Z, Horrocks MH, Laohakunakorn N, Regan L. Self-Assembling Protein Surfaces for In Situ Capture of Cell-Free-Synthesized Proteins. Front Bioeng Biotechnol 2022; 10:915035. [PMID: 35875503 PMCID: PMC9300835 DOI: 10.3389/fbioe.2022.915035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/16/2022] [Indexed: 11/13/2022] Open
Abstract
We present a new method for the surface capture of proteins in cell-free protein synthesis (CFPS). We demonstrate the spontaneous self-assembly of the protein BslA into functionalizable surfaces on the surface of a CFPS reaction chamber. We show that proteins can be covalently captured by such surfaces, using “Catcher/Tag” technology. Importantly, proteins of interest can be captured either when synthesised in situ by CFPS above the BslA surfaces, or when added as pure protein. The simplicity and cost efficiency of this method suggest that it will find many applications in cell-free-based methods.
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Affiliation(s)
- Ella Lucille Thornton
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Sarah Maria Paterson
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Zoe Gidden
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Nadanai Laohakunakorn
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Nadanai Laohakunakorn, ; Lynne Regan,
| | - Lynne Regan
- Centre for Synthetic and Systems Biology, Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Nadanai Laohakunakorn, ; Lynne Regan,
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9
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Janson N, Heinks T, Beuel T, Alam S, Höhne M, Bornscheuer UT, Fischer von Mollard G, Sewald N. Efficient Site‐Selective Immobilization of Aldehyde‐Tagged Peptides and Proteins by Knoevenagel Ligation. ChemCatChem 2021. [DOI: 10.1002/cctc.202101485] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Nils Janson
- Faculty of Chemistry Organic and Bioorganic Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Tobias Heinks
- TFaculty of Chemistry, Biochemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Tobias Beuel
- TFaculty of Chemistry, Biochemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Sarfaraz Alam
- TFaculty of Chemistry, Biochemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
| | - Matthias Höhne
- Institute of Biochemistry Greifswald University Felix-Hausdorff-Straße 4 17487 Greifswald Germay
| | - Uwe T. Bornscheuer
- Institute of Biochemistry Greifswald University Felix-Hausdorff-Straße 4 17487 Greifswald Germay
| | | | - Norbert Sewald
- Faculty of Chemistry Organic and Bioorganic Chemistry Bielefeld University Universitätsstraße 25 33615 Bielefeld Germany
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10
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Di Natale C, Battista E, Lettera V, Reddy N, Pitingolo G, Vecchione R, Causa F, Netti PA. Easy Surface Functionalization and Bioconjugation of Peptides as Capture Agents of a Microfluidic Biosensing Platform for Multiplex Assay in Serum. Bioconjug Chem 2021; 32:1593-1601. [PMID: 34114801 PMCID: PMC8382222 DOI: 10.1021/acs.bioconjchem.1c00146] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/28/2021] [Indexed: 12/11/2022]
Abstract
The development of assays for protein biomarkers in complex matrices is a demanding task that still needs implementation of new approaches. Antibodies as capture agents have been largely used in bioassays but their low stability, low-efficiency production, and cross-reactivity in multiplex approaches impairs their larger applications. Instead, synthetic peptides, even with higher stability and easily adapted amino acid sequences, still remain largely unexplored in this field. Here, we provide a proof-of-concept of a microfluidic device for direct detection of biomarker overexpression. The multichannel microfluidic polydimethylsiloxane (PDMS) device was first derivatized with PAA (poly(acrylic acid)) solution. CRP-1, VEGF-114, and ΦG6 peptides were preliminarily tested to respectively bind the biomarkers, C-reactive protein (CRP), vascular endothelial growth factor (VEGF), and tumor necrosis factor-alpha (TNF-α). Each PDMS microchannel was then respectively bioconjugated with a specific peptide (CRP-1, VEGF-114, or ΦG6) to specifically capture CRP, VEGF, and TNF-α. With such microdevices, a fluorescence bioassay has been set up with sensitivity in the nanomolar range, both in buffered solution and in human serum. The proposed multiplex assay worked with a low amount of sample (25 μL) and detected biomarker overexpression (above nM concentration), representing a noninvasive and inexpensive screening platform.
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Affiliation(s)
- Concetta Di Natale
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Edmondo Battista
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Vincenzo Lettera
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- Biopox
srl, Viale Maria Bakunin
12, 80125 Naples, Italy
| | - Narayana Reddy
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Gabriele Pitingolo
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Raffaele Vecchione
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
| | - Filippo Causa
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica del Materiali e della Produzione Industriale
(DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Paolo Antonio Netti
- Center
for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Largo Barsanti e Matteucci 53, 80125 Naples, Italy
- InterdisciplinaryResearch
Centre on Biomaterials (CRIB), Università
degli Studi di Napoli “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
- Dipartimento
di Ingegneria Chimica del Materiali e della Produzione Industriale
(DICMAPI), University “Federico II”, Piazzale Tecchio 80, 80125 Naples, Italy
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11
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McSweeney MA, Styczynski MP. Effective Use of Linear DNA in Cell-Free Expression Systems. Front Bioeng Biotechnol 2021; 9:715328. [PMID: 34354989 PMCID: PMC8329657 DOI: 10.3389/fbioe.2021.715328] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/06/2021] [Indexed: 12/27/2022] Open
Abstract
Cell-free expression systems (CFEs) are cutting-edge research tools used in the investigation of biological phenomena and the engineering of novel biotechnologies. While CFEs have many benefits over in vivo protein synthesis, one particularly significant advantage is that CFEs allow for gene expression from both plasmid DNA and linear expression templates (LETs). This is an important and impactful advantage because functional LETs can be efficiently synthesized in vitro in a few hours without transformation and cloning, thus expediting genetic circuit prototyping and allowing expression of toxic genes that would be difficult to clone through standard approaches. However, native nucleases present in the crude bacterial lysate (the basis for the most affordable form of CFEs) quickly degrade LETs and limit expression yield. Motivated by the significant benefits of using LETs in lieu of plasmid templates, numerous methods to enhance their stability in lysate-based CFEs have been developed. This review describes approaches to LET stabilization used in CFEs, summarizes the advancements that have come from using LETs with these methods, and identifies future applications and development goals that are likely to be impactful to the field. Collectively, continued improvement of LET-based expression and other linear DNA tools in CFEs will help drive scientific discovery and enable a wide range of applications, from diagnostics to synthetic biology research tools.
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Affiliation(s)
- Megan A McSweeney
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
| | - Mark P Styczynski
- Georgia Institute of Technology, School of Chemical & Biomolecular Engineering, Atlanta, GA, United States
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12
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Hook AL, Hogwood J, Gray E, Mulloy B, Merry CLR. High sensitivity analysis of nanogram quantities of glycosaminoglycans using ToF-SIMS. Commun Chem 2021; 4:67. [PMID: 36697531 PMCID: PMC9814553 DOI: 10.1038/s42004-021-00506-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/07/2021] [Indexed: 01/28/2023] Open
Abstract
Glycosaminoglycans (GAGs) are important biopolymers that differ in the sequence of saccharide units and in post polymerisation alterations at various positions, making these complex molecules challenging to analyse. Here we describe an approach that enables small quantities (<200 ng) of over 400 different GAGs to be analysed within a short time frame (3-4 h). Time of flight secondary ion mass spectrometry (ToF-SIMS) together with multivariate analysis is used to analyse the entire set of GAG samples. Resultant spectra are derived from the whole molecules and do not require pre-digestion. All 6 possible GAG types are successfully discriminated, both alone and in the presence of fibronectin. We also distinguish between pharmaceutical grade heparin, derived from different animal species and from different suppliers, to a sensitivity as low as 0.001 wt%. This approach is likely to be highly beneficial in the quality control of GAGs produced for therapeutic applications and for characterising GAGs within biomaterials or from in vitro cell culture.
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Affiliation(s)
- Andrew L. Hook
- grid.4563.40000 0004 1936 8868Advanced Materials and Healthcare Technology, University of Nottingham, Nottingham, UK
| | - John Hogwood
- grid.70909.370000 0001 2199 6511National Institute for Biological Standards and Control, Potters Bar, UK
| | - Elaine Gray
- grid.70909.370000 0001 2199 6511National Institute for Biological Standards and Control, Potters Bar, UK ,grid.13097.3c0000 0001 2322 6764Institute for Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, Stamford Street, London, UK
| | - Barbara Mulloy
- grid.13097.3c0000 0001 2322 6764Institute for Pharmaceutical Science, King’s College London, Franklin-Wilkins Building, Stamford Street, London, UK
| | - Catherine L. R. Merry
- grid.4563.40000 0004 1936 8868Stem Cell Glycobiology Group, Biodiscovery Institute, Faculty of Medicine and Health Sciences, University of Nottingham, Nottingham, UK
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13
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Evans SE, Harrington T, Rodriguez Rivero MC, Rognin E, Tuladhar T, Daly R. 2D and 3D inkjet printing of biopharmaceuticals - A review of trends and future perspectives in research and manufacturing. Int J Pharm 2021; 599:120443. [PMID: 33675921 DOI: 10.1016/j.ijpharm.2021.120443] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/24/2021] [Accepted: 02/25/2021] [Indexed: 12/13/2022]
Abstract
There is an ongoing global shift in pharmaceutical business models from small molecule drugs to biologics. This increase in complexity is in response to advancements in our diagnoses and understanding of diseases. With the more targeted approach coupled with its inherently more costly development and manufacturing, 2D and 3D printing are being explored as suitable techniques to deliver more personalised and affordable routes to drug discovery and manufacturing. In this review, we explore first the business context underlying this shift to biopharmaceuticals and provide an update on the latest work exploring discovery and pharmaceutics. We then draw on multiple disciplines to help reveal the shared challenges facing researchers and firms aiming to develop biopharmaceuticals, specifically when using the most commonly explored manufacturing routes of drop-on-demand inkjet printing and pneumatic extrusion. This includes separating out how to consider mechanical and chemical influences during manufacturing, the role of the chosen hardware and the challenges of aqueous formulation based on similar challenges being faced by the printing industry. Together, this provides a review of existing work and guidance for researchers and industry to help with the de-risking and rapid development of future biopharmaceutical products.
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Affiliation(s)
| | | | | | - Etienne Rognin
- Institute for Manufacturing, Department of Engineering, University of Cambridge (UK), UK
| | | | - Ronan Daly
- Institute for Manufacturing, Department of Engineering, University of Cambridge (UK), UK.
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14
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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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15
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Toren P, Smolka M, Haase A, Palfinger U, Nees D, Ruttloff S, Kuna L, Schaude C, Jauk S, Rumpler M, Hierschlager B, Katzmayr I, Sonnleitner M, Thesen MW, Lohse M, Horn M, Weigel W, Strbac M, Bijelic G, Hemanth S, Okulova N, Kafka J, Kostler S, Stadlober B, Hesse J. High-throughput roll-to-roll production of polymer biochips for multiplexed DNA detection in point-of-care diagnostics. LAB ON A CHIP 2020; 20:4106-4117. [PMID: 33090158 DOI: 10.1039/d0lc00751j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Roll-to-roll UV nanoimprint lithography has superior advantages for high-throughput manufacturing of micro- or nano-structures on flexible polymer foils with various geometries and configurations. Our pilot line provides large-scale structure imprinting for cost-effective polymer biochips (4500 biochips/hour), enabling rapid and multiplexed detections. A complete high-volume process chain of the technology for producing structures like μ-sized, triangular optical out-couplers or capillary channels (width: from 1 μm to 2 mm, height: from 200 nm up to 100 μm) to obtain biochips (width: 25 mm, length: 75 mm, height: 100 μm to 1.5 mm) was described. The imprinting process was performed with custom-developed resins on polymer foils with resin thicknesses ranging between 125-190 μm. The produced chips were tested in a commercial point-of-care diagnostic system for multiplexed DNA analysis of methicillin resistant Staphylococcus aureus (e.g., mecA, mecC gene detections). Specific target DNA capturing was based on hybridisation between surface bound DNA probes and biotinylated targets from the sample. The immobilised biotinylated targets subsequently bind streptavidin-horseradish peroxidase conjugates, which in turn generate light upon incubation with a chemiluminescent substrate. To enhance the light out-coupling thus to improve the system performance, optical structures were integrated into the design. The limits-of-detection of mecA (25 bp) for chips with and without structures were calculated as 0.06 and 0.07 μM, respectively. Further, foil-based chips with fluidic channels were DNA functionalised in our roll-to-roll micro-array spotter following the imprinting. This straightforward approach of sequential imprinting and multiplexed DNA functionalisation on a single foil was also realised for the first time. The corresponding foil-based chips were able to detect mecA gene DNA sequences down to a 0.25 μM concentration.
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Affiliation(s)
- Pelin Toren
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Martin Smolka
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Anja Haase
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Ursula Palfinger
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Dieter Nees
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Stephan Ruttloff
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Ladislav Kuna
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Cindy Schaude
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Sandra Jauk
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Markus Rumpler
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Health - Institute for Biomedicine and Health Sciences, 8010 Graz, Austria
| | | | | | | | | | - Mirko Lohse
- micro resist technology GmbH, 12555 Berlin, Germany
| | | | | | - Matija Strbac
- TECNALIA Research & Innovation, E-48160 Derio, Bizkaia, Spain
| | - Goran Bijelic
- TECNALIA Research & Innovation, E-48160 Derio, Bizkaia, Spain
| | | | | | - Jan Kafka
- INMOLD A/S, Savsvinget 4B, DK-2970 Horsholm, Denmark
| | - Stefan Kostler
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Barbara Stadlober
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
| | - Jan Hesse
- JOANNEUM RESEARCH Forschungsgesellschaft mbH, Materials-Institute for Surface Technologies and Photonics, A-8160 Weiz, Austria.
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16
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Li BW, Zhang Y, Wang YC, Xue Y, Nie XY. Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes. ACS Synth Biol 2020; 9:2267-2273. [PMID: 32810400 DOI: 10.1021/acssynbio.0c00343] [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
A streamlined approach toward the rapid fabrication of streptavidin-biotin-based protein microarrays was investigated. First, using our engineered versatile plasmid (pBADcM-tBirA) and an optimal coexpression strategy for biotin ligase and biotin acceptor peptide (BAP) chimeric recombinant protein, an autogeneration system for biotinylated probes was developed. This system permitted an advantageous biotinylation of BAP chimeric recombinant proteins, providing a strategy for the high-throughput synthesis of biotinylated probes. Then, to bypass the conventional rate-limiting steps, we employed an on-chip purification process to immobilize the biotinylated probes with high-throughput recombinant lysates. The integration of the autogeneration of probes and on-chip purification not only contributed to the effective and reliable fabrication of the protein microarray, but also enabled simplification of the process and an automated throughput format. This labor- and cost-effective approach may facilitate the use of protein microarrays for diagnosis, pharmacology, proteomics, and other laboratory initiatives.
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Affiliation(s)
- Bo-Wen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yi Zhang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yin-Chun Wang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yang Xue
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Xin-Yi Nie
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
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17
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Li X, Li L, Liu X, Wu J, Sun X, Li Z, Geng YJ, Liu F, Zhou Y. Attenuation of Cardiac Ischaemia-reperfusion Injury by Treatment with Hydrogen-rich Water. Curr Mol Med 2020; 19:294-302. [PMID: 30907314 PMCID: PMC7061975 DOI: 10.2174/1566524019666190321113544] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 02/18/2019] [Accepted: 03/19/2019] [Indexed: 02/07/2023]
Abstract
Background: Hydrogen has been shown to exert a bioactive effect on the myocardium. This study examined the signalling pathways for hydrogen attenuating ischaemia-reperfusion injury. Methods: In total, 20 male Wistar rats were evaluated for the effects of hydrogen-rich water on ischaemia-reperfusion in hearts. Left ventricular tissue was taken for screening and analysis of active protein factors by protein chip technology. The enrichment of the KEGG pathway was obtained by using the Gene Ontology (GO) enrichment principle. The expression of JAK2, STAT1, STAT3, p-STAT1, p-JAK2, p-STAT3 in rat myocardium was detected by Western blot analysis and immunohistochemistry. The apoptosis rates of the control and hydrogen-rich water groups were detected by TUNEL staining. Results: The expression levels of 25 proteins, including five transduction pathways, were downregulated in the hydrogen-rich water group. The expression levels of p-JAK2/JAK2, p-STAT3/STAT3 were upregulated in the hydrogen-rich water group compared with the control group, and p-STAT1/STAT1 was downregulated in the hydrogen-rich water group compared with the control group. Furthermore, the apoptosis rate was significantly decreased in the hydrogen-rich water group, as well. Conclusion: Hydrogen-rich water may inhibit the apoptosis of cardiomyocytes after ischaemia-reperfusion by upregulating the expression of the JAK2-STAT3 signalling pathway, which reduces ischaemia-reperfusion injury.
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Affiliation(s)
- Xiangzi Li
- School of Medicine, Hebei University, Baoding 071000, China
| | - Liangtong Li
- School of Medicine, Hebei University, Baoding 071000, China
| | - Xuanchen Liu
- School of Medicine, Hebei University, Baoding 071000, China
| | - Jiawen Wu
- School of Medicine, Hebei University, Baoding 071000, China
| | - Xiaoyu Sun
- School of Medicine, Hebei University, Baoding 071000, China
| | - Zhilin Li
- School of Chemistry, Hebei University, Baoding 071000, China
| | - Yong-Jian Geng
- Centre for Cardiovascular Biology and Atherosclerosis Research, Division of Cardiovascular Medicine, Department of Internal Medicine, University of Texas Medical School at Houston, Houston, TX 77030, United States
| | - Fulin Liu
- School of Medicine, Hebei University, Baoding 071000, China.,Department of Cardiac Surgery, Affiliated Hospital of Hebei University, Baoding 071000, China
| | - Yujuan Zhou
- School of Medicine, Hebei University, Baoding 071000, China
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18
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Fauser J, Savitskiy S, Fottner M, Trauschke V, Gulen B. Sortase-Mediated Quantifiable Enzyme Immobilization on Magnetic Nanoparticles. Bioconjug Chem 2020; 31:1883-1892. [DOI: 10.1021/acs.bioconjchem.0c00322] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Joel Fauser
- Department of Biochemistry and Signaltransduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20251, Hamburg, Germany
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Sergey Savitskiy
- Department of Biochemistry and Signaltransduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20251, Hamburg, Germany
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Maximilian Fottner
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
| | - Vanessa Trauschke
- Department of Chemistry, Center for Nanoscience (CeNS), Ludwig Maximilians-Universität, Schellingstrasse 4, 80799, Munich, Germany
| | - Burak Gulen
- Department of Biochemistry and Signaltransduction, University Medical Center Hamburg-Eppendorf (UKE), Martinistrasse 52, 20251, Hamburg, Germany
- Center for Integrated Protein Science Munich (CIPSM), Department Chemistry, Technical University of Munich, Lichtenbergstrasse 4, 85748, Garching, Germany
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19
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Affiliation(s)
- Christin Bednarek
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Ilona Wehl
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
| | - Nicole Jung
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Functional Interfaces, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, D-76131 Karlsruhe, Germany
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology (KIT), Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
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20
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Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S. Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection. J Am Chem Soc 2019; 141:12974-12978. [PMID: 31373491 DOI: 10.1021/jacs.9b06061] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
O-GlcNAc is an abundant post-translational modification found on nuclear and cytoplasmic proteins in all metazoans. This modification regulates a wide variety of cellular processes, and elevated O-GlcNAc levels have been implicated in cancer progression. A single essential enzyme, O-GlcNAc transferase (OGT), is responsible for all nucleocytoplasmic O-GlcNAcylation. Understanding how this enzyme chooses its substrates is critical for understanding, and potentially manipulating, its functions. Here we use protein microarray technology and proteome-wide glycosylation profiling to show that conserved aspartate residues in the tetratricopeptide repeat (TPR) lumen of OGT drive substrate selection. Changing these residues to alanines alters substrate selectivity and unexpectedly increases rates of protein glycosylation. Our findings support a model where sites of glycosylation for many OGT substrates are determined by TPR domain contacts to substrate side chains five to fifteen residues C-terminal to the glycosite. In addition to guiding design of inhibitors that target OGT's TPR domain, this information will inform efforts to engineer substrates to explore biological functions.
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Affiliation(s)
- Cassandra M Joiner
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
| | - Zebulon G Levine
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
| | - Chanat Aonbangkhen
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology , Harvard University , 12 Oxford Street , Cambridge , Massachusetts 02138 , United States
| | - Suzanne Walker
- Department of Microbiology , Harvard Medical School , 4 Blackfan Circle , Boston , Massachusetts 02115 , United States
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21
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Xiao Q, Bi Z, Yao L, Lei J, Yan Y, Zhou J, Yan L. Novel protein microarray for the detection of avian influenza virus antibodies and simultaneous distinction of antibodies against H5 and H7 subtypes. Avian Pathol 2019; 48:528-536. [PMID: 31232095 DOI: 10.1080/03079457.2019.1634791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Avian influenza virus (AIV) can cause serious zoonotic disease, thereby threatening the poultry industry and human health. An efficient and rapid detection approach is crucial to prevent and control the spread of avian influenza. In this study, a novel protein microarray was developed. Haemagglutinin proteins of H5 and H7 subtypes and nucleoprotein (NP) were purified and spotted onto the initiator-integrated poly-(dimethylsiloxane) as antigens. Monoclonal antibodies with inhibition effect were screened and utilized for the synchronous detection of three avian influenza antibodies in different species. In the protein microarray, the cut-off values were 40%, 50% and 30% inhibition for H5 antibody detection; 50%, 50% and 20% for NP antibody detection; 40%, 50% and 40% for H7 antibody detection in chicken, peacock and duck sera, respectively. The 95 serum samples were detected by microarray, and results were compared with the findings of AIV antibody test enzyme-linked immunosorbent assay (ELISA) or haemagglutination inhibition (HI) test. NP antibody detection in the microarray showed 100% (55/55) agreement ratio in chicken using ELISA. Compared with HI, H5 antibody detection in the microarray showed 100% (95/95) agreement ratio in chicken, peacock and duck, whilst those of H7 displayed 98.18% (54/55) agreement in chicken, 100% (20/20) in peacock and 90% (18/20) in duck. In conclusion, this novel protein microarray is a high-throughput and specific method for the detection of AIV antibodies and simultaneous distinction of antibodies against H5 and H7 subtypes. It can be applied to the serological diagnosis and epidemiological investigation of AIV. RESEARCH HIGHLIGHTS A novel protein microarray method has been developed. The microarray can detect AIV antibodies and distinguish between H5 and H7 subtypes. The study lays the foundation for simultaneous identification of multiple pathogens.
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Affiliation(s)
- Qian Xiao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Jiangsu Detection Center of Terrestrial Wildlife Disease, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , People's Republic of China
| | - Zhenwei Bi
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Jiangsu Detection Center of Terrestrial Wildlife Disease, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , People's Republic of China
| | - Lu Yao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Jiangsu Detection Center of Terrestrial Wildlife Disease, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , People's Republic of China
| | - Jing Lei
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Jiangsu Detection Center of Terrestrial Wildlife Disease, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , People's Republic of China
| | - Yan Yan
- Key Laboratory of Animal Virology and Department of Veterinary Medicine, Zhejiang University , Hangzhou , People's Republic of China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology and Department of Veterinary Medicine, Zhejiang University , Hangzhou , People's Republic of China
| | - Liping Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Jiangsu Detection Center of Terrestrial Wildlife Disease, Institute of Immunology and College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , People's Republic of China
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Cao Y, Li Z, Mao L, Cao H, Kong J, Yu B, Yu C, Liao W. The use of proteomic technologies to study molecular mechanisms of multidrug resistance in cancer. Eur J Med Chem 2019; 162:423-434. [DOI: 10.1016/j.ejmech.2018.10.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 01/18/2023]
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23
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Chen GQ, Xu Y, Shen SM, Zhang J. Phenotype and target-based chemical biology investigations in cancers. Natl Sci Rev 2018; 6:1111-1127. [PMID: 34691990 PMCID: PMC8291603 DOI: 10.1093/nsr/nwy124] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/27/2018] [Accepted: 09/27/2018] [Indexed: 12/14/2022] Open
Abstract
Chemical biology has been attracting a lot of attention because of the key roles of chemical methods and techniques in helping to decipher and manipulate biological systems. Although chemical biology encompasses a broad field, this review will focus on chemical biology aimed at using exogenous chemical probes to interrogate, modify and manipulate biological processes, at the cellular and organismal levels, in a highly controlled and dynamic manner. In this area, many advances have been achieved for cancer biology and therapeutics, from target identification and validation based on active anticancer compounds (forward approaches) to discoveries of anticancer molecules based on some important targets including protein-protein interaction (reverse approaches). Herein we attempt to summarize some recent progresses mainly from China through applying chemical biology approaches to explore molecular mechanisms of carcinogenesis. Additionally, we also outline several new strategies for chemistry to probe cellular activities such as proximity-dependent labeling methods for identifying protein-protein interactions, genetically encoded sensors, and light activating or repressing gene expression system.
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Affiliation(s)
- Guo-Qiang Chen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Ying Xu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Shao-Ming Shen
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine (SJTU-SM), Shanghai 200025, China
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Abstract
Exposure of protein modified surfaces to air may be necessary in several applications. For example, air contact may be inevitable during the implantation of biomedical devices, for analysis of protein modified surfaces, or for sensor applications. Protein coatings are very sensitive to dehydration and can undergo significant and irreversible alterations of their conformations upon exposure to air. With the use of two compatible solutes from extremophilic bacteria, ectoine and hydroxyectoine, the authors were able to preserve the activity of dried protein monolayers for up to >24 h. The protective effect can be explained by the preferred exclusion model; i.e., the solutes trap a thin water layer around the protein, retaining an aqueous environment and preventing unfolding of the protein. Horseradish peroxidase (HRP) immobilized on compact TiO2 was used as a model system. Structural differences between the compatible solute stabilized and unstabilized protein films, and between different solutes, were analyzed by static time-of-flight secondary ion mass spectrometry (ToF-SIMS). The biological activity difference observed in a colorimetric activity assay was correlated to changes in protein conformation by application of principal component analysis to the static ToF-SIMS data. Additionally, rehydration of the denatured HRP was observed in ToF-SIMS with an exposure of denatured protein coatings to ectoine and hydroxyectoine solutions.
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25
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Grawe RW, Knotts TA. The effects of tether placement on antibody stability on surfaces. J Chem Phys 2018; 146:215102. [PMID: 28576081 DOI: 10.1063/1.4983705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.
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Affiliation(s)
- Rebecca W Grawe
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
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26
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Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC. Current applications of antibody microarrays. Clin Proteomics 2018; 15:7. [PMID: 29507545 PMCID: PMC5830343 DOI: 10.1186/s12014-018-9184-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 02/19/2018] [Indexed: 12/14/2022] Open
Abstract
The concept of antibody microarrays is one of the most versatile approaches within multiplexed immunoassay technologies. These types of arrays have increasingly become an attractive tool for the exploratory detection and study of protein abundance, function, pathways, and potential drug targets. Due to the properties of the antibody microarrays and their potential use in basic research and clinical analytics, various types of antibody microarrays have already been developed. In spite of the growing number of studies utilizing this technique, few reviews about antibody microarray technology have been presented to reflect the quality and future uses of the generated data. In this review, we provide a summary of the recent applications of antibody microarray techniques in basic biology and clinical studies, providing insights into the current trends and future of protein analysis.
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Affiliation(s)
- Ziqing Chen
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
| | - Tea Dodig-Crnković
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Jochen M. Schwenk
- Affinity Proteomics, SciLifeLab, KTH - Royal Institute of Technology, 171 65 Solna, Sweden
| | - Sheng-ce Tao
- Key Laboratory of Systems Biomedicine, (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240 China
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
- State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University, Shanghai, 200240 China
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27
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Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes 2018; 11:156. [PMID: 29482592 PMCID: PMC5828362 DOI: 10.1186/s13104-018-3266-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. Electronic supplementary material The online version of this article (10.1186/s13104-018-3266-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Da Gama Duarte
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Tumour Immunology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ryan W Goosen
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Peter J Lawry
- Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Blackburn Laboratory, N3.03, Wernher & Beit Building North, Institute of Infectious Disease & Molecular Medicine, UCT Faculty of Health Sciences, Observatory, Cape Town, 7925, South Africa
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28
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Wang X, Guo T, Chen J, Li X, Zhou Y, Pan Z. Covalent and selective immobilization of GST fusion proteins with fluorophosphonate-based probes. Chem Commun (Camb) 2018. [DOI: 10.1039/c7cc08888d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fluorophosphonate probes covalently immobilize proteins onto solid support by reacting with tyrosine 111 in the GST tag.
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Affiliation(s)
- Xiafeng Wang
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
| | - Tianlin Guo
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
| | - Jiahui Chen
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
| | - Xiaofeng Li
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
| | - Yiqing Zhou
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
| | - Zhengying Pan
- State Key Laboratory of Chemical Oncogenomics
- Key Laboratory of Chemical Genomics
- School of Chemical Biology and Biotechnology
- Shenzhen Graduate School
- Peking University Xili University Town
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29
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Sievers S, Cretich M, Gagni P, Ahrens B, Grishina G, Sampson HA, Niggemann B, Chiari M, Beyer K. Performance of a polymer coated silicon microarray for simultaneous detection of food allergen-specific IgE and IgG4. Clin Exp Allergy 2017; 47:1057-1068. [DOI: 10.1111/cea.12929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 02/13/2017] [Accepted: 03/20/2017] [Indexed: 01/26/2023]
Affiliation(s)
- S. Sievers
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
- Department of Biology, Chemistry and Pharmacy; Free University; Berlin Germany
| | - M. Cretich
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - P. Gagni
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - B. Ahrens
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
| | - G. Grishina
- Icahn School of Medicine at Mount Sinai; New York NY USA
| | - H. A. Sampson
- Icahn School of Medicine at Mount Sinai; New York NY USA
| | - B. Niggemann
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
| | - M. Chiari
- Istituto di Chimica del Riconoscimento Molecolare (ICRM); Consiglio Nazionale delle Ricerche; Milano Italy
| | - K. Beyer
- Pediatric Pneumology and Immunology; Charité Universitätsmedizin; Berlin Germany
- Icahn School of Medicine at Mount Sinai; New York NY USA
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30
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Guo X, Deng Y, Zhu C, Cai J, Zhu X, Landry JP, Zheng F, Cheng X, Fei Y. Characterization of protein expression levels with label-free detected reverse phase protein arrays. Anal Biochem 2016; 509:67-72. [PMID: 27372609 DOI: 10.1016/j.ab.2016.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/24/2016] [Accepted: 06/27/2016] [Indexed: 01/12/2023]
Abstract
In reverse-phase protein arrays (RPPA), one immobilizes complex samples (e.g., cellular lysate, tissue lysate or serum etc.) on solid supports and performs parallel reactions of antibodies with immobilized protein targets from the complex samples. In this work, we describe a label-free detection of RPPA that enables quantification of RPPA data and thus facilitates comparison of studies performed on different samples and on different solid supports. We applied this detection platform to characterization of phosphoserine aminotransferase (PSAT) expression levels in Acanthamoeba lysates treated with artemether and the results were confirmed by Western blot studies.
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Affiliation(s)
- Xuexue Guo
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Yihong Deng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Chenggang Zhu
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China
| | - Junlong Cai
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Xiangdong Zhu
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - James P Landry
- Department of Physics, University of California, Davis, CA, 95616, USA
| | - Fengyun Zheng
- Institutes of Biomedical Science, Fudan University, Shanghai, 200032, China
| | - Xunjia Cheng
- Department of Medical Microbiology and Parasitology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center for Ultra-Precision Optical Manufacturing, Green Photoelectron Platform, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, 200433, China.
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31
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Meldal M, Schoffelen S. Recent advances in covalent, site-specific protein immobilization. F1000Res 2016; 5:F1000 Faculty Rev-2303. [PMID: 27785356 PMCID: PMC5022707 DOI: 10.12688/f1000research.9002.1] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/07/2016] [Indexed: 01/25/2023] Open
Abstract
The properties of biosensors, biomedical implants, and other materials based on immobilized proteins greatly depend on the method employed to couple the protein molecules to their solid support. Covalent, site-specific immobilization strategies are robust and can provide the level of control that is desired in this kind of application. Recent advances include the use of enzymes, such as sortase A, to couple proteins in a site-specific manner to materials such as microbeads, glass, and hydrogels. Also, self-labeling tags such as the SNAP-tag can be employed. Last but not least, chemical approaches based on bioorthogonal reactions, like the azide-alkyne cycloaddition, have proven to be powerful tools. The lack of comparative studies and quantitative analysis of these immobilization methods hampers the selection process of the optimal strategy for a given application. However, besides immobilization efficiency, the freedom in selecting the site of conjugation and the size of the conjugation tag and the researcher's expertise regarding molecular biology and/or chemical techniques will be determining factors in this regard.
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Affiliation(s)
- Morten Meldal
- Center for Evolutionary Chemical Biology, Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
| | - Sanne Schoffelen
- Center for Evolutionary Chemical Biology, Department of Chemistry & Nano-Science Center, University of Copenhagen, Copenhagen, Denmark
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32
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Schinn SM, Broadbent A, Bradley WT, Bundy BC. Protein synthesis directly from PCR: progress and applications of cell-free protein synthesis with linear DNA. N Biotechnol 2016; 33:480-7. [PMID: 27085957 DOI: 10.1016/j.nbt.2016.04.002] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 03/30/2016] [Accepted: 04/07/2016] [Indexed: 11/18/2022]
Abstract
A rapid, versatile method of protein expression and screening can greatly facilitate the future development of therapeutic biologics, proteomic drug targets and biocatalysts. An attractive candidate is cell-free protein synthesis (CFPS), a cell-lysate-based in vitro expression system, which can utilize linear DNA as expression templates, bypassing time-consuming cloning steps of plasmid-based methods. Traditionally, such linear DNA expression templates (LET) have been vulnerable to degradation by nucleases present in the cell lysate, leading to lower yields. This challenge has been significantly addressed in the recent past, propelling LET-based CFPS as a useful tool for studying, screening and engineering proteins in a high-throughput manner. Currently, LET-based CFPS has promise in fields such as functional proteomics, protein microarrays, and the optimization of complex biological systems.
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Affiliation(s)
- Song-Min Schinn
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Andrew Broadbent
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - William T Bradley
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA
| | - Bradley C Bundy
- Department of Chemical Engineering, Brigham Young University, Provo, UT, USA.
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33
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Wang Y, Li H, Xu D. Aptamers-based sandwich assay for silver-enhanced fluorescence multiplex detection. Anal Chim Acta 2015; 905:149-55. [PMID: 26755149 DOI: 10.1016/j.aca.2015.12.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/04/2015] [Accepted: 12/12/2015] [Indexed: 12/26/2022]
Abstract
In this work, aptamers-modified silver nanoparticles (AgNPs) were prepared as capture substrate, and fluorescent dyes-modified aptamers were synthesized as detection probes. The sandwich assay was based on dual aptamers, which was aimed to accomplish the highly sensitive detection of single protein and multiplex detection of proteins on one-spot. We found that aptamers-modified AgNPs based microarray was much superior to the aptamer based microarray in fluorescence detection of proteins. The result shows that the detection limit of the sandwich assay using AgNPs probes for thrombin or platelet-derived growth factor-BB (PDGF-BB) is 80 or 8 times lower than that of aptamers used directly. For multiplex detection of proteins, the detection limit was 625 pM for PDGF-BB and 21 pM for thrombin respectively. The sandwich assay based on dual aptamers and AgNPs was sensitive and specific.
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Affiliation(s)
- Ying Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China; School of Environmental Science, Nanjing Xiaozhuang University, China.
| | - Hui Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
| | - Danke Xu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, China.
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34
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Luo Y, Zhu X, Zhang P, Shen Q, Wang Z, Wen X, Wang L, Gao J, Dong J, Yang C, Wu T, Zhu Z, Tian Y. The clinical performance evaluation of novel protein chips for eleven biomarkers detection and the diagnostic model study. Int J Clin Exp Med 2015; 8:20413-20423. [PMID: 26884957 PMCID: PMC4723802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 10/25/2015] [Indexed: 06/05/2023]
Abstract
We aimed to develop and validate two novel protein chips, which are based on microarray chemiluminescence immunoassay and can simultaneously detected 11 biomarkers, and then to evaluate their clinical diagnostic value by comparing with the traditional methods. Protein chips were evaluated for limit of detection, specificity, common interferences, linearity, precision and accuracy. 11 biomarkers were simultaneously detected by traditional methods and protein chips in 3683 samples, which included 1723 cancer patients, 1798 benign diseases patients and 162 healthy controls. After assay validation, protein chips demonstrated high sensitivity, high specificity, good linearity, low imprecision and were free of common interferences. Compared with the traditional methods, protein chips have good correlation in the detection of all the 13 kinds of biomarkers (r≥0.935, P<0.001). For specific cancer detection, there were no statistically significant differences between the traditional method and novel protein chips, except that male protein chip showed significantly better diagnostic value on NSE detection (P=0.004) but significantly worse value on pro-GRP detection (P=0.012), female chip showed significantly better diagnostic value on pro-GRP detection (P=0.005). Furthermore, both male and female multivariate diagnostic models had significantly better diagnostic value than single detection of PGI, PG II, pro-GRP, NSE and CA125 (P<0.05). In addition, male models had significantly better diagnostic value than single CA199 and free-PSA (P<0.05), while female models observed significantly better diagnostic value than single CA724 and β-HCG (P<0.05). For total disease or cancer detection, the AUC of multivariate logistic regression for the male and female disease detection was 0.981 (95% CI: 0.975-0.987) and 0.836 (95% CI: 0.798-0.874), respectively. While, that for total cancer detection was 0.691 (95% CI: 0.666-0.717) and 0.753 (95% CI: 0.731-0.775), respectively. The new designed protein chips are simple, multiplex and reliable clinical assays and the multi-parameter diagnostic models based on them could significantly improve their clinical performance.
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Affiliation(s)
- Yuan Luo
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General HospitalBeijing, P. R. China
| | - Xu Zhu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital&InstituteBeijing, P. R. China
| | - Pengjun Zhang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Interventional Therapy Department, Peking University Cancer Hospital&InstituteBeijing, P. R. China
| | - Qian Shen
- Department of Laboratory Diagnosis, Changhai Hospital, The Second Military Medical UniversityShanghai, P. R. China
| | - Zi Wang
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General HospitalBeijing, P. R. China
| | - Xinyu Wen
- Department of Clinical Biochemistry, Chinese PLA General HospitalBeijing, P. R. China
| | - Ling Wang
- Department of Clinical Biochemistry, Chinese PLA General HospitalBeijing, P. R. China
| | - Jing Gao
- Department of Clinical Biochemistry, Chinese PLA General HospitalBeijing, P. R. China
| | - Jin Dong
- Department of Clinical Biochemistry, Chinese PLA General HospitalBeijing, P. R. China
| | - Caie Yang
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General HospitalBeijing, P. R. China
| | - Tangming Wu
- Jiangsu Sunlant Bioengineering Co., LtdWuxi, P. R. China
| | - Zheng Zhu
- Jiangsu Sunlant Bioengineering Co., LtdWuxi, P. R. China
| | - Yaping Tian
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General HospitalBeijing, P. R. China
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35
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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36
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Yao C, Wang T, Zhang B, He D, Na N, Ouyang J. Screening of the binding of small molecules to proteins by desorption electrospray ionization mass spectrometry combined with protein microarray. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1950-1958. [PMID: 26174365 DOI: 10.1007/s13361-015-1221-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 06/04/2023]
Abstract
The interaction between bioactive small molecule ligands and proteins is one of the important research areas in proteomics. Herein, a simple and rapid method is established to screen small ligands that bind to proteins. We designed an agarose slide to immobilize different proteins. The protein microarrays were allowed to interact with different small ligands, and after washing, the microarrays were screened by desorption electrospray ionization mass spectrometry (DESI MS). This method can be applied to screen specific protein binding ligands and was shown for seven proteins and 34 known ligands for these proteins. In addition, a high-throughput screening was achieved, with the analysis requiring approximately 4 s for one sample spot. We then applied this method to determine the binding between the important protein matrix metalloproteinase-9 (MMP-9) and 88 small compounds. The molecular docking results confirmed the MS results, demonstrating that this method is suitable for the rapid and accurate screening of ligands binding to proteins. Graphical Abstract ᅟ.
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Affiliation(s)
- Chenxi Yao
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Tao Wang
- Department of Pharmacy, Changzhi Medical College, Changzhi, 046000, People's Republic of China
| | - Buqing Zhang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Dacheng He
- Key Laboratory for Cell Proliferation and Regulation Biology, Ministry of Education Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Na Na
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China
| | - Jin Ouyang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, 100875, People's Republic of China.
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37
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Multiplexed In-cell Immunoassay for Same-sample Protein Expression Profiling. Sci Rep 2015; 5:13651. [PMID: 26328896 PMCID: PMC4556981 DOI: 10.1038/srep13651] [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: 06/18/2015] [Accepted: 08/03/2015] [Indexed: 12/15/2022] Open
Abstract
In-cell immunoassays have become a valuable tool for protein expression analysis complementary to established assay formats. However, comprehensive molecular characterization of individual specimens has proven challenging and impractical due to, in part, a singleplex nature of reporter enzymes and technical complexity of alternative assay formats. Herein, we describe a simple and robust methodology for multiplexed protein expression profiling on the same intact specimen, employing a well-characterized enzyme alkaline phosphatase for accurate quantification of all targets of interest, while overcoming fundamental limitations of enzyme-based techniques by implementing the DNA-programmed release mechanism for segregation of sub-sets of target-bound reporters. In essence, this methodology converts same-sample multi-target labeling into a set of isolated singleplex measurements performed in a parallel self-consistent fashion. For a proof-of-principle, multiplexed detection of three model proteins was demonstrated on cultured HeLa cells, and two clinically-relevant markers of dementia, β-amyloid and PHF-tau, were profiled in formalin-fixed paraffin embedded brain tissue sections, uncovering correlated increase in abundance of both markers in the “Alzheimer’s disease” cohort. Featuring an analytically powerful yet technically simple and robust methodology, multiplexed in-cell immunoassay is expected to enable insightful same-sample protein profiling studies and become broadly adopted in biomedical research and clinical diagnostics.
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38
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Fasolo J, Im H, Snyder MP. Probing High-density Functional Protein Microarrays to Detect Protein-protein Interactions. J Vis Exp 2015:e51872. [PMID: 26274875 DOI: 10.3791/51872] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
High-density functional protein microarrays containing ~4,200 recombinant yeast proteins are examined for kinase protein-protein interactions using an affinity purified yeast kinase fusion protein containing a V5-epitope tag for read-out. Purified kinase is obtained through culture of a yeast strain optimized for high copy protein production harboring a plasmid containing a Kinase-V5 fusion construct under a GAL inducible promoter. The yeast is grown in restrictive media with a neutral carbon source for 6 hr followed by induction with 2% galactose. Next, the culture is harvested and kinase is purified using standard affinity chromatographic techniques to obtain a highly purified protein kinase for use in the assay. The purified kinase is diluted with kinase buffer to an appropriate range for the assay and the protein microarrays are blocked prior to hybridization with the protein microarray. After the hybridization, the arrays are probed with monoclonal V5 antibody to identify proteins bound by the kinase-V5 protein. Finally, the arrays are scanned using a standard microarray scanner, and data is extracted for downstream informatics analysis to determine a high confidence set of protein interactions for downstream validation in vivo.
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Affiliation(s)
| | - Hogune Im
- Department of Genetics, Stanford University
| | - Michael P Snyder
- Department of Genetics, Stanford University; Stanford Center for Genomics and Personalized Medicine, Stanford University;
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Lindsey ML, Mayr M, Gomes AV, Delles C, Arrell DK, Murphy AM, Lange RA, Costello CE, Jin YF, Laskowitz DT, Sam F, Terzic A, Van Eyk J, Srinivas PR. Transformative Impact of Proteomics on Cardiovascular Health and Disease: A Scientific Statement From the American Heart Association. Circulation 2015. [PMID: 26195497 DOI: 10.1161/cir.0000000000000226] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The year 2014 marked the 20th anniversary of the coining of the term proteomics. The purpose of this scientific statement is to summarize advances over this period that have catalyzed our capacity to address the experimental, translational, and clinical implications of proteomics as applied to cardiovascular health and disease and to evaluate the current status of the field. Key successes that have energized the field are delineated; opportunities for proteomics to drive basic science research, facilitate clinical translation, and establish diagnostic and therapeutic healthcare algorithms are discussed; and challenges that remain to be solved before proteomic technologies can be readily translated from scientific discoveries to meaningful advances in cardiovascular care are addressed. Proteomics is the result of disruptive technologies, namely, mass spectrometry and database searching, which drove protein analysis from 1 protein at a time to protein mixture analyses that enable large-scale analysis of proteins and facilitate paradigm shifts in biological concepts that address important clinical questions. Over the past 20 years, the field of proteomics has matured, yet it is still developing rapidly. The scope of this statement will extend beyond the reaches of a typical review article and offer guidance on the use of next-generation proteomics for future scientific discovery in the basic research laboratory and clinical settings.
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A nanocoaxial-based electrochemical sensor for the detection of cholera toxin. Biosens Bioelectron 2015; 74:406-10. [PMID: 26164012 DOI: 10.1016/j.bios.2015.06.069] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Accepted: 06/26/2015] [Indexed: 11/21/2022]
Abstract
Sensitive, real-time detection of biomarkers is of critical importance for rapid and accurate diagnosis of disease for point of care (POC) technologies. Current methods do not allow for POC applications due to several limitations, including sophisticated instrumentation, high reagent consumption, limited multiplexing capability, and cost. Here, we report a nanocoaxial-based electrochemical sensor for the detection of bacterial toxins using an electrochemical enzyme-linked immunosorbent assay (ELISA) and differential pulse voltammetry (DPV) or square wave voltametry (SWV). The device architecture is composed of vertically-oriented, nanoscale coaxial electrodes in array format (~10(6) coaxes per square millimeter). The coax cores and outer shields serve as integrated working and counter electrodes, respectively, exhibiting a nanoscale separation gap corresponding to ~100 nm. Proof-of-concept was demonstrated for the detection of cholera toxin (CT). The linear dynamic range of detection was 10 ng/ml-1 µg/ml, and the limit of detection (LOD) was found to be 2 ng/ml. This level of sensitivity is comparable to the standard optical ELISA used widely in clinical applications, which exhibited a linear dynamic range of 10 ng/ml-1 µg/ml and a LOD of 1 ng/ml. In addition to matching the detection profile of the standard ELISA, the nanocoaxial array provides a simple electrochemical readout and a miniaturized platform with multiplexing capabilities for the simultaneous detection of multiple biomarkers, giving the nanocoax a desirable advantage over the standard method towards POC applications.
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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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Krizkova S, Heger Z, Zalewska M, Moulick A, Adam V, Kizek R. Nanotechnologies in protein microarrays. Nanomedicine (Lond) 2015; 10:2743-55. [PMID: 26039143 DOI: 10.2217/nnm.15.81] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.
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Affiliation(s)
- Sona Krizkova
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Zbynek Heger
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Marta Zalewska
- Department of Biomedical & Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland, European Union
| | - Amitava Moulick
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Vojtech Adam
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Rene Kizek
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
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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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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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Fischer T, Dietrich PM, Streeck C, Ray S, Nutsch A, Shard A, Beckhoff B, Unger WES, Rurack K. Quantification of Variable Functional-Group Densities of Mixed-Silane Monolayers on Surfaces via a Dual-Mode Fluorescence and XPS Label. Anal Chem 2015; 87:2685-92. [DOI: 10.1021/ac503850f] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Tobias Fischer
- Division
1.9 Chemical and Optical Sensing, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
| | - Paul M. Dietrich
- Division
6.8 Surface Analysis and Interfacial Chemistry, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Cornelia Streeck
- X-ray
and IR Spectrometry Group, Physikalisch-Technische Bundesanstalt PTB, Abbestrasse
2-12, 10587 Berlin, Germany
| | - Santanu Ray
- Surface
and Nanoanalysis Group, Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Andreas Nutsch
- X-ray
and IR Spectrometry Group, Physikalisch-Technische Bundesanstalt PTB, Abbestrasse
2-12, 10587 Berlin, Germany
| | - Alex Shard
- Surface
and Nanoanalysis Group, Analytical Science Division, National Physical Laboratory, Hampton Road, Teddington, Middlesex TW11 0LW, United Kingdom
| | - Burkhard Beckhoff
- X-ray
and IR Spectrometry Group, Physikalisch-Technische Bundesanstalt PTB, Abbestrasse
2-12, 10587 Berlin, Germany
| | - Wolfgang E. S. Unger
- Division
6.8 Surface Analysis and Interfacial Chemistry, BAM Federal Institute for Materials Research and Testing, Unter den Eichen 44-46, 12203 Berlin, Germany
| | - Knut Rurack
- Division
1.9 Chemical and Optical Sensing, BAM Federal Institute for Materials Research and Testing, Richard-Willstätter-Strasse 11, 12489 Berlin, Germany
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Groh KJ, Suter MJF. Stressor-induced proteome alterations in zebrafish: a meta-analysis of response patterns. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2015; 159:1-12. [PMID: 25498419 DOI: 10.1016/j.aquatox.2014.11.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2014] [Revised: 11/05/2014] [Accepted: 11/18/2014] [Indexed: 06/04/2023]
Abstract
Proteomics approaches are being increasingly applied in ecotoxicology on the premise that the identification of specific protein expression changes in response to a particular chemical would allow elucidation of the underlying molecular pathways leading to an adverse effect. This in turn is expected to promote the development of focused testing strategies for specific groups of toxicants. Although both gel-based and gel-free global characterization techniques provide limited proteome coverage, the conclusions regarding the cellular processes affected are still being drawn based on the few changes detected. To investigate how specific the detected responses are, we analyzed a set of studies that characterized proteome alterations induced by various physiological, chemical and biological stressors in zebrafish, a popular model organism. Our analysis highlights several proteins and protein groups, including heat shock and oxidative stress defense proteins, energy metabolism enzymes and cytoskeletal proteins, to be most frequently identified as responding to diverse stressors. In contrast, other potentially more specifically responding protein groups are detected much less frequently. Thus, zebrafish proteome responses to stress reported by different studies appear to depend mostly on the level of stress rather than on the specific stressor itself. This suggests that the most broadly used current proteomics technologies do not provide sufficient proteome coverage to allow in-depth investigation of specific mechanisms of toxicant action. We suggest that the results of any differential proteomics experiment performed with zebrafish should be interpreted keeping in mind the list of the most frequent responders that we have identified. Similar reservations should apply to any other species where proteome responses are analyzed by global proteomics methods. Careful consideration of the reliability and significance of observed changes is necessary in order not to over-interpret the experimental results and to prevent the proliferation of false positive linkages between the chemical and the cellular functions it perturbs. We further discuss the implications of the identified "top lists" of frequently responding proteins and protein families, and suggest further directions for proteomics research in ecotoxicology. Apart from improving the proteome coverage, further research should focus on defining the significance of the observed stress response patterns for organism phenotypes and on searching for common upstream regulators that can be targeted by specific assays.
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Affiliation(s)
- Ksenia J Groh
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Chemistry and Applied Biosciences, 8093 Zürich, Switzerland.
| | - Marc J-F Suter
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, 8600 Dübendorf, Switzerland; ETH Zürich, Swiss Federal Institute of Technology, Department of Environmental Systems Science, 8092 Zürich, Switzerland
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Wang JC, Liu W, Tu Q, Ma C, Zhao L, Wang Y, Ouyang J, Pang L, Wang J. High throughput and multiplex localization of proteins and cells for in situ micropatterning using pneumatic microfluidics. Analyst 2015; 140:827-36. [DOI: 10.1039/c4an01972e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We present a micropatterning method for protein/cell localization by using pneumatically controllable microstructures in an integrated microfluidic device.
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Affiliation(s)
- Jian-Chun Wang
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
- Energy Research Institute of Shandong Academy of Sciences
| | - Wenming Liu
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Qin Tu
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Chao Ma
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Lei Zhao
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Yaolei Wang
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Jia Ouyang
- School of Materials Science and Engineering
- Northwestern Polytechnical University
- Xi'an
- China
| | - Long Pang
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
| | - Jinyi Wang
- Colleges of Science and Veterinary Medicine
- Northwest A&F University
- Yangling
- China
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Bidlingmaier S, Liu B. Utilizing Yeast Surface Human Proteome Display Libraries to Identify Small Molecule-Protein Interactions. Methods Mol Biol 2015; 1319:203-14. [PMID: 26060077 PMCID: PMC4838597 DOI: 10.1007/978-1-4939-2748-7_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The identification of proteins that interact with small bioactive molecules is a critical but often difficult and time-consuming step in understanding cellular signaling pathways or molecular mechanisms of drug action. Numerous methods for identifying small molecule-interacting proteins have been developed and utilized, including affinity-based purification followed by mass spectrometry analysis, protein microarrays, phage display, and three-hybrid approaches. Although all these methods have been used successfully, there remains a need for additional techniques for analyzing small molecule-protein interactions. A promising method for identifying small molecule-protein interactions is affinity-based selection of yeast surface-displayed human proteome libraries. Large and diverse libraries displaying human protein fragments on the surface of yeast cells have been constructed and subjected to FACS-based enrichment followed by comprehensive exon microarray-based output analysis to identify protein fragments with affinity for small molecule ligands. In a recent example, a proteome-wide search has been successfully carried out to identify cellular proteins binding to the signaling lipids PtdIns(4,5)P2 and PtdIns(3,4,5)P3. Known phosphatidylinositide-binding proteins such as pleckstrin homology domains were identified, as well as many novel interactions. Intriguingly, many novel nuclear phosphatidylinositide-binding proteins were discovered. Although the existence of an independent pool of nuclear phosphatidylinositides has been known about for some time, their functions and mechanism of action remain obscure. Thus, the identification and subsequent study of nuclear phosphatidylinositide-binding proteins is expected to bring new insights to this important biological question. Based on the success with phosphatidylinositides, it is expected that the screening of yeast surface-displayed human proteome libraries will be of general use for the discovery of novel small molecule-protein interactions, thus facilitating the study of cellular signaling pathways and mechanisms of drug action or toxicity.
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Affiliation(s)
- Scott Bidlingmaier
- Department of Anesthesia, UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 1001 Potrero Avenue, Box 1305, San Francisco, CA, 94110, USA
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Credou J, Volland H, Berthelot T. Photolinker-free photoimmobilization of antibodies onto cellulose for the preparation of immunoassay membranes. J Mater Chem B 2015; 3:1079-1088. [DOI: 10.1039/c4tb01138d] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Immunoassay membranes were produced by photoimmobilization of antibodies onto cellulose without any photocoupling intermediate nor any biomolecule or substrate pretreatment.
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Affiliation(s)
- Julie Credou
- CEA Saclay
- IRAMIS
- NIMBE
- LICSEN (Laboratory of Innovation in Surface Chemistry and Nanosciences)
- F-91191 Gif sur Yvette
| | - Hervé Volland
- CEA Saclay
- iBiTec-S
- SPI
- LERI (Laboratory of Study and Research in Immunoanalysis)
- F-91191 Gif sur Yvette
| | - Thomas Berthelot
- CEA Saclay
- IRAMIS
- NIMBE
- LICSEN (Laboratory of Innovation in Surface Chemistry and Nanosciences)
- F-91191 Gif sur Yvette
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