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McMahon R, Hill C, Rudge J, Herbert B, Karsten E. Stability of inflammation markers in human blood collected using volumetric absorptive microsampling (VAMS) under typical laboratory storage temperatures. Cytokine 2023; 171:156355. [PMID: 37690424 DOI: 10.1016/j.cyto.2023.156355] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 08/28/2023] [Accepted: 08/29/2023] [Indexed: 09/12/2023]
Abstract
Dried blood spots (DBS) collected on filter paper such as Guthrie cards are stored for years at room temperature. The assumption is that once dried, the samples remain stable and quantifiable indefinitely since the metabolites these were initially designed to measure, are known for their extended stability. The concentration of other blood proteins such as cytokines, however, are known to vary with storage even in liquid samples stored at -80 °C for extended periods of time. We sought to determine if cytokines are stable for up to 5 months when stored as a dried blood sample using volumetric absorptive microsampling (VAMS) devices. To test this, blood was collected from 4 healthy participants, spiked with recombinant cytokines, and collected into 30 µL VAMS devices. These prepared VAMS devices were stored at room temperature, 4 °C, or -20 °C for up to 5 months and matching VAMS liquid extracts were stored at -80 °C for the same period of time. At each timepoint, the samples were extracted from the VAMS devices and the extracts were analysed by Luminex® for quantification of up to 31 cytokines. These methods were also tested in a remote clinical study over a period of up to 8 months. Cytokine analysis revealed that room temperature, the current standard for DBS and VAMS storage, performed the poorest out of all storage temperatures with significant losses in 13/21 analytes compared to 4 °C at 5 months. Storage at 4 °C or colder performed well for the majority of analytes tested, however out of those, the optimal storage temperature differed for each analyte. There were a small number of analytes that performed poorly regardless of storage conditions and for fractalkine, this was found to be caused by inefficient recovery during extraction. Cytokine concentrations from finger-prick samples were also found to be much more variable that those in venous blood samples. Our results highlight the need to understand the stability of analytes of interest before committing to longitudinal collection and storage of samples in VAMS devices. These data give confidence that storage at 4 °C or colder was beneficial for cytokine stability. Wherein 25/31 cytokines were quantifiably stable at -20 °C when stored for 3 months and 17/21 were quantifiably stable after 5 months when stored at 4 °C.
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Affiliation(s)
- R McMahon
- Sangui Bio Pty Ltd, Sydney, Australia; The Kolling Institute, Sydney, Australia.
| | - C Hill
- Sangui Bio Pty Ltd, Sydney, Australia; The Kolling Institute, Sydney, Australia
| | - J Rudge
- Trajan Scientific and Medical (Neoteryx), Australia
| | - B Herbert
- Sangui Bio Pty Ltd, Sydney, Australia; The Kolling Institute, Sydney, Australia
| | - E Karsten
- Sangui Bio Pty Ltd, Sydney, Australia; The Kolling Institute, Sydney, Australia; University of Sydney, Australia
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2
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Kuşat K, Bağlamış S, Kuru Cİ, Ulucan F, Uygun M, Akgöl S. p(HEMA)-RR241 hydrogel membranes with micron network for IgG depletion in proteomic studies. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2022; 33:1181-1197. [PMID: 35192441 DOI: 10.1080/09205063.2022.2045666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Serum proteins can generally be considered a good source for the illness' indication and are precious resources to detect diseases such as inflammation, cancer, diabetes, malnutrition, cardiovascular diseases, Alzheimer's, other autoimmune diseases, and infections. However, one of the biggest difficulties for proteomic studies is that the majority of serum protein mass consists of only a few proteins. Albumin and Immunoglobulin (IgG) constitute 80% of total serum protein. In this study, dye ligand affinity-based hydrogel membranes were proposed as new materials with micron mesh structures. Micron mesh p(HEMA) hydrogel membranes were synthesized by using the UV-photopolymerization method, then modified with Reactive Red 241 (RR241) dye ligand to increase the affinity towards IgG. Characterizations of synthesized micron mesh p(HEMA)-RR241 hydrogel membranes were also performed. It was demonstrated by the characterization studies that; the dye was successfully incorporated into the membrane structure with the amount of 119.38 mg/g. The hydrophilic property of the hydrogel membrane was demonstrated by swelling tests and the swelling value of dye modified membrane was found to be 8 times higher than that of the plain membrane. Micron network structure, as well as the porosity, were demonstrated with SEM/ESEM studies. Optimization of IgG adsorption conditions was also studied at different parameters (pH, temperature, ion strength, initial IgG concentration). Optimum pH, temperature, and ionic strength were found to be 6.5, 25 °C, 0.05 M, respectively, and the maximum IgG absorption value was 10.27 mg/g. Finally, it was shown that the proposed materials can be used repeatedly by 5 adsorption-desorption cycles.
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Affiliation(s)
- Kevser Kuşat
- Chemistry Department, Faculty of Science, Dokuz Eylül University, Izmir, Turkey
| | - Selami Bağlamış
- Biochemistry Department, Faculty of Science, Ege University, Izmir, Turkey
| | - Cansu İlke Kuru
- Biochemistry Department, Faculty of Science, Ege University, Izmir, Turkey
| | - Fulden Ulucan
- Biochemistry Department, Faculty of Science, Ege University, Izmir, Turkey
| | - Murat Uygun
- Chemistry Department, Faculty of Science and Arts, Adnan Menderes University, Aydın, Turkey
| | - Sinan Akgöl
- Biochemistry Department, Faculty of Science, Ege University, Izmir, Turkey
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3
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Becktell L, Matuska AM, Hon S, Delco ML, Cole BJ, Begum L, Zhang S, Fortier LA. Proteomic Analysis and Cell Viability of Nine Amnion, Chorion, Umbilical Cord, and Amniotic Fluid-Derived Products. Cartilage 2021; 13:495S-507S. [PMID: 33356465 PMCID: PMC8804846 DOI: 10.1177/1947603520976767] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE Amnion products are used in various musculoskeletal surgeries and as injections for joint pain with conflicting reports of cell viability and protein contents. The objective of this study was to determine the full proteome and examine cell viability in 9 commercial amnion products using an unbiased bottom-up shotgun proteomics approach and confocal microscopy. DESIGN Products were subjected to liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis and searched against a UniProt Homo sapiens database. Relative protein abundance was determined for each sample. Based on proteomics results, lumican was measured by enzyme-linked immunosorbent assay (ELISA) and Western blot analysis was performed for interleukin-1 receptor antagonist (IL-1Ra) and tissue inhibitor of matrix metalloproteinase-2 (TIMP-2). Cell viability was determined by calcein AM (live) and ethidium homodimer (dead) staining and confocal microscopy. RESULTS Proteomic analysis revealed 919 proteins in the nine products. Proteins were primarily collagens, keratin, and albumin. Lumican, a small leucine-rich proteoglycan (SLRP) was found in all samples. Western blot analysis for IL-1Ra and TIMP-2 indicated presence of both proteins, with nonspecific antibody binding also present in all samples. No live cells were identified in any product. CONCLUSIONS Several novel proteins were identified through proteomics that might impart the beneficial effects of amnion products, including SLRPs, collagens, and regulators of fibroblast activity. IL-1Ra and TIMP-2 were identified, but concentrations measured by ELISA may be falsely increased due to nonspecific antibody binding. The concept that the amnion tissues provide live cells to aid in tissue regeneration cannot be supported by the findings of this study.
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Affiliation(s)
- Liliya Becktell
- College of Veterinary Medicine, Cornell
University, Ithaca, NY, USA
| | | | - Stephanie Hon
- College of Veterinary Medicine, Cornell
University, Ithaca, NY, USA
| | | | - Brian J. Cole
- Midwest Orthopedics at Rush, Rush
University Medical Center, Chicago, IL, USA
| | - Laila Begum
- College of Veterinary Medicine, Cornell
University, Ithaca, NY, USA
| | - Sheng Zhang
- Proteomics and Metabolomics Facility,
Institute of Biotechnology, Cornell University, Ithaca, NY, USA
| | - Lisa A. Fortier
- College of Veterinary Medicine, Cornell
University, Ithaca, NY, USA,Lisa A. Fortier, Department of Clinical
Sciences, College of Veterinary Medicine, Cornell University, 930 Campus Road,
Ithaca, NY 14853, USA.
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Fatangare A, Glässner A, Sachs B, Sickmann A. Future perspectives on in-vitro diagnosis of drug allergy by the lymphocyte transformation test. J Immunol Methods 2021; 495:113072. [PMID: 34000289 DOI: 10.1016/j.jim.2021.113072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/22/2021] [Accepted: 05/12/2021] [Indexed: 11/26/2022]
Abstract
This article aims to envisage future perspectives of the lymphocyte transformation test (LTT). We describe the select innovative techniques, which can be integrated at different stages of the LTT to potentially improve the sensitivity, specificity, or practicability of the LTT. We first focus upon the cell sorting techniques comprising immunomagnetic cell separation and flow cytometry, which can be implemented prior and after the LTT culturing step to concentrate and quantify specific immune cell types. Further, we elaborate upon three important omics techniques such as transcriptomics, proteomics, and metabolomics, which can be integrated downstream of the LTT to analyze molecular changes in specific immune cells following drug induced activation and proliferation. We also develop visions, how state of the art techniques used in other scientific fields, can be transferred and applied in the context of in-vitro detection of drug allergy.
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Affiliation(s)
- Amol Fatangare
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany
| | - Andreas Glässner
- Federal Institute for Drugs and Medical Devices, Research Division, Bonn, Germany
| | - Bernhardt Sachs
- Federal Institute for Drugs and Medical Devices, Research Division, Bonn, Germany; Department for Dermatology and Allergology, University Hospital Aachen, Germany
| | - Albert Sickmann
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Straße 11, 44139 Dortmund, Germany; Medizinische Fakultät, Medizinisches Proteom-Center (MPC), Ruhr-Universität Bochum, 44801 Bochum, Germany; Department of Chemistry, College of Physical Sciences, University of Aberdeen, Aberdeen, AB243FX, Scotland, UK.
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5
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Ahn SB, Kamath KS, Mohamedali A, Noor Z, Wu JX, Pascovici D, Adhikari S, Cheruku HR, Guillemin GJ, McKay MJ, Nice EC, Baker MS. Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins. J Proteome Res 2021; 20:2374-2389. [PMID: 33752330 DOI: 10.1021/acs.jproteome.0c00898] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).
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Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Zainab Noor
- ProCan, Children's Medical Research Institute, The University of Sydney, Westmead, Newtown, NSW 2042, Australia
| | - Jemma X Wu
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Harish R Cheruku
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
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Solís-Fernández G, Montero-Calle A, Alonso-Navarro M, Fernandez-Torres MÁ, Lledó VE, Garranzo-Asensio M, Barderas R, Guzman-Aranguez A. Protein Microarrays for Ocular Diseases. Methods Mol Biol 2021; 2344:239-265. [PMID: 34115364 DOI: 10.1007/978-1-0716-1562-1_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The eye is a multifaceted organ organized in several compartments with particular properties that reflect their diverse functions. The prevalence of ocular diseases is increasing, mainly because of its relationship with aging and of generalized lifestyle changes. However, the pathogenic molecular mechanisms of many common eye pathologies remain poorly understood. Considering the unquestionable importance of proteins in cellular processes and disease progression, proteomic techniques, such as protein microarrays, represent a valuable approach to analyze pathophysiological protein changes in the ocular environment. This technology enables to perform multiplex high-throughput protein expression profiling with minimal sample volume requirements broadening our knowledge of ocular proteome network in eye diseases.In this review, we present a brief summary of the main types of protein microarrays (antibody microarrays, reverse-phase protein microarrays, and protein microarrays) and their application for protein change detection in chronic ocular diseases such as dry eye, age-related macular degeneration, diabetic retinopathy, and glaucoma. The validation of these specific protein changes in eye pathologies may lead to the identification of new biomarkers, depiction of ocular disease pathways, and assistance in the diagnosis, prognosis, and development of new therapeutic options for eye pathologies.
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Affiliation(s)
- Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Molecular Imaging and Photonics Division, Chemistry Department, Faculty of Sciences, KU Leuven, Leuven, Belgium
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Miren Alonso-Navarro
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Miguel Ángel Fernandez-Torres
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Victoria Eugenia Lledó
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - María Garranzo-Asensio
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain.,Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, Madrid, Spain.
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7
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Mendoza-Porras O, Pires PRL, Goswami H, Meirelles FV, Colgrave ML, Wijffels G. Cytokines in the grass, a lesson learnt: Measuring cytokines in plasma using multiple reaction monitoring mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8723. [PMID: 31922636 DOI: 10.1002/rcm.8723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Cytokines are cell regulatory molecules of high importance as indicators for homeostasis and pathology in many species. The current method to measure cytokines in body fluids is reagent dependent, requiring highly specific paired antibodies. METHODS A liquid chromatography/multiple reaction monitoring mass spectrometry (LC/MRM-MS)-based approach was developed to simultaneously establish the limits of detection (LODs) and quantification (LOQs) for recombinant cytokines IL-1β, IL-6, IFNγ and TNFα as pure standards and in bovine sera. All experimental LC/MRM-MS data are available at CSIRO Data Access Portal repository under identifier doi.org/10.25919/5de8a0232a862. RESULTS The present method enabled LODs and LOQs as low as 1.05 and 1.12 fmol/μL in the experiment comprised of pure standards. Comparable results were obtained in the experiment where digested cytokines were mixed with pre-digested sera proteins. The intrinsic matrix effects were evident when intact cytokines were co-digested within undiluted and undigested sera decreasing the ability to detect and quantify cytokines by 10,000-fold compared with pure standards and pre-digested sera. CONCLUSIONS The developed LC/MRM-MS method provided insights into the difficulties in detecting the target peptides when embedded in complex matrices. Nonetheless, the method may potentially be readily applied in biomarker-focused research interrogating fluids of lesser complexity such as synovial fluid, cerebrospinal fluid and tissue culture media.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Pedro R L Pires
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Hareshwar Goswami
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Flavio V Meirelles
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
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8
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Plasma/serum proteomics: depletion strategies for reducing high-abundance proteins for biomarker discovery. Bioanalysis 2019; 11:1799-1812. [PMID: 31617391 DOI: 10.4155/bio-2019-0145] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Plasma and serum are widely used for proteomics-based biomarker discovery. However, analysis of these biofluids is highly challenging due to the complexity and wide dynamic range of their proteomes. Notably, highly abundant proteins tend to obscure the detection of potential biomarkers that are usually of lower concentrations. Among the strategies to resolve this problem are: depletion of high-abundance proteins, enrichment of low abundant proteins of interest and prefractionation. In this review, we focus on current and emerging depletion techniques used to enhance the detection and identification of the less abundant proteins in plasma and serum. We discuss the applications and contributions of these methods to proteomics analysis of plasma and serum alongside their limitations and future perspectives.
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9
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Häussler RS, Bendes A, Iglesias M, Sanchez-Rivera L, Dodig-Crnković T, Byström S, Fredolini C, Birgersson E, Dale M, Edfors F, Fagerberg L, Rockberg J, Tegel H, Uhlén M, Qundos U, Schwenk JM. Systematic Development of Sandwich Immunoassays for the Plasma Secretome. Proteomics 2019; 19:e1900008. [PMID: 31278833 DOI: 10.1002/pmic.201900008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 06/17/2019] [Indexed: 12/15/2022]
Abstract
The plasma proteome offers a clinically useful window into human health. Recent advances from highly multiplexed assays now call for appropriate pipelines to validate individual candidates. Here, a workflow is developed to build dual binder sandwich immunoassays (SIA) and for proteins predicted to be secreted into plasma. Utilizing suspension bead arrays, ≈1800 unique antibody pairs are first screened against 209 proteins with recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies, dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets are obtained. For 22 protein assays, the longitudinal, interindividual, and technical performance is determined in a set of plasma samples collected from 18 healthy subjects every third month over 1 year. Finally, 14 of these assays are compared with with SIAs composed of other binders, proximity extension assays, and affinity-free targeted mass spectrometry. The workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, and the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.
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Affiliation(s)
- Ragna S Häussler
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Annika Bendes
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - MariaJesus Iglesias
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- K.G. Jebsen - Thrombosis Research and Expertise Center (TREC), Department of Clinical Medicine, UiT - The Arctic University of Norway, 9010, Tromsø, Norway
- Division of Internal Medicine, University Hospital of North Norway, 9010, Tromsø, Norway
| | - Laura Sanchez-Rivera
- Division of Cellular and Clinical Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Tea Dodig-Crnković
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Sanna Byström
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Claudia Fredolini
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Elin Birgersson
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Matilda Dale
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Fredrik Edfors
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Linn Fagerberg
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
| | - Johan Rockberg
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Hanna Tegel
- Division of Protein Technology, Department of Protein Science, KTH - Royal Institute of Technology, 106 91, Stockholm, Sweden
| | - Mathias Uhlén
- Division of Systems Biology, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2970, Hørsholm, Denmark
| | | | - Jochen M Schwenk
- Division of Affinity Proteomics, Science for Life Laboratory, KTH - Royal Institute of Technology, Box 1031, 171 21, Solna, Sweden
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10
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Garranzo-Asensio M, Montero-Calle A, Solís-Fernández G, Barderas R, Guzman-Aranguez A. Protein Microarrays: Valuable Tools for Ocular Diseases Research. Curr Med Chem 2019; 27:4549-4566. [PMID: 31244416 DOI: 10.2174/0929867326666190627131300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/07/2019] [Accepted: 05/14/2019] [Indexed: 11/22/2022]
Abstract
The eye is a complex organ comprised of several compartments with exclusive and specialized properties that reflect their diverse functions. Although the prevalence of eye pathologies is increasing, mainly because of its correlation with aging and of generalized lifestyle changes, the pathogenic molecular mechanisms of many common ocular diseases remain poorly understood. Therefore, there is an unmet need to delve into the pathogenesis, diagnosis, and treatment of eye diseases to preserve ocular health and reduce the incidence of visual impairment or blindness. Proteomics analysis stands as a valuable tool for deciphering protein profiles related to specific ocular conditions. In turn, such profiles can lead to real breakthroughs in the fields of ocular science and ophthalmology. Among proteomics techniques, protein microarray technology stands out by providing expanded information using very small volumes of samples. In this review, we present a brief summary of the main types of protein microarrays and their application for the identification of protein changes in chronic ocular diseases such as dry eye, glaucoma, age-related macular degeneration, or diabetic retinopathy. The validation of these specific protein alterations could provide new biomarkers, disclose eye diseases pathways, and help in the diagnosis and development of novel therapies for eye pathologies.
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Affiliation(s)
- María Garranzo-Asensio
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
| | - Ana Montero-Calle
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Guillermo Solís-Fernández
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Rodrigo Barderas
- Functional Proteomics Unit, Chronic Disease Programme (UFIEC), Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Ana Guzman-Aranguez
- Department of Biochemistry and Molecular Biology, Faculty of Optics and Optometry, Universidad Complutense de Madrid, C/Arcos de Jalon 118, Madrid 28037, Spain
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11
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Kim B, Araujo R, Howard M, Magni R, Liotta LA, Luchini A. Affinity enrichment for mass spectrometry: improving the yield of low abundance biomarkers. Expert Rev Proteomics 2018. [PMID: 29542338 DOI: 10.1080/14789450.2018.1450631] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Mass spectrometry (MS) is the premier tool for discovering novel disease-associated protein biomarkers. Unfortunately, when applied to complex body fluid samples, MS has poor sensitivity for the detection of low abundance biomarkers (≪10 ng/mL), derived directly from the diseased tissue cells or pathogens. Areas covered: Herein we discuss the strengths and drawbacks of technologies used to concentrate low abundance analytes in body fluids, with the aim to improve the effective sensitivity for MS discovery. Solvent removal by dry-down or dialysis, and immune-depletion of high abundance serum or plasma proteins, is shown to have disadvantages compared to positive selection of the candidate biomarkers by affinity enrichment. A theoretical analysis of affinity enrichment reveals that the yield for low abundance biomarkers is a direct function of the binding affinity (Association/Dissociation rates) used for biomarker capture. In addition, a high affinity capture pre processing step can effectively dissociate the candidate biomarker from partitioning with high abundance proteins such as albumin. Expert commentary: Properly designed high affinity capture materials can enrich the yield of low abundance (0.1-10 picograms/mL) candidate biomarkers for MS detection. Affinity capture and concentration, as an upfront step in sample preparation for MS, combined with MS advances in software and hardware that improve the resolution of the chromatographic separation can yield a transformative new class of low abundance biomarkers predicting disease risk or disease latency.
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Affiliation(s)
| | - Robyn Araujo
- b School of Mathematical Sciences , Queensland University of Technology , Brisbane , Australia
| | - Marissa Howard
- c Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Ruben Magni
- c Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Lance A Liotta
- c Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
| | - Alessandra Luchini
- c Center for Applied Proteomics and Molecular Medicine , George Mason University , Manassas , VA , USA
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12
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Garranzo-Asensio M, San Segundo-Acosta P, Martínez-Useros J, Montero-Calle A, Fernández-Aceñero MJ, Häggmark-Månberg A, Pelaez-Garcia A, Villalba M, Rabano A, Nilsson P, Barderas R. Identification of prefrontal cortex protein alterations in Alzheimer's disease. Oncotarget 2018. [PMID: 29541381 PMCID: PMC5834268 DOI: 10.18632/oncotarget.24303] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia in developed countries. A better understanding of the events taking place at the molecular level would help to identify novel protein alterations, which might be used in diagnosis or for treatment development. In this study, we have performed the high-throughput analysis of 706 molecules mostly implicated in cell-cell communication and cell signaling processes by using two antibody microarray platforms. We screened three AD pathological groups -each one containing four pooled samples- from Braak stages IV, V and VI, and three control groups from two healthy subjects, five frontotemporal and two vascular dementia patients onto Panorama and L-Series antibody microarrays to identify AD-specific alterations not common to other dementias. Forty altered proteins between control and AD groups were detected, and validated by i) meta-analysis of mRNA alterations, ii) WB, and iii) FISH and IHC using an AD-specific tissue microarray containing 44 samples from AD patients at different Braak stages, and frontotemporal and vascular dementia patients and healthy individuals as controls. We identified altered proteins in AD not common to other dementias like the E3 ubiquitin-protein ligase TOPORS, Layilin and MICB, and validated the association to AD of the previously controverted proteins DDIT3 and the E3 ubiquitin-protein ligase XIAP. These altered proteins constitute interesting targets for further immunological analyses using sera, plasma and CSF to identify AD blood- or cerebrospinal fluid-biomarkers and to perform functional analysis to determine their specific role in AD, and their usefulness as potential therapeutic targets of intervention.
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Affiliation(s)
- Maria Garranzo-Asensio
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Pablo San Segundo-Acosta
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Madrid, Spain
| | - Ana Montero-Calle
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - María Jesús Fernández-Aceñero
- Servicio de Anatomía Patológica Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Departamento de Anatomía Patològica, Facultad de Medicina, Complutense University of Madrid, Madrid, Spain
| | - Anna Häggmark-Månberg
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Mayte Villalba
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Alberto Rabano
- Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Barderas
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain.,UFIEC, National Institute of Health Carlos III, Majadahonda, Madrid, Spain
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13
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Chen WCW, Wang Z, Missinato MA, Park DW, Long DW, Liu HJ, Zeng X, Yates NA, Kim K, Wang Y. Decellularized zebrafish cardiac extracellular matrix induces mammalian heart regeneration. SCIENCE ADVANCES 2016; 2:e1600844. [PMID: 28138518 PMCID: PMC5262469 DOI: 10.1126/sciadv.1600844] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 10/20/2016] [Indexed: 05/03/2023]
Abstract
Heart attack is a global health problem that leads to significant morbidity, mortality, and health care burden. Adult human hearts have very limited regenerative capability after injury. However, evolutionarily primitive species generally have higher regenerative capacity than mammals. The extracellular matrix (ECM) may contribute to this difference. Mammalian cardiac ECM may not be optimally inductive for cardiac regeneration because of the fibrotic, instead of regenerative, responses in injured adult mammalian hearts. Given the high regenerative capacity of adult zebrafish hearts, we hypothesize that decellularized zebrafish cardiac ECM (zECM) made from normal or healing hearts can induce mammalian heart regeneration. Using zebrafish and mice as representative species of lower vertebrates and mammals, we show that a single administration of zECM, particularly the healing variety, enables cardiac functional recovery and regeneration of adult mouse heart tissues after acute myocardial infarction. zECM-treated groups exhibit proliferation of the remaining cardiomyocytes and multiple cardiac precursor cell populations and reactivation of ErbB2 expression in cardiomyocytes. Furthermore, zECM exhibits pro-proliferative and chemotactic effects on human cardiac precursor cell populations in vitro. These contribute to the structural preservation and correlate with significantly higher cardiac contractile function, notably less left ventricular dilatation, and substantially more elastic myocardium in zECM-treated hearts than control animals treated with saline or decellularized adult mouse cardiac ECM. Inhibition of ErbB2 activity abrogates beneficial effects of zECM administration, indicating the possible involvement of ErbB2 signaling in zECM-mediated regeneration. This study departs from conventional focuses on mammalian ECM and introduces a new approach for cardiac tissue regeneration.
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Affiliation(s)
- William C. W. Chen
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Zhouguang Wang
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Maria Azzurra Missinato
- Department of Developmental Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Dae Woo Park
- Center for Ultrasound Molecular Imaging and Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
| | - Daniel Ward Long
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Heng-Jui Liu
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Biomedical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, PA 15213, USA
| | - Nathan A. Yates
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, Pittsburgh, PA 15213, USA
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA
| | - Kang Kim
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Center for Ultrasound Molecular Imaging and Therapeutics, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
- Heart and Vascular Institute, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Yadong Wang
- Department of Bioengineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Vascular Medicine Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Department of Surgery, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Chemical and Petroleum Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Clinical Translational Science Institute, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
- Corresponding author.
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14
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El Rassi Z, Puangpila C. Liquid-phase based separation systems for depletion, prefractionation, and enrichment of proteins in biological fluids and matrices for in-depth proteomics analysis-An update covering the period 2014-2016. Electrophoresis 2016; 38:150-161. [DOI: 10.1002/elps.201600413] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 10/03/2016] [Accepted: 10/04/2016] [Indexed: 12/14/2022]
Affiliation(s)
- Ziad El Rassi
- Department of Chemistry; Oklahoma State University; Stillwater OK USA
| | - Chanida Puangpila
- Department of Chemistry, Faculty of Science; Chiang Mai University; Chiang Mai Thailand
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15
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Stenzel C. Deployment of precise and robust sensors on board ISS-for scientific experiments and for operation of the station. Anal Bioanal Chem 2016; 408:6517-36. [PMID: 27526089 PMCID: PMC5012259 DOI: 10.1007/s00216-016-9789-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 06/03/2016] [Accepted: 07/12/2016] [Indexed: 11/23/2022]
Abstract
The International Space Station (ISS) is the largest technical vehicle ever built by mankind. It provides a living area for six astronauts and also represents a laboratory in which scientific experiments are conducted in an extraordinary environment. The deployed sensor technology contributes significantly to the operational and scientific success of the station. The sensors on board the ISS can be thereby classified into two categories which differ significantly in their key features: (1) sensors related to crew and station health, and (2) sensors to provide specific measurements in research facilities. The operation of the station requires robust, long-term stable and reliable sensors, since they assure the survival of the astronauts and the intactness of the station. Recently, a wireless sensor network for measuring environmental parameters like temperature, pressure, and humidity was established and its function could be successfully verified over several months. Such a network enhances the operational reliability and stability for monitoring these critical parameters compared to single sensors. The sensors which are implemented into the research facilities have to fulfil other objectives. The high performance of the scientific experiments that are conducted in different research facilities on-board demands the perfect embedding of the sensor in the respective instrumental setup which forms the complete measurement chain. It is shown that the performance of the single sensor alone does not determine the success of the measurement task; moreover, the synergy between different sensors and actuators as well as appropriate sample taking, followed by an appropriate sample preparation play an essential role. The application in a space environment adds additional challenges to the sensor technology, for example the necessity for miniaturisation, automation, reliability, and long-term operation. An alternative is the repetitive calibration of the sensors. This approach, however, increases the operational overhead significantly. But meeting especially these requirements offers unique opportunities for testing these sensor technologies in harsh and dedicated environments which are not available on Earth, therefore pushing the related technologies and methodologies to their limits. The scientific objectives for selected experiments, representing a wide range of research fields, are presented, including the instrument setups and the implemented sensor technologies, and where available, the first scientific results are presented.
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Affiliation(s)
- Christian Stenzel
- Airbus DS GmbH-TSPOE, Claude-Dornier-Str. 1, 88090, Immenstaad, Germany.
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16
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Hoare R, Thompson KD, Herath T, Collet B, Bron JE, Adams A. Development, Characterisation and Application of Monoclonal Antibodies for the Detection and Quantification of Infectious Salmon Anaemia Virus in Plasma Samples Using Luminex Bead Array Technology. PLoS One 2016; 11:e0159155. [PMID: 27434377 PMCID: PMC4951118 DOI: 10.1371/journal.pone.0159155] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/28/2016] [Indexed: 11/19/2022] Open
Abstract
Infectious salmon anaemia virus (ISAV) is an orthomyxovirus that has had a significant economic impact on Atlantic salmon farming in Europe, North America and Chile. Monoclonal antibodies (mAbs) were developed against Segment 3 (encoding the viral nucleoprotein, NP) of the virus. Six of the mAbs were shown to be specific to ISAV and recognised all isolates from Scotland, Norway and Canada. They reacted with ISAV in enzyme-linked immunosorbent assay (ELISA), indirect fluorescent antibody technique (IFAT) and western blotting. They were also used to develop a novel detection method based on Luminex (Bio-Plex) bead-based flow cytometric technology for the detection of ISAV in the plasma of Atlantic salmon (Salmo salar L.) smolts experimentally infected with ISAV. Fish were challenged by intraperitoneal (i.p.) injection of virus at 50% Tissue Culture Infective Dose (TCID50) = 2.8 x106 per animal. Virus present in plasma of infected fish, collected at 0, 4, 8, 12, 16, 21 and 28 days post infection using a non-lethal sampling method (n = 12 at each time point), was quantified using the optimised Bio-Plex assay. The results obtained with this assay were compared with absolute quantification of the virus by RT-qPCR using SYBR Green I and TaqMan chemistries. The Bio-Plex assay developed using the NP mAbs appears to be a rapid, sensitive method for detecting and quantifying ISAV in small volumes of fish plasma and has the potential to be multiplexed for the detection of other fish pathogens (e.g. during co-infections). To our knowledge this is the first report of the use of Luminex (Bio-Plex) technology for the detection of a fish pathogen.
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Affiliation(s)
- R. Hoare
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - K. D. Thompson
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, United Kingdom
| | - T. Herath
- Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, United Kingdom
| | - B. Collet
- Marine Scotland, Marine Laboratory, 375 Victoria Road, Aberdeen AB11 9PA, United Kingdom
| | - J. E. Bron
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
| | - A. Adams
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, United Kingdom
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