1
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Aggarwal RT, Lai L, Li H. Microarray fabrication techniques for multiplexed bioassay applications. Anal Biochem 2023; 683:115369. [PMID: 37914004 DOI: 10.1016/j.ab.2023.115369] [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: 08/28/2023] [Revised: 10/19/2023] [Accepted: 10/23/2023] [Indexed: 11/03/2023]
Abstract
Microarrays are powerful tools for high-throughput bioassays that can extract information from tens of thousands of micro-spots consisting of biomolecules. This information is invaluable to many applications, such as drug discovery and disease diagnostics. Different applications of these microarrays need spots of different shapes, sizes, and chemistries to achieve their goals. Micro/nano-fabrication techniques are used to make microarrays with different feature structures and array densities for required assay procedures. Understanding these fabrication methods is essential to creating an effective microarray. The purpose of this article is to critically review fabrication methods used in recent microarray-based bioassay studies. We summarized commonly used microarray fabrication techniques and filled the gap in recent literature on relevant topics. We discussed recent examples of how microarrays were fabricated and used in a variety of bioassays. Specifically, we examined microarray printing, various microlithography techniques, and microfluidics-based microarray fabrication. We evaluated how their application shaped the fabrication methods and compared their performance based on different applications. In the end, we discussed current challenges and outlined potential future directions. This review addressed the gap in literature and provided important insights for choosing appropriate fabrication techniques towards different applications.
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Affiliation(s)
| | - Leyun Lai
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Huiyan Li
- School of Engineering, University of Guelph, Guelph, Ontario, N1G2W1, Canada.
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2
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Itri S, del Giudice D, Mugnano M, Tkachenko V, Uusitalo S, Kokkonen A, Päkkilä I, Ottevaere H, Nie Y, Mazzon E, Gugliandolo A, Ferraro P, Grilli S. A pin-based pyro-electrohydrodynamic jet sensor for tuning the accumulation of biomolecules down to sub-picogram level detection. SENSING AND BIO-SENSING RESEARCH 2022. [DOI: 10.1016/j.sbsr.2022.100536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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3
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Cathcart AM, Smith H, Labrie M, Mills GB. Characterization of anticancer drug resistance by reverse-phase protein array: new targets and strategies. Expert Rev Proteomics 2022; 19:115-129. [PMID: 35466854 PMCID: PMC9215307 DOI: 10.1080/14789450.2022.2070065] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Drug resistance is the main barrier to achieving cancer cures with medical therapy. Cancer drug resistance occurs, in part, due to adaptation of the tumor and microenvironment to therapeutic stress at a proteomic level. Reverse-phase protein arrays (RPPA) are well suited to proteomic analysis of drug resistance due to high sample throughput, sensitive detection of phosphoproteins, and validation for a large number of critical cellular pathways. AREAS COVERED This review summarizes contributions of RPPA to understanding and combating drug resistance. In particular, contributions of RPPA to understanding resistance to PARP inhibitors, BRAF inhibitors, immune checkpoint inhibitors, and breast cancer investigational therapies are discussed. Articles reviewed were identified by MEDLINE, Scopus, and Cochrane search for keywords 'proteomics,' 'reverse-phase protein array,' 'drug resistance,' 'PARP inhibitor,' 'BRAF inhibitor,' 'immune checkpoint inhibitor,' and 'I-SPY' spanning October 1, 1960 - October 1, 2021. EXPERT OPINION Precision oncology has thus far failed to convert the armament of targeted therapies into durable responses for most patients, highlighting that genetic sequencing alone is insufficient to guide therapy selection and overcome drug resistance. Combined genomic and proteomic analyses paired with creative drug combinations and dosing strategies hold promise for maturing precision oncology into an era of improved patient outcomes.
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Affiliation(s)
- Ann M Cathcart
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA
| | - Hannah Smith
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
| | - Marilyne Labrie
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Immunology and Cellular Biology, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Gordon B Mills
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA
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4
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Heggestad JT, Kinnamon DS, Liu J, Joh DY, Fontes CM, Wei Q, Ozcan A, Hucknall AM, Chilkoti A. Smartphone Enabled Point-of-Care Detection of Serum Biomarkers. Methods Mol Biol 2022; 2393:343-365. [PMID: 34837189 DOI: 10.1007/978-1-0716-1803-5_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Sandwich immunoassays are the gold standard for detection of protein analytes. Here, we describe an ultrasensitive point-of-care sandwich immunoassay platform for the detection of biomarkers directly from blood or serum using a custom-built smartphone detector. Testing undiluted blood or serum is challenging due to the complexity of the matrix. Proteins nonspecifically adsorb to and cells often adhere to the assay surface, which can drastically impact the analytical sensitivity of the assay. To address this problem, our assay is built upon a "nonfouling" polymer brush "grafted from" a glass slide, which eliminates nearly all nonspecific binding and therefore increases the signal-to-noise ratio and greatly improves the analytical performance of the test. The two components required to perform a sandwich immunoassay are inkjet-printed directly onto the surface: (1) "stable" capture antibodies that remain entrapped in the brush even after exposure to a liquid sample and (2) fluorescently labeled "soluble" detection antibodies that dissolve upon exposure to a liquid sample. The polymer brush provides hydration to the antibodies, allowing them to remain stable and active over prolonged periods of time. When a liquid sample containing a biomarker of interest is dispensed onto the chip, the detection antibodies dissolve and diffuse to the stable capture spots forming a complex that sandwiches the analyte and that has a fluorescence intensity proportional to the concentration of the biomarker in solution, which can be measured using a custom-built smartphone detector. As multiple capture antibodies can be printed as discrete capture spots, the assay can be easily multiplexed without the need for multiple fluorophores. This chip and detector platform can be utilized for the point-of-care detection of low-abundance biomarkers directly from blood or serum in low-resource settings.
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Affiliation(s)
- Jacob T Heggestad
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - David S Kinnamon
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Jason Liu
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Daniel Y Joh
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Cassio M Fontes
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, College of Engineering, NC State University, Raleigh, NC, USA
| | - Aydogan Ozcan
- Electrical and Computer Engineering and Bioengineering Departments, Henry Samueli School of Engineering and Applied Science, University of California, Los Angeles, CA, USA
| | - Angus M Hucknall
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
| | - Ashutosh Chilkoti
- Department of Biomedical Engineering, Pratt School of Engineering, Duke University, Durham, NC, USA.
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5
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Reverse Phase Protein Arrays. Methods Mol Biol 2021; 2237:103-122. [PMID: 33237412 DOI: 10.1007/978-1-0716-1064-0_9] [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: 12/03/2022]
Abstract
Reverse phase protein arrays (RPPA) are used to quantify proteins and protein posttranslational modifications in cellular lysates and body fluids. RPPA technology is suitable for biomarker discovery, protein pathway profiling, functional phenotype analysis, and drug discovery mechanism of action. The principles of RPPA technology are (a) immobilizing protein-containing specimens on a coated slide in discrete spots, (b) antibody recognition of proteins, (c) amplification chemistries to detect the protein-antibody complex, and (d) quantifying spot intensity. Construction of a RPPA begins with the robotic liquid transfer of protein-containing specimens from microtiter plates onto nitrocellulose-coated slides. The robotic arrayer deposits each sample as discrete spots in an array format. Specimens, controls, and calibrators are printed on each array, thus providing a complete calibrated assay on a single slide. Each RPPA slide is subsequently probed with catalyzed signal amplification chemistries and a single primary antibody, a secondary antibody, and either fluorescent or colorimetric dyes. The focus of this chapter is to describe RPPA detection and imaging using a colorimetric (diaminobenzidine (DAB)) detection strategy.
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Padmanabhan S, Sposito A, Yeh M, Everitt M, White I, DeVoe DL. Reagent integration and controlled release for multiplexed nucleic acid testing in disposable thermoplastic 2D microwell arrays. BIOMICROFLUIDICS 2021; 15:014103. [PMID: 33520047 PMCID: PMC7816768 DOI: 10.1063/5.0039146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/05/2021] [Indexed: 06/12/2023]
Abstract
The seamless integration of reagents into microfluidic devices can serve to significantly reduce assay complexity and cost for disposable diagnostics. In this work, the integration of multiplexed reagents into thermoplastic 2D microwell arrays is demonstrated using a scalable pin spotting technique. Using a simple and low-cost narrow-bore capillary spotting pin, high resolution deposition of concentrated reagents within the arrays of enclosed nanoliter-scale wells is achieved. The pin spotting method is further employed to encapsulate the deposited reagents with a chemically modified wax layer that serves to prevent disruption of the dried assay components during sample introduction through a shared microchannel, while also enabling temperature-controlled release after sample filling is complete. This approach supports the arbitrary patterning and release of different reagents within individual wells without crosstalk for multiplexed analyses. The performance of the in-well spotting technique is characterized using on-chip rolling circle amplification to evaluate its potential for nucleic acid-based diagnostics.
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Affiliation(s)
- S. Padmanabhan
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - A. Sposito
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - M. Yeh
- Department of Mechanical Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - M. Everitt
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - I. White
- Department of Bioengineering, University of Maryland, College Park, Maryland 20742, USA
| | - D. L. DeVoe
- Author to whom correspondence should be addressed:. Tel.: +1-301-405-8125
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7
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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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Awanye AM, Chang CM, Wheeler JX, Chan H, Marsay L, Dold C, Rollier CS, Bird LE, Nettleship JE, Owens RJ, Pollard AJ, Derrick JP. Immunogenicity profiling of protein antigens from capsular group B Neisseria meningitidis. Sci Rep 2019; 9:6843. [PMID: 31048732 PMCID: PMC6497663 DOI: 10.1038/s41598-019-43139-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 04/11/2019] [Indexed: 11/29/2022] Open
Abstract
Outer membrane vesicle (OMV)- based vaccines have been used to provide strain-specific protection against capsular group B Neisseria meningitidis infections, but the full breadth of the immune response against the components of the OMV has not been established. Sera from adults vaccinated with an OMV vaccine were used to screen 91 outer membrane proteins (OMPs) incorporated in an antigen microarray panel. Antigen-specific IgG levels were quantified pre-vaccination, and after 12 and 18 weeks. These results were compared with IgG levels from mice vaccinated with the same OMV vaccine. The repertoires of highly responding antigens in humans and mice overlapped, but were not identical. The highest responding antigens to human IgG comprised four integral OMPs (PorA, PorB, OpcA and PilQ), a protein which promotes the stability of PorA and PorB (RmpM) and two lipoproteins (BamC and GNA1162). These observations will assist in evaluating the role of minor antigen components within OMVs in providing protection against meningococcal infection. In addition, the relative dominance of responses to integral OMPs in humans emphasizes the importance of this subclass and points to the value of maintaining conformational epitopes from integral membrane proteins in vaccine formulations.
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Affiliation(s)
- Amaka M Awanye
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Chun-Mien Chang
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK
| | - Jun X Wheeler
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Hannah Chan
- National Institute for Biological Standards and Control, Blanche Lane, South Mimms, Hertfordshire, EN6 3QG, UK
| | - Leanne Marsay
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Christina Dold
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Christine S Rollier
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Louise E Bird
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Joanne E Nettleship
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Raymond J Owens
- Oxford Protein Production Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell, Didcot, OX11 0FA, UK
| | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of Oxford, and the NIHR Oxford Biomedical Research Centre, Oxford, OX3 7LE, UK
| | - Jeremy P Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, M13 9PL, UK.
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Clancy KF, Dery S, Laforte V, Shetty P, Juncker D, Nicolau DV. Protein microarray spots are modulated by patterning method, surface chemistry and processing conditions. Biosens Bioelectron 2019; 130:397-407. [DOI: 10.1016/j.bios.2018.09.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 09/05/2018] [Accepted: 09/06/2018] [Indexed: 01/13/2023]
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10
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Frosiniuk A, Kolchanov DS, Milichko VA, Vinogradov AV, Vinogradov VV. Optical interference-based sensors for the visual detection of nano-scale objects. NANOSCALE 2019; 11:6343-6351. [PMID: 30887996 DOI: 10.1039/c9nr00616h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we present a new concept for the simple visual detection of nano-scale objects in solutions. To achieve this goal, we developed chromogen-free interference-based sensors that provided a color visible reaction directly after the interaction of the analyte with the substrate. The effect is based on the strong optical interference occurring at the interface between the inkjet printed sol-gel titania film (a layer with high refractive index) and the adsorbed nano-sized objects (layer with low refractive index), which can be detected even with the naked eye. Herein, we have developed a synthetic strategy for the inkjet printing of interference sensors with controllable color change through thickness adjustment.
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Affiliation(s)
- Anna Frosiniuk
- ITMO University, International Laboratory "Solution Chemistry of Advanced Materials and Technologies", Lomonosova 9, 191002, Saint Petersburg, Russia.
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Byron A. Reproducibility and Crossplatform Validation of Reverse-Phase Protein Array Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1188:181-201. [PMID: 31820389 DOI: 10.1007/978-981-32-9755-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Reverse-phase protein array (RPPA) technology is a high-throughput antibody- and microarray-based approach for the rapid profiling of levels of proteins and protein posttranslational modifications in biological specimens. The technology consumes small amounts of samples, can sensitively detect low-abundance proteins and posttranslational modifications, enables measurements of multiple signaling pathways in parallel, has the capacity to analyze large sample numbers, and offers robust interexperimental reproducibility. These features of RPPA experiments have motivated and enabled the use of RPPA technology in various biomedical, translational, and clinical applications, including the delineation of molecular mechanisms of disease, profiling of druggable signaling pathway activation, and search for new prognostic markers. Owing to the complexity of many of these applications, such as developing multiplex protein assays for diagnostic laboratories or integrating posttranslational modification-level data using large-scale proteogenomic approaches, robust and well-validated data are essential. There are many distinct components of an RPPA workflow, and numerous possible technical setups and analysis parameter options exist. The differences between RPPA platform setups around the world offer opportunities to assess and minimize interplatform variation. Crossplatform validation may also aid in the evaluation of robust, platform-independent protein markers of disease and response to therapy.
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Affiliation(s)
- Adam Byron
- Cancer Research UK Edinburgh Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
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12
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Samson AAS, Lee J, Song JM. Inkjet printing-based photo-induced electron transfer reaction on parchment paper using riboflavin as a photosensitizer. Anal Chim Acta 2018; 1012:49-59. [DOI: 10.1016/j.aca.2018.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Revised: 01/16/2018] [Accepted: 02/05/2018] [Indexed: 01/14/2023]
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13
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Sierra-Sánchez Á, Garrido-Martín D, Lourido L, González-González M, Díez P, Ruiz-Romero C, Sjöber R, Droste C, De Las Rivas J, Nilsson P, Blanco F, Fuentes M. Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies. J Proteome Res 2017; 16:1890-1899. [DOI: 10.1021/acs.jproteome.6b00980] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Lucía Lourido
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
| | | | | | - Cristina Ruiz-Romero
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
| | - Ronald Sjöber
- Affinity
Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), SE-17165 Stockholm, Sweden
| | | | | | - Peter Nilsson
- Affinity
Proteomics, Science for Life Laboratory, School of Biotechnology, Royal Institute of Technology (KTH), SE-17165 Stockholm, Sweden
| | - Francisco Blanco
- Proteomics
Group-PBR2-ProteoRed/ISCIII, Rheumatology Division, Instituto de Investigación Biomédica de A Coruña (INIBIC/CHUAC/Sergas/UDC), 15001 A Coruña, Spain
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14
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Hellström C, Dodig-Crnković T, Hong MG, Schwenk JM, Nilsson P, Sjöberg R. High-Density Serum/Plasma Reverse Phase Protein Arrays. Methods Mol Biol 2017; 1619:229-238. [PMID: 28674890 DOI: 10.1007/978-1-4939-7057-5_18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In-depth exploration and characterization of human serum and plasma proteomes is an attractive strategy for the identification of potential prognostic or diagnostic biomarkers. The possibility of analyzing larger numbers of samples in a high-throughput fashion has markedly increased with affinity-based microarrays, thus providing higher statistical power to these biomarker studies. Here, we describe a protocol for high-density serum and plasma reverse phase protein arrays (RPPAs). We demonstrate how a biobank of 12,392 samples was immobilized and analyzed on a single microarray slide, allowing high-quality profiling of abundant target proteins across all samples in one assay.
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Affiliation(s)
- Cecilia Hellström
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Tea Dodig-Crnković
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Box 1031, 17121, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden.
| | - Ronald Sjöberg
- Affinity Proteomics, School of Biotechnology, SciLifeLab, KTH-Royal Institute of Technology, Box 1031, SE-17121, Stockholm, Sweden
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Abstract
There is a huge potential interest to use synthetic polymers as versatile solid supports for analytical microarraying. Chemical modification of polycarbonate (PC) for covalent immobilization of probes, micro-printing of protein or nucleic acid probes, development of indirect immunoassay, and development of hybridization protocols are described and discussed.
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Affiliation(s)
- María-José Bañuls
- Departamento de Química, Instituto interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Sergi B Morais
- Departamento de Química, Instituto interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Luis A Tortajada-Genaro
- Departamento de Química, Instituto interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain
| | - Ángel Maquieira
- Departamento de Química, Instituto interuniversitario de Reconocimiento Molecular y Desarrollo Tecnológico, Universitat Politècnica de València, Camino de Vera s/n, 46022, Valencia, Spain.
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16
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Li H, Munzar JD, Ng A, Juncker D. A versatile snap chip for high-density sub-nanoliter chip-to-chip reagent transfer. Sci Rep 2015; 5:11688. [PMID: 26148566 PMCID: PMC4493572 DOI: 10.1038/srep11688] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/05/2015] [Indexed: 01/15/2023] Open
Abstract
The coordinated delivery of minute amounts of different reagents is important for microfluidics and microarrays, but is dependent on advanced equipment such as microarrayers. Previously, we developed the snap chip for the direct transfer of reagents, thus realizing fluidic operations by only manipulating microscope slides. However, owing to the misalignment between arrays spotted on different slides, millimeter spacing was needed between spots and the array density was limited. In this work, we have developed a novel double transfer method and have transferred 625 spots cm(-2), corresponding to >10000 spots for a standard microscope slide. A user-friendly snapping system was manufactured to make liquid handling straightforward. Misalignment, which for direct transfer ranged from 150-250 μm, was reduced to <40 μm for double transfer. The snap chip was used to quantify 50 proteins in 16 samples simultaneously, yielding limits of detection in the pg/mL range for 35 proteins. The versatility of the snap chip is illustrated with a 4-plex homogenous enzyme inhibition assay analyzing 128 conditions with precise timing. The versatility and high density of the snap chip with double transfer allows for the development of high throughput reagent transfer protocols compatible with a variety of applications.
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Affiliation(s)
- Huiyan Li
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - Jeffrey D. Munzar
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - Andy Ng
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
| | - David Juncker
- Biomedical Engineering Department, McGill University, Montréal, QC, H3A 0G1, Canada
- McGill University and Genome Quebec Innovation Centre, McGill University, Montréal, QC, H3A 0G1, Canada
- Department of Neurology and Neurosurgery, McGill University, Montréal, QC, H3A 0G1, Canada
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17
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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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Daly R, Harrington TS, Martin GD, Hutchings IM. Inkjet printing for pharmaceutics - A review of research and manufacturing. Int J Pharm 2015; 494:554-567. [PMID: 25772419 DOI: 10.1016/j.ijpharm.2015.03.017] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/17/2015] [Accepted: 03/09/2015] [Indexed: 11/27/2022]
Abstract
Global regulatory, manufacturing and consumer trends are driving a need for change in current pharmaceutical sector business models, with a specific focus on the inherently expensive research costs, high-risk capital-intensive scale-up and the traditional centralised batch manufacturing paradigm. New technologies, such as inkjet printing, are being explored to radically transform pharmaceutical production processing and the end-to-end supply chain. This review provides a brief summary of inkjet printing technologies and their current applications in manufacturing before examining the business context driving the exploration of inkjet printing in the pharmaceutical sector. We then examine the trends reported in the literature for pharmaceutical printing, followed by the scientific considerations and challenges facing the adoption of this technology. We demonstrate that research activities are highly diverse, targeting a broad range of pharmaceutical types and printing systems. To mitigate this complexity we show that by categorising findings in terms of targeted business models and Active Pharmaceutical Ingredient (API) chemistry we have a more coherent approach to comparing research findings and can drive efficient translation of a chosen drug to inkjet manufacturing.
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Affiliation(s)
- Ronan Daly
- Inkjet Research Centre, Institute for Manufacturing, Department of Engineering, University of Cambridge, UK.
| | - Tomás S Harrington
- Centre for International Manufacturing, Institute for Manufacturing, Department of Engineering, University of Cambridge, UK
| | - Graham D Martin
- Inkjet Research Centre, Institute for Manufacturing, Department of Engineering, University of Cambridge, UK
| | - Ian M Hutchings
- Inkjet Research Centre, Institute for Manufacturing, Department of Engineering, University of Cambridge, UK
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Protein Microarrays with Novel Microfluidic Methods: Current Advances. MICROARRAYS 2014; 3:180-202. [PMID: 27600343 PMCID: PMC4996363 DOI: 10.3390/microarrays3030180] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 06/10/2014] [Accepted: 06/16/2014] [Indexed: 01/08/2023]
Abstract
Microfluidic-based micromosaic technology has allowed the pattering of recognition elements in restricted micrometer scale areas with high precision. This controlled patterning enabled the development of highly multiplexed arrays multiple analyte detection. This arraying technology was first introduced in the beginning of 2001 and holds tremendous potential to revolutionize microarray development and analyte detection. Later, several microfluidic methods were developed for microarray application. In this review we discuss these novel methods and approaches which leverage the property of microfluidic technologies to significantly improve various physical aspects of microarray technology, such as enhanced imprinting homogeneity, stability of the immobilized biomolecules, decreasing assay times, and reduction of the costs and of the bulky instrumentation.
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Abstract
Almost all plant cells are surrounded by glycan-rich cell walls, which form much of the plant body and collectively are the largest source of biomass on earth. Plants use polysaccharides for support, defense, signaling, cell adhesion, and as energy storage, and many plant glycans are also important industrially and nutritionally. Understanding the biological roles of plant glycans and the effective exploitation of their useful properties requires a detailed understanding of their structures, occurrence, and molecular interactions. Microarray technology has revolutionized the massively high-throughput analysis of nucleotides, proteins, and increasingly carbohydrates. Using microarrays, the abundance of and interactions between hundreds and thousands of molecules can be assessed simultaneously using very small amounts of analytes. Here we show that carbohydrate microarrays are multifunctional tools for plant research and can be used to map glycan populations across large numbers of samples to screen antibodies, carbohydrate binding proteins, and carbohydrate binding modules and to investigate enzyme activities.
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Pedersen HL, Fangel JU, McCleary B, Ruzanski C, Rydahl MG, Ralet MC, Farkas V, von Schantz L, Marcus SE, Andersen MCF, Field R, Ohlin M, Knox JP, Clausen MH, Willats WGT. Versatile high resolution oligosaccharide microarrays for plant glycobiology and cell wall research. J Biol Chem 2012; 287:39429-38. [PMID: 22988248 PMCID: PMC3501085 DOI: 10.1074/jbc.m112.396598] [Citation(s) in RCA: 175] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/10/2012] [Indexed: 12/13/2022] Open
Abstract
Microarrays are powerful tools for high throughput analysis, and hundreds or thousands of molecular interactions can be assessed simultaneously using very small amounts of analytes. Nucleotide microarrays are well established in plant research, but carbohydrate microarrays are much less established, and one reason for this is a lack of suitable glycans with which to populate arrays. Polysaccharide microarrays are relatively easy to produce because of the ease of immobilizing large polymers noncovalently onto a variety of microarray surfaces, but they lack analytical resolution because polysaccharides often contain multiple distinct carbohydrate substructures. Microarrays of defined oligosaccharides potentially overcome this problem but are harder to produce because oligosaccharides usually require coupling prior to immobilization. We have assembled a library of well characterized plant oligosaccharides produced either by partial hydrolysis from polysaccharides or by de novo chemical synthesis. Once coupled to protein, these neoglycoconjugates are versatile reagents that can be printed as microarrays onto a variety of slide types and membranes. We show that these microarrays are suitable for the high throughput characterization of the recognition capabilities of monoclonal antibodies, carbohydrate-binding modules, and other oligosaccharide-binding proteins of biological significance and also that they have potential for the characterization of carbohydrate-active enzymes.
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Affiliation(s)
- Henriette L. Pedersen
- From the Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Jonatan U. Fangel
- From the Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Barry McCleary
- Megazyme International Ireland Ltd., Bray Business Park, Bray, County Wicklow, Ireland
| | - Christian Ruzanski
- the John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
| | - Maja G. Rydahl
- From the Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
| | | | - Vladimir Farkas
- the Institute of Chemistry, Centre for Glycobiology, Slovak Academy of Sciences, SK-84538, Bratislava, Slovakia
| | - Laura von Schantz
- the Department of Immunotechnology, Lund University, BMC D13, S-22184 Lund, Sweden
| | - Susan E. Marcus
- the Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom, and
| | - Mathias C. F. Andersen
- the Center for Nanomedicine and Theranostics and Department of Chemistry, Technical University of Denmark, Building 201, 2800 Kongens Lyngby, Denmark
| | - Rob Field
- the John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, United Kingdom
| | - Mats Ohlin
- the Department of Immunotechnology, Lund University, BMC D13, S-22184 Lund, Sweden
| | - J. Paul Knox
- the Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom, and
| | - Mads H. Clausen
- the Center for Nanomedicine and Theranostics and Department of Chemistry, Technical University of Denmark, Building 201, 2800 Kongens Lyngby, Denmark
| | - William G. T. Willats
- From the Department of Plant Biology and Biotechnology, University of Copenhagen, 1871 Frederiksberg, Denmark
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Rahmanian O, Chen CF, DeVoe DL. Microscale patterning of thermoplastic polymer surfaces by selective solvent swelling. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12923-9. [PMID: 22900539 PMCID: PMC3443563 DOI: 10.1021/la302704t] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
A new method for the fabrication of microscale features in thermoplastic substrates is presented. Unlike traditional thermoplastic microfabrication techniques, in which bulk polymer is displaced from the substrate by machining or embossing, a unique process termed orogenic microfabrication has been developed in which selected regions of a thermoplastic surface are raised from the substrate by an irreversible solvent swelling mechanism. The orogenic technique allows thermoplastic surfaces to be patterned using a variety of masking methods, resulting in three-dimensional features that would be difficult to achieve through traditional microfabrication methods. Using cyclic olefin copolymer as a model thermoplastic material, several variations of this process are described to realize growth heights ranging from several nanometers to tens of micrometers, with patterning techniques include direct photoresist masking, patterned UV/ozone surface passivation, elastomeric stamping, and noncontact spotting. Orogenic microfabrication is also demonstrated by direct inkjet printing as a facile photolithography-free masking method for rapid desktop thermoplastic microfabrication.
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Affiliation(s)
- Omid Rahmanian
- Department of Bioengineering, University of Maryland, College Park, MD 20742
| | - Chien-Fu Chen
- Department of Bioengineering, University of Maryland, College Park, MD 20742
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taiwan
| | - Don L. DeVoe
- Department of Bioengineering, University of Maryland, College Park, MD 20742
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742
- Corresponding author
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Gallotta A, Orzes E, Fassina G. Biomarkers Quantification with Antibody Arrays in Cancer Early Detection. Clin Lab Med 2012; 32:33-45. [DOI: 10.1016/j.cll.2011.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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