1
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Courson R, Bratash O, Maziz A, Desmet C, Meza RA, Leroy L, Engel E, Buhot A, Malaquin L, Leïchlé T. Rapid prototyping of a polymer MEMS droplet dispenser by laser-assisted 3D printing. MICROSYSTEMS & NANOENGINEERING 2023; 9:85. [PMID: 37408536 PMCID: PMC10318032 DOI: 10.1038/s41378-023-00559-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/01/2023] [Accepted: 05/23/2023] [Indexed: 07/07/2023]
Abstract
In this work, we introduce a polymer version of a previously developed silicon MEMS drop deposition tool for surface functionalization that consists of a microcantilever integrating an open fluidic channel and a reservoir. The device is fabricated by laser stereolithography, which offers the advantages of low-cost and fast prototyping. Additionally, thanks to the ability to process multiple materials, a magnetic base is incorporated into the cantilever for convenient handling and attachment to the holder of a robotized stage used for spotting. Droplets with diameters ranging from ∼50 µm to ∼300 µm are printed upon direct contact of the cantilever tip with the surface to pattern. Liquid loading is achieved by fully immersing the cantilever into a reservoir drop, where a single load results in the deposition of more than 200 droplets. The influences of the size and shape of the cantilever tip and the reservoir on the printing outcome are studied. As a proof-of-concept of the biofunctionalization capability of this 3D printed droplet dispenser, microarrays of oligonucleotides and antibodies displaying high specificity and no cross-contamination are fabricated, and droplets are deposited at the tip of an optical fiber bundle.
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Affiliation(s)
- Rémi Courson
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Oleksii Bratash
- Université Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France
| | - Ali Maziz
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
| | - Cloé Desmet
- Université Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France
| | | | - Loïc Leroy
- Université Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France
| | - Elodie Engel
- Université Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France
| | - Arnaud Buhot
- Université Grenoble Alpes, CNRS, CEA, IRIG, SyMMES, 38000 Grenoble, France
| | | | - Thierry Leïchlé
- LAAS-CNRS, Université de Toulouse, CNRS, 31400 Toulouse, France
- Georgia Tech−CNRS International Research Laboratory, Atlanta, GA 30332 USA
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2
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Victorious A, Zhang Z, Chang D, Maclachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022; 61:e202204252. [DOI: 10.1002/anie.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Amanda Victorious
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Zijie Zhang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | | | - Richa Pandey
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
| | - Jianrun Xia
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Jimmy Gu
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
| | - Todd Hoare
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Chemical Engineering McMaster University Canada
| | - Leyla Soleymani
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Engineering Physics McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
| | - Yingfu Li
- School of Biomedical Engineering McMaster University 1280 Main Street West, Hamilton Ontario L8S 4K1 Canada
- Department of Biochemistry and Biomedical Sciences McMaster University Canada
- Michael G. DeGroote Institute for Infectious Disease Research McMaster University Canada
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3
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Victorious A, Zhang Z, Chang D, Malachlan R, Pandey R, Xia J, Gu J, Hoare T, Soleymani L, Li Y. A DNA Barcode‐Based Aptasensor Enables Rapid Testing of Porcine Epidemic Diarrhea Viruses in Swine Saliva Using Electrochemical Readout. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202204252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
| | - Zijie Zhang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Dingran Chang
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | | | | | - Jianrun Xia
- McMaster University Biochemistry and Biomedical Sciences CANADA
| | - Jimmy Gu
- McMurry University Biochemistry and Biomedical Sciences CANADA
| | - Todd Hoare
- McMurry University Chemical Engineering CANADA
| | - Leyla Soleymani
- McMastser University Engineering Physics 1280 Main Street W. L8S 4M1 Hamilton CANADA
| | - Yingfu Li
- McMaster University Biochemistry and Biomedical Sciences CANADA
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4
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Temme JS, Gildersleeve JC. General Strategies for Glycan Microarray Data Processing and Analysis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2460:67-87. [PMID: 34972931 DOI: 10.1007/978-1-0716-2148-6_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Glycan microarrays provide a high-throughput technology for rapidly profiling interactions between carbohydrates and glycan-binding proteins (GBPs). Use of glycan microarrays involves several general steps, including construction of the microarray, carrying out the assay, detection of binding events, and analysis of the results. While multiple platforms have been developed to construct microarrays, most utilize fluorescence for detection of binding events. This chapter describes methods to acquire and process microarray images, including generating GAL files, imaging of the slide, aligning the grid, detecting problematic spots, and evaluating the quality of the data. The chapter focuses on processing our neoglycoprotein microarrays, but many of the lessons we have learned are applicable to other array formats.
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Affiliation(s)
- J Sebastian Temme
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA.
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5
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Delamarche E, Pereiro I, Kashyap A, Kaigala GV. Biopatterning: The Art of Patterning Biomolecules on Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9637-9651. [PMID: 34347483 DOI: 10.1021/acs.langmuir.1c00867] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Patterning biomolecules on surfaces provides numerous opportunities for miniaturizing biological assays; biosensing; studying proteins, cells, and tissue sections; and engineering surfaces that include biological components. In this Feature Article, we summarize the themes presented in our recent Langmuir Lecture on patterning biomolecules on surfaces, miniaturizing surface assays, and interacting with biointerfaces using three key technologies: microcontact printing, microfluidic networks, and microfluidic probes.
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Affiliation(s)
- Emmanuel Delamarche
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Iago Pereiro
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Aditya Kashyap
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
| | - Govind V Kaigala
- IBM Research Europe-Zurich, Säumerstrasse 4, Rüschlikon CH-8803, Switzerland
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6
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Kalli M, Blok A, Jiang L, Starr N, Alcocer MJC, Falcone FH. Development of a protein microarray-based diagnostic chip mimicking the skin prick test for allergy diagnosis. Sci Rep 2020; 10:18208. [PMID: 33097775 PMCID: PMC7584649 DOI: 10.1038/s41598-020-75226-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 10/12/2020] [Indexed: 01/16/2023] Open
Abstract
Protein microarrays have been successfully used for detection of allergen-specific IgE in patient sera. Here, we demonstrate proof-of-concept of a solid-phase technique coupling the high-throughput potential of protein microarrays with the biologically relevant readout provided by IgE reporter cells, creating a novel allergic sensitization detection system. Three proteins (κ-casein, timothy grass pollen extract, polyclonal anti-human IgE) were printed onto three different polymer-coated surfaces (aldehyde-, epoxy- and NHS ester-coated). ToF-SIMs analysis was performed to assess printed protein stability and retention during washing steps. NFAT-DsRed rat basophil leukemia cell attachment and retention during washing steps was assessed after treatment with various extracellular matrix proteins. NFAT-DsRed IgE reporter cells were sensitized with serum of an allergic donor, incubated on the printed slides, and cell activation determined using a microarray laser scanner. NFAT DsRed IgE reporter cell binding was significantly increased on all polymer surfaces after incubation with fibronectin and vitronectin, but not collagen or laminin. All surfaces supported printed protein stability during washing procedure, with epoxy- and NHS ester-coated surfaces showing best protein retention. Cell activation was significantly higher in NHS ester-coated slides after timothy grass pollen extract stimulation appearing a suitable substrate for further development of an automated allergy diagnosis system.
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Affiliation(s)
- Marina Kalli
- Molecular Therapeutics and Formulation Division, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Andrew Blok
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Long Jiang
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, UK
| | - Nichola Starr
- Advanced Materials and Healthcare Technologies Division, School of Pharmacy, University of Nottingham, Nottingham, UK
| | | | - Franco H Falcone
- Molecular Therapeutics and Formulation Division, School of Pharmacy, University of Nottingham, Nottingham, UK.
- Institute for Parasitology, Justus-Liebig-University of Giessen, Biomedizinisches Forschungszentrum Am Seltersberg, Schubertstr. 81, 35392, Giessen, Germany.
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7
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Shpilevaya MV, Runina AV, Filippova MA, Kubanov AA. [Сomparison of immunoarrays for syphilis diagnostics produced by co-polymerization immobilization and non-contact printing techniques.]. Klin Lab Diagn 2020; 65:16-23. [PMID: 32155002 DOI: 10.18821/0869-2084-2020-65-1-16-23] [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: 11/11/2019] [Accepted: 11/19/2019] [Indexed: 11/17/2022]
Abstract
The aim of the study was to investigate the characteristics of immunoarrays (microarrays) produced by co-polymerization immobilization and non-contact printing techniques for enhancing the capacities of syphilis diagnostics. In diagnostic context immunoarrays of both protein immobilization techniques have shown high sensitivity and specificity together with potency to differentiate syphilis stages in serologic assays. The article discloses the advantages and limitations of non-contact printing techniques as well as the results and problems revealed in the study. Solution of these problems in future may provide the development of new serodiagnostic tools with higher accuracy of the results.
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Affiliation(s)
- M V Shpilevaya
- State Research Center of Dermatovenereology and Cosmetology, 107076, Moscow, Russia
| | - A V Runina
- State Research Center of Dermatovenereology and Cosmetology, 107076, Moscow, Russia
| | - M A Filippova
- The V.A. Engelhardt Institute of Molecular Biology, 119991, Moscow, Russia
| | - A A Kubanov
- State Research Center of Dermatovenereology and Cosmetology, 107076, Moscow, Russia
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8
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Alvarado RE, Nguyen HT, Pepin-Donat B, Lombard C, Roupioz Y, Leroy L. Optically Assisted Surface Functionalization for Protein Arraying in Aqueous Media. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10511-10516. [PMID: 28899097 DOI: 10.1021/acs.langmuir.7b02965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Protein surface patterning is employed in a broad spectrum of applications ranging from protein microarray analysis to 2D cell organization. However, limitations arise because of the highly sensitive nature of proteins requiring careful handling to ensure their structural and functional integrity during the grafting process. Here, we describe a patterning protocol that keeps proteins in an aqueous environment during their immobilization, avoiding the loss of their biological activity. The procedure is based on the UV-mediated removal of polyethylene glycol self-assembled monolayers in a transparent microfluidic chamber, giving access to micrometric motifs of predefined geometries. Afterward, modified proteins can be grafted on the photopatterned domains. We also studied the influence of reactive oxygen species for a better understanding of the chemical mechanism involved in this process. Finally, as a proof of concept, a protein microarray was created with this process using cell-capturing antibodies to immobilize human blood cells, confirming the functionality of the arrayed proteins.
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Affiliation(s)
- Ricardo E Alvarado
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | - Hoang T Nguyen
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | | | - Christian Lombard
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | - Yoann Roupioz
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
| | - Loïc Leroy
- Univ. Grenoble Alpes, CEA, CNRS, INAC, SyMMES , F-38000 Grenoble, France
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9
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Manuel G, Lupták A, Corn RM. A Microwell-Printing Fabrication Strategy for the On-Chip Templated Biosynthesis of Protein Microarrays for Surface Plasmon Resonance Imaging. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2016; 120:20984-20990. [PMID: 28706572 PMCID: PMC5504410 DOI: 10.1021/acs.jpcc.6b03307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A two-step templated, ribosomal biosynthesis/printing method for the fabrication of protein microarrays for surface plasmon resonance imaging (SPRI) measurements is demonstrated. In the first step, a sixteen component microarray of proteins is created in microwells by cell free on chip protein synthesis; each microwell contains both an in vitro transcription and translation (IVTT) solution and 350 femtomoles of a specific DNA template sequence that together are used to create approximately 40 picomoles of a specific hexahistidine-tagged protein. In the second step, the protein microwell array is used to contact print one or more protein microarrays onto nitrilotriacetic acid (NTA)-functionalized gold thin film SPRI chips for real-time SPRI surface bioaffinity adsorption measurements. Even though each microwell array element only contains approximately 40 picomoles of protein, the concentration is sufficiently high for the efficient bioaffinity adsorption and capture of the approximately 100 femtomoles of hexahistidine-tagged protein required to create each SPRI microarray element. As a first example, the protein biosynthesis process is verified with fluorescence imaging measurements of a microwell array containing His-tagged green fluorescent protein (GFP), yellow fluorescent protein (YFP) and mCherry (RFP), and then the fidelity of SPRI chips printed from this protein microwell array is ascertained by measuring the real-time adsorption of various antibodies specific to these three structurally related proteins. This greatly simplified two-step synthesis/printing fabrication methodology eliminates most of the handling, purification and processing steps normally required in the synthesis of multiple protein probes, and enables the rapid fabrication of SPRI protein microarrays from DNA templates for the study of protein-protein bioaffinity interactions.
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Affiliation(s)
| | - Andrej Lupták
- Corresponding Authors: Robert M. Corn,
, phone: 1-949-824-1746 and Andrej Luptak,
, phone: 1-949-824-9132
| | - Robert M. Corn
- Corresponding Authors: Robert M. Corn,
, phone: 1-949-824-1746 and Andrej Luptak,
, phone: 1-949-824-9132
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10
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Bergeron S, Laforte V, Lo PS, Li H, Juncker D. Evaluating mixtures of 14 hygroscopic additives to improve antibody microarray performance. Anal Bioanal Chem 2015; 407:8451-62. [PMID: 26345442 DOI: 10.1007/s00216-015-8992-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Revised: 08/17/2015] [Accepted: 08/19/2015] [Indexed: 11/27/2022]
Abstract
Microarrays allow the miniaturization and multiplexing of biological assays while only requiring minute amounts of samples. As a consequence of the small volumes used for spotting and the assays, evaporation often deteriorates the quality, reproducibility of spots, and the overall assay performance. Glycerol is commonly added to antibody microarray printing buffers to decrease evaporation; however, it often decreases the binding of antibodies to the surface, thereby negatively affecting assay sensitivity. Here, combinations of 14 hygroscopic chemicals were used as additives to printing buffers for contact-printed antibody microarrays on four different surface chemistries. The ability of the additives to suppress evaporation was quantified by measuring the residual buffer volume in open quill pins over time. The seven best additives were then printed either individually or as a 1:1 mixture of two additives, and the homogeneity, intensity, and reproducibility of both the spotted protein and of a fluorescently labeled analyte in an assay were quantified. Among the 28 combinations on the four slides, many were found to outperform glycerol, and the best additive mixtures were further evaluated by changing the ratio of the two additives. We observed that the optimal additive mixture was dependent on the slide chemistry, and that it was possible to increase the binding of antibodies to the surface threefold compared to 50 % glycerol, while decreasing whole-slide coefficient of variation to 5.9 %. For the two best slides, improvements were made for both the limit of detection (1.6× and 5.9×, respectively) and the quantification range (1.2× and 2.1×, respectively). The additive mixtures identified here thus help improve assay reproducibility and performance, and might be beneficial to all types of microarrays that suffer from evaporation of the printing buffers.
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Affiliation(s)
- Sébastien Bergeron
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Veronique Laforte
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
- Neurology and Neurosurgery Department, McGill University, 3801 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Pik-Shan Lo
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - Huiyan Li
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4
| | - David Juncker
- McGill University & Genome Quebec Innovation Centre, McGill University, 740 Dr. Penfield Avenue, Montreal, Quebec, Canada, H3A 0G1.
- Biomedical Engineering Department, McGill University, 3775 University Street, Montreal, Quebec, Canada, H3A 2B4.
- Neurology and Neurosurgery Department, McGill University, 3801 University Street, Montreal, Quebec, Canada, H3A 2B4.
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11
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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: 95] [Impact Index Per Article: 10.6] [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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12
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Stenken JA, Poschenrieder AJ. Bioanalytical chemistry of cytokines--a review. Anal Chim Acta 2015; 853:95-115. [PMID: 25467452 PMCID: PMC4717841 DOI: 10.1016/j.aca.2014.10.009] [Citation(s) in RCA: 194] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/30/2014] [Accepted: 10/08/2014] [Indexed: 02/06/2023]
Abstract
Cytokines are bioactive proteins produced by many different cells of the immune system. Due to their role in different inflammatory disease states and maintaining homeostasis, there is enormous clinical interest in the quantitation of cytokines. The typical standard methods for quantitation of cytokines are immunoassay-based techniques including enzyme-linked immusorbent assays (ELISA) and bead-based immunoassays read by either standard or modified flow cytometers. A review of recent developments in analytical methods for measurements of cytokine proteins is provided. This review briefly covers cytokine biology and the analysis challenges associated with measurement of these biomarker proteins for understanding both health and disease. New techniques applied to immunoassay-based assays are presented along with the uses of aptamers, electrochemistry, mass spectrometry, optical resonator-based methods. Methods used for elucidating the release of cytokines from single cells as well as in vivo collection methods are described.
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Affiliation(s)
- Julie A Stenken
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA.
| | - Andreas J Poschenrieder
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA; Pharmaceutical Radiochemistry, Technische Universität München, Walther-Meißner-Street 3, D-85748 Garching, Germany
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13
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Hamid Mujawar L, van Amerongen A, Norde W. Influence of Pluronic F127 on the distribution and functionality of inkjet-printed biomolecules in porous nitrocellulose substrates. Talanta 2015; 131:541-7. [DOI: 10.1016/j.talanta.2014.08.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/30/2014] [Accepted: 08/02/2014] [Indexed: 10/24/2022]
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14
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Mujawar LH, Kuerten JGM, Siregar DP, van Amerongen A, Norde W. Influence of the relative humidity on the morphology of inkjet printed spots of IgG on a non-porous substrate. RSC Adv 2014. [DOI: 10.1039/c4ra01327a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
During the drying of inkjet printed droplets, the solute particles (IgG-Alexa-635 molecules) in the drop may distribute unevenly on the substrate, resulting in a “coffee-stain” spot morphology.
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Affiliation(s)
- Liyakat Hamid Mujawar
- Food and Biobased Research, Biomolecular Sensing and Diagnostics
- Wageningen University and Research Centre
- 6708 AA Wageningen, The Netherlands
- Laboratory of Physical Chemistry and Colloid Science
- Wageningen University
| | - J. G. M. Kuerten
- Department of Mechanical Engineering
- Eindhoven University of Technology
- 5600 MB Eindhoven, The Netherlands
- Faculty EEMCS
- University of Twente
| | - D. P. Siregar
- Department of Mechanical Engineering
- Eindhoven University of Technology
- 5600 MB Eindhoven, The Netherlands
| | - Aart van Amerongen
- Food and Biobased Research, Biomolecular Sensing and Diagnostics
- Wageningen University and Research Centre
- 6708 AA Wageningen, The Netherlands
| | - Willem Norde
- Laboratory of Physical Chemistry and Colloid Science
- Wageningen University
- 6703 HB Wageningen, The Netherlands
- University Medical Center Groningen
- University of Groningen
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15
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Ruwona TB, Mcbride R, Chappel R, Head SR, Ordoukhanian P, Burton DR, Law M. Optimization of peptide arrays for studying antibodies to hepatitis C virus continuous epitopes. J Immunol Methods 2013; 402:35-42. [PMID: 24269751 DOI: 10.1016/j.jim.2013.11.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/22/2013] [Accepted: 11/12/2013] [Indexed: 02/02/2023]
Abstract
Accurate and in-depth mapping of antibody responses is of great value in vaccine and antibody research. Using hepatitis C virus (HCV) as a model, we developed an affordable and high-throughput microarray-based assay for mapping antibody specificities to continuous antibody epitopes of HCV at high resolution. Important parameters in the chemistry for conjugating peptides/antigens to the array surface, the array layout, fluorophore choice and the methods for data analysis were investigated. Microscopic glass slide pre-coated with N-Hydroxysuccinimide (NHS)-ester (Slide H) was the preferred surface for conjugation of aminooxy-tagged peptides. This combination provides a simple chemical means to orient the peptides to the conjugation surface via an orthogonal covalent linkage at the N- or C-terminus of each peptide. The addition of polyvinyl alcohol to printing buffer gave uniform spot morphology and improved sensitivity and specificity of binding signals. Libraries of overlapping peptides covering the HCV E1 and E2 glycoprotein polypeptides (15-mer, 10 amino acids overlap) of 6 major HCV genotypes and the entire polypeptide sequence of the prototypic strain H77 were synthesized and printed in quadruplets in the assays. The utility of the peptide arrays was confirmed using HCV monoclonal antibodies (mAbs) specific to known continuous epitopes and immune sera of rabbits immunized with HCV antigens. The methods developed here can be easily adapted to studying antibody responses to antigens relevant in vaccine and autoimmune research.
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Affiliation(s)
- Tinashe B Ruwona
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Ryan Mcbride
- Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, United States
| | - Rebecca Chappel
- Center for Protein and Nucleic Acids Research, The Scripps Research Institute, La Jolla, CA, United States
| | - Steven R Head
- Microarray Core Facility, The Scripps Research Institute, La Jolla, CA, United States
| | - Phillip Ordoukhanian
- Center for Protein and Nucleic Acids Research, The Scripps Research Institute, La Jolla, CA, United States
| | - Dennis R Burton
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States
| | - Mansun Law
- Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA, United States.
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16
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Mujawar LH, Maan AA, Khan MKI, Norde W, van Amerongen A. Distribution of Biomolecules in Porous Nitrocellulose Membrane Pads Using Confocal Laser Scanning Microscopy and High-Speed Cameras. Anal Chem 2013; 85:3723-9. [DOI: 10.1021/ac400076p] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Liyakat Hamid Mujawar
- Food and Biobased Research,
Biomolecular Sensing and Diagnostics, Wageningen University and Research Centre, Bornse Weilanden 9, 6708 WG Wageningen,
The Netherlands
- Laboratory
of Physical Chemistry
and Colloid Science, Wageningen University, Dreijenplein 6, 6703 HB Wageningen, The Netherlands
| | - Abid Aslam Maan
- Food and Bioprocess Engineering
Group, Wageningen University, Bomenweg
2, 6703 HD Wageningen, Netherlands
| | - Muhammad Kashif Iqbal Khan
- Food and Bioprocess Engineering
Group, Wageningen University, Bomenweg
2, 6703 HD Wageningen, Netherlands
| | - Willem Norde
- University Medical Center Groningen, University of Groningen, A. Deusinglaan 1, 9713 AV
Groningen, The Netherlands
| | - Aart van Amerongen
- Food and Biobased Research,
Biomolecular Sensing and Diagnostics, Wageningen University and Research Centre, Bornse Weilanden 9, 6708 WG Wageningen,
The Netherlands
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17
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Zauber H, Schüler V, Schulze W. Systematic evaluation of reference protein normalization in proteomic experiments. FRONTIERS IN PLANT SCIENCE 2013; 4:25. [PMID: 23450762 PMCID: PMC3583035 DOI: 10.3389/fpls.2013.00025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 02/04/2013] [Indexed: 06/01/2023]
Abstract
Quantitative comparative analyses of protein abundances using peptide ion intensities and their modifications have become a widely used technique in studying various biological questions. In the past years, several methods for quantitative proteomics were established using stable-isotope labeling and label-free approaches. We systematically evaluated the application of reference protein normalization (RPN) for proteomic experiments using a high mass accuracy LC-MS/MS platform. In RPN all sample peptide intensities were normalized to an average protein intensity of a spiked reference protein. The main advantage of this method is that it avoids fraction of total based relative analysis of proteomic data, which is often very much dependent on sample complexity. We could show that reference protein ion intensity sums are sufficiently reproducible to ensure a reliable normalization. We validated the RPN strategy by analyzing changes in protein abundances induced by nutrient starvation in Arabidopsis thaliana. Beyond that, we provide a principle guideline for determining optimal combination of sample protein and reference protein load on individual LC-MS/MS systems.
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Affiliation(s)
- Henrik Zauber
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
| | - Vivian Schüler
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
| | - Waltraud Schulze
- Max Planck Institute of Molecular Plant PhysiologyGolm, Germany
- Plant Systems Biology, University of HohenheimStuttgart, Germany
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18
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Improvement of protein immobilization for the elaboration of tumor-associated antigen microarrays: application to the sensitive and specific detection of tumor markers from breast cancer sera. Biosens Bioelectron 2012; 40:385-92. [PMID: 23017679 DOI: 10.1016/j.bios.2012.08.019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2012] [Revised: 07/25/2012] [Accepted: 08/07/2012] [Indexed: 01/27/2023]
Abstract
There is an urgent need to identify relevant tumor markers showing high sensitivity and specificity for early diagnosis and prognosis of breast cancer. Protein microarrays have demonstrated to be cost-effective, high through-put and powerful tools for screening and identifying tumor markers with only minute samples. Autoantibodies directed against tumor-associated antigens (TAAs) were shown to be relevant tumor markers. However, due to the variability of immune response from one individual to another and depending on the type of cancer, detection of only one type of anti-TAA autoantibody is not sufficient to give a reliable and precise diagnosis. It is necessary to use a set of several TAAs for determining specific autoimmune profiles. Therefore, combining various TAAs on different surfaces could improve sensitivity and specificity for anti-TAA autoantibody detection. Herein a panel of 10 proteins, including well-known tumor-associated antigens (TAAs) and potential new biomarkers of breast cancer, were immobilized onto microstructured microarray under optimized conditions (spotting pH buffer, surface chemistry, blocking procedure), in order to determine an autoimmune signature of breast cancer. Sera from 29 breast cancer patients and 28 healthy donors were screened in sandwich immunoassays on the miniaturized system to detect the eventual presence of anti-TAAs autoantibodies. Results indicated that the detection level of each anti-TAA autoantibody in a given serum sample was strongly dependant on the surface chemistry. Combining five TAAs (p53, Hsp60, Hsp70, Her2-Fc, NY-ESO-1) on two different surface chemistries (NHS and APDMES) allowed the significant detection of more than 82% breast cancer sera.
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19
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Phillips CO, Govindarajan S, Hamblyn SM, Conlan RS, Gethin DT, Claypole TC. Patterning of antibodies using flexographic printing. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:9878-9884. [PMID: 22616757 DOI: 10.1021/la300867m] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Antibodies were patterned onto flexible plastic films using the flexographic printing process. An ink formulation was developed using high molecular weight polyvinyl alcohol in carbonate-bicarbonate buffer. In order to aid both antibody adhesion and the quality of definition in the printed features, a nitrocellulose coating was developed that was capable of being discretely patterned, thus increasing the signal-to-noise ratio of an antibody array. Printing antibody features such as dots, squares, text, and fine lines were reproduced effectively. Furthermore, this process could be easily adapted for printing of other biological materials, including, but not limited to, enzymes, DNA, proteins, aptamers, and cells.
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Affiliation(s)
- Christopher O Phillips
- Welsh Centre for Printing and Coating, College of Engineering, Swansea University, Singleton Park, Swansea, SA2 8PP, UK.
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20
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A comparative evaluation of microarray slides as substrates for the development of protease assay biosensors. Exp Mol Pathol 2011; 91:714-7. [DOI: 10.1016/j.yexmp.2011.09.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2011] [Accepted: 09/06/2011] [Indexed: 11/20/2022]
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21
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Gervais L, de Rooij N, Delamarche E. Microfluidic chips for point-of-care immunodiagnostics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2011; 23:H151-76. [PMID: 21567479 DOI: 10.1002/adma.201100464] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Indexed: 05/03/2023]
Abstract
We might be at the turning point where research in microfluidics undertaken in academia and industrial research laboratories, and substantially sponsored by public grants, may provide a range of portable and networked diagnostic devices. In this Progress Report, an overview on microfluidic devices that may become the next generation of point-of-care (POC) diagnostics is provided. First, we describe gaps and opportunities in medical diagnostics and how microfluidics can address these gaps using the example of immunodiagnostics. Next, we conceptualize how different technologies are converging into working microfluidic POC diagnostics devices. Technologies are explained from the perspective of sample interaction with components of a device. Specifically, we detail materials, surface treatment, sample processing, microfluidic elements (such as valves, pumps, and mixers), receptors, and analytes in the light of various biosensing concepts. Finally, we discuss the integration of components into accurate and reliable devices.
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Affiliation(s)
- Luc Gervais
- IBM Research-Zurich, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland
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22
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Rodríguez-Seguí SA, Pons Ximénez JI, Sevilla L, Ruiz A, Colpo P, Rossi F, Martínez E, Samitier J. Quantification of protein immobilization on substrates for cellular microarray applications. J Biomed Mater Res A 2011; 98:245-56. [PMID: 21626656 DOI: 10.1002/jbm.a.33089] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 10/11/2010] [Accepted: 02/03/2011] [Indexed: 11/07/2022]
Abstract
Cellular microarray developments and its applications are the next step after DNA and protein microarrays. The choice of the surface chemistry of the substrates used for the implementation of this technique, that must favor proper protein immobilization while avoiding cell adhesion on the nonspotted areas, presents a complex challenge. This is a key issue since usually the best nonfouling surfaces are also the ones that retain immobilized the smallest amounts of printed protein. To quantitatively assess the amount of protein immobilization, in this study several combinations of fluorescently labeled fibronectin (Fn*) and streptavidin (SA*) were microspotted, with and without glycerol addition in the printing buffer, on several substrates suitable for cellular microarrays. The substrates assayed included chemically activated surfaces as well as Poly ethylene oxide (PEO) films that are nonfouling in solution but accept adhesion of proteins in dry conditions. The results showed that the spotted Fn* was retained by all the surfaces, although the PEO surface did show smaller amounts of immobilization. The SA*, on the other hand, was only retained by the chemically activated surfaces. The inclusion of glycerol in the printing buffer significantly reduced the immobilization of both proteins. The results presented in this article provide quantitative evidence of the convenience of using a chemically activated surface to immobilize proteins relevant for cellular microarray applications, particularly when ECM proteins are cospotted with smaller factors which are more difficult to be retained by the surfaces.
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Affiliation(s)
- Santiago A Rodríguez-Seguí
- Nanobioengineering group, Institute for Bioengineering of Catalonia, Baldiri i Reixac 10-12, 08028 Barcelona, Spain.
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23
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Katz C, Levy-Beladev L, Rotem-Bamberger S, Rito T, Rüdiger SGD, Friedler A. Studying protein–protein interactions using peptide arrays. Chem Soc Rev 2011; 40:2131-45. [DOI: 10.1039/c0cs00029a] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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McWilliam I, Chong Kwan M, Hall D. Inkjet printing for the production of protein microarrays. Methods Mol Biol 2011; 785:345-61. [PMID: 21901611 DOI: 10.1007/978-1-61779-286-1_23] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A significant proportion of protein microarray researchers would like the arrays they develop to become widely used research, screening, validation or diagnostic devices. For this to be achievable the arrays must be compatible with high-throughput techniques that allow manufacturing scale production. In order to simplify the transition from laboratory bench to market, Arrayjet have developed a range of inkjet microarray printers, which, at one end of the scale, are suitable for R&D and, at the other end, are capable of true high-throughput array output. To maintain scalability, all Arrayjet microarray printers utilise identical core technology comprising a JetSpyder™ liquid handling adaptor, which enables automated loading of an industry standard inkjet printhead compatible with non-contact on-the-fly printing. This chapter contains a detailed explanation of Arrayjet technology followed by a historical look at the development of inkjet technologies for protein microarray production. The method described subsequently is a simple example of an antibody array printed onto nitrocellulose-coated slides with specific detection with fluorescently labelled IgG. The method is linked to a notes section with advice on best practice and sources of useful information for protein microarray production using inkjet technology.
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25
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Yue C, Oelke M, Paulaitis ME, Schneck JP. Novel cellular microarray assay for profiling T-cell peptide antigen specificities. J Proteome Res 2010; 9:5629-37. [PMID: 20836567 DOI: 10.1021/pr100447b] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a novel cellular microarray assay using soluble peptide-loaded HLA A2-Ig dimer complexes that optimizes the avidity of peptide-HLA binding by preserving the molecular flexibility of the dimer complex while attaining much higher concentrations of the complex relative to cognate T-cell receptors. A seminal advance in assay development is made by separating the molecular T-cell receptor recognition event from the binding interactions that lead to antigen-specific cell capture on the microarray. This advance enables the quantitative determination of antigen-specific frequencies in heterogeneous T-cell populations without enumerating the number of cells captured on the microarray. The specificity of cell capture, sensitivity to low antigen-specific frequencies, and quantitation of antigenic T-cell specificities are established using CD8 T-cell populations with prepared antigen-specific CTL frequencies and heterogeneous T cells isolated from peripheral blood. The results demonstrate several advantages for high-throughput broad-based, quantitative assessments of low-frequency antigen specificities. The assay enables the use of cellular microarrays to determine the stability and flux of antigen-specific T-cell responses within and across populations.
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Affiliation(s)
- C Yue
- Lowrie Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, OH 43210, USA
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26
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Gervais L, Delamarche E. Toward one-step point-of-care immunodiagnostics using capillary-driven microfluidics and PDMS substrates. LAB ON A CHIP 2009; 9:3330-7. [PMID: 19904397 DOI: 10.1039/b906523g] [Citation(s) in RCA: 157] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Point-of-care diagnostics will strongly benefit from miniaturization based on microfluidics because microfluidics integrate functions that can together preserve valuable samples and reagents, increase sensitivity of a test, and accelerate mass transport limited reactions. But a main challenge is to incorporate reagents into microfluidics and to make microfluidics simple to use. Here, we integrate microfluidic functional elements, some of which were developed earlier, and reagents such as detection antibodies (dAbs), capture antibodies (cAbs) and analyte molecules for making one-step immunoassays: the integrated device only requires the addition of sample to trigger a cascade of events powered by capillary forces for effecting a sandwich immunoassay that is read using a fluorescence microscope. The microfluidic elements comprise a sample collector, delay valves, flow resistors, a deposition zone for dAbs, a reaction chamber sealed with a polydimethylsiloxane (PDMS) substrate, and a capillary pump and vents. Parameters for depositing 3.6 nL of a solution of dAb on the chip using an inkjet are optimized and the PDMS substrate is patterned with analytes, which provide a positive control, and cAbs. Various storage conditions of the patterned PDMS are investigated for up to 6 months revealing that storage with a desiccant preserved at least 51% of the activity of the cAbs. C-reactive protein (CRP), a general inflammation and cardiac marker, is detected using this one-step chip using only 5 microL of human serum by measuring fluorescent signals from 30 x 100 microm(2) areas of the PDMS substrate in the wet reaction chamber. The one-step chip can detect CRP at a concentration of 10 ng mL(-1) in less than 3 min and below 1 ng mL(-1) within 14 min. The work presented here may spur the adoption of fluorescence immunoassays using capillary driven microfluidics and PDMS substrates for point-of-care diagnostics.
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Affiliation(s)
- Luc Gervais
- University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
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27
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Stoevesandt O, Taussig MJ, He M. Protein microarrays: high-throughput tools for proteomics. Expert Rev Proteomics 2009; 6:145-57. [PMID: 19385942 PMCID: PMC7105755 DOI: 10.1586/epr.09.2] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein microarrays are versatile tools for parallel, miniaturized screening of binding events involving large numbers of immobilized proteins in a time- and cost-effective manner. They are increasingly applied for high-throughput protein analyses in many research areas, such as protein interactions, expression profiling and target discovery. While conventionally made by the spotting of purified proteins, recent advances in technology have made it possible to produce protein microarrays through in situ cell-free synthesis directly from corresponding DNA arrays. This article reviews recent developments in the generation of protein microarrays and their applications in proteomics and diagnostics.
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Affiliation(s)
- Oda Stoevesandt
- Babraham Bioscience Technologies Ltd., Babraham Research Campus, Cambridge, CB22 3AT, UK.
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28
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Hurst R, Hook B, Slater MR, Hartnett J, Storts DR, Nath N. Protein-protein interaction studies on protein arrays: effect of detection strategies on signal-to-background ratios. Anal Biochem 2009; 392:45-53. [PMID: 19464993 DOI: 10.1016/j.ab.2009.05.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/15/2009] [Accepted: 05/16/2009] [Indexed: 01/19/2023]
Abstract
Protein arrays hold great promise for proteome-scale analysis of protein-protein interaction networks, but the technical challenges have hindered their adoption by proteomics researchers. The crucial issue of design and fabrication of protein arrays have been addressed in several studies, but the detection strategies used for identifying protein-protein interactions have received little attention. In this study, we evaluated six different detection strategies to identify four different protein-protein interaction pairs. We discuss each detection approach in terms of signal-to-background (S/B) ratio, ease of use, and adaptability to high-throughput format. Protein arrays for this study were made by expressing both the bait proteins (proteins captured at the surface) and prey proteins (probes) in cell-free rabbit reticulocyte lysate (RRL) systems. Bait proteins were expressed as HaloTag fusions that allow covalent capture on a HaloTag ligand-coated glass without any prior protein purification step. Prey proteins were expressed and modified with either tags (protein or peptides) or labels (fluorescent or radiometric) for detection. This simple method for creating protein arrays in combination with our analyses of several detection strategies should increase the usefulness of protein array technologies.
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Affiliation(s)
- Robin Hurst
- Research and Development, Promega Corporation, Madison, WI 53711, USA
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29
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Liu J, Eddings MA, Miles AR, Bukasov R, Gale BK, Shumaker-Parry JS. In Situ Microarray Fabrication and Analysis Using a Microfluidic Flow Cell Array Integrated with Surface Plasmon Resonance Microscopy. Anal Chem 2009; 81:4296-301. [DOI: 10.1021/ac900181f] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jianping Liu
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Mark A. Eddings
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Adam R. Miles
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Rostislav Bukasov
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Bruce K. Gale
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
| | - Jennifer S. Shumaker-Parry
- Department of Chemistry, Department of Bioengineering, and Department of Mechanical Engineering, University of Utah, Salt Lake City, Utah 84112, and Wasatch Microfluidics, 825 N. 300 W. Street NE 129, North Salt Lake City, Utah 84054
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30
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Apparent thixotropic properties of saline/glycerol drops with biotinylated antibodies on streptavidin-coated glass slides: implications for bacterial capture on antibody microarrays. SENSORS 2009; 9:995-1011. [PMID: 22399952 PMCID: PMC3280844 DOI: 10.3390/s90200995] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2008] [Accepted: 02/11/2009] [Indexed: 11/20/2022]
Abstract
The thixotropic-like properties of saline/glycerol drops, containing biotinylated capture antibodies, on streptavidin-coated glass slides have been investigated, along with their implications for bacterial detection in a fluorescent microarray immunoassay. The thixotropic-like nature of 60:40 saline-glycerol semisolid droplets (with differing amounts of antibodies) was observed when bacteria were captured, and their presence detected using a fluorescently-labeled antibody. Semisolid, gel-like drops of biotinylated capture antibody became liquefied and moved, and then returned to semisolid state, during the normal immunoassay procedures for bacterial capture and detection. Streaking patterns were observed that indicated thixotropic-like characteristics, and this appeared to have allowed excess biotinylated capture antibody to participate in bacterial capture and detection. When developing a microarray for bacterial detection, this must be considered for optimization. For example, with the appropriate concentration of antibody (in this study, 0.125 ng/nL), spots with increased diameter at the point of contact printing (and almost no streaking) were produced, resulting in a maximal signal. With capture antibody concentrations greater than 0.125 ng/nL, the excess biotinylated capture antibody (i.e., that which was residing in the three-dimensional, semisolid droplet space above the surface) was utilized to capture more bacteria. Similarly, when the immunoassay was performed within a hydrophobic barrier (i.e., without a coverslip), brighter spots with increased signal were observed. In addition, when higher concentrations of cells (∼108 cells/mL) were available for capture, the importance of unbound capture antibody in the semisolid droplets became apparent because washing off the excess, unbound biotinylated capture antibody before the immunoassay was performed reduced the signal intensity by nearly 50%. This reduction in signal was not observed with lower concentrations of cells (∼106 cells/mL). With increased volumes of capture antibody, abnormal spots were visualized, along with decreased signal intensity, after bacterial detection, indicating that the increased droplet volume detrimentally affected the immunoassay.
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31
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Mace CR, Yadav AR, Miller BL. Investigation of non-nucleophilic additives for the reduction of morphological anomalies in protein arrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12754-7. [PMID: 18925757 PMCID: PMC2836230 DOI: 10.1021/la801712m] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Uniform spot morphology is of critical importance in the fabrication and successful use of protein arrays, and solution additives are often needed to ensure good spot quality. Whereas hydroxyl-bearing molecules such as glycerol have found wide use, in our experience these reduce the efficiency of probe immobilization (particularly in the context of aldehyde-terminated surfaces). Here, we report a series of non-nucleophilic molecules that can be used as additives to improve spot homogeneity in protein arrays. Arrayed imaging reflectometry, a label-free optical biosensing technique, has been used along with spectroscopic ellipsometry to test the spot homogeneity, antibody immobilization efficiency, and activity of antihuman IgG arrays prepared with these non-nucleophilic additives on glutaraldehyde surfaces. It has been determined that 0.1% v/v 12-crown-4 performs optimally in MPBS buffer.
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Affiliation(s)
- Charles R. Mace
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
| | - Amrita R. Yadav
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14642
| | - Benjamin L. Miller
- Department of Dermatology, University of Rochester, Rochester, New York 14642
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642
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32
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Nath N, Hurst R, Hook B, Meisenheimer P, Zhao KQ, Nassif N, Bulleit RF, Storts DR. Improving Protein Array Performance: Focus on Washing and Storage Conditions. J Proteome Res 2008; 7:4475-82. [DOI: 10.1021/pr800323j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nidhi Nath
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Robin Hurst
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Brad Hook
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Poncho Meisenheimer
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Kate Q. Zhao
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Nadine Nassif
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Robert F. Bulleit
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
| | - Douglas R. Storts
- Research and Development, Promega Corporation, Madison, Wisconsin 53711 and Promega Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401
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Wu P, Castner DG, Grainger DW. Diagnostic devices as biomaterials: a review of nucleic acid and protein microarray surface performance issues. JOURNAL OF BIOMATERIALS SCIENCE-POLYMER EDITION 2008; 19:725-53. [PMID: 18534094 DOI: 10.1163/156856208784522092] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
This review of current DNA and protein microarray diagnostic and bio-analytical technologies focuses on the different surface chemistries used in these miniaturized surface-capture formats. Description of current strategies in bio-immobilization and coupling to create multiplexed affinity bioassays in micrometer-sized printed spots, problems with current formats and review of some detection methods are included. Recommendations for improving long-standing challenges in DNA- and protein-based arrays are forwarded. The biomaterials community can contribute relevant expertise to these formidable bio-interfacial problems that represent significant barriers to clinical implementation of microarray assays.
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Affiliation(s)
- Peng Wu
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
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Egas DA, Wirth MJ. Fundamentals of protein separations: 50 years of nanotechnology, and growing. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2008; 1:833-855. [PMID: 20636099 DOI: 10.1146/annurev.anchem.1.031207.112912] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The separation of proteins in biology samples has long been recognized as an important and daunting endeavor that continues to have enormous impact on human health. Today's technology for protein separations has its origins in the early nanotechnology of the 1950s and 1960s, and the methods include immunoassays and other affinity extractions, electrophoresis, and chromatography. What is different today is the need to resolve and identify many low-abundance proteins within complex biological matrices. Multidimensional separations are the rule, high speed is needed, and the separations must be able to work with mass spectrometry for protein identification. Hybrid approaches that combine disparate separation tools (including recognition, electrophoresis, and chromatography) take advantage of the fact that no single class of separation can resolve the proteins in a biological matrix. Protein separations represent a developing area technologically, and understanding the principles of protein separations from a molecular and nanoscale viewpoint will enable today's researchers to invent tomorrow's technology.
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Affiliation(s)
- David A Egas
- Department of Chemistry, University of Arizona, Tucson, 85721, USA.
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Abstract
The antibody microarray is an intrinsically robust and quantitative system that delivers high-throughput and parallel measurements on particular sets of known proteins. It has become an important proteomics research tool, complementary to the conventional unbiased separation-based and mass spectrometry-based approaches. This review summarizes the technical aspects of production and the application for quantitative proteomic analysis with an emphasis on disease proteomics, especially the identification of biomarkers. Quality control, data analysis methods and the challenges for quantitative assays are also discussed.
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Affiliation(s)
- Lin-Li Lv
- Institute of Nephrology, Zhong Da Hospital, Southeast University, Nanjing, China.
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