1
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Gray A, Bradbury ARM, Knappik A, Plückthun A, Borrebaeck CAK, Dübel S. Animal-free alternatives and the antibody iceberg. Nat Biotechnol 2020; 38:1234-1239. [DOI: 10.1038/s41587-020-0687-9] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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2
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Matsushita T, Arai H, Koyama T, Hatano K, Nemoto N, Matsuoka K. Iodoacetyl-functionalized pullulan: A supplemental enhancer for single-domain antibody-polyclonal antibody sandwich enzyme-linked immunosorbent assay for detection of survivin. Bioorg Med Chem Lett 2017; 27:4844-4848. [PMID: 28974337 DOI: 10.1016/j.bmcl.2017.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/20/2017] [Accepted: 09/22/2017] [Indexed: 11/19/2022]
Abstract
Survivin, an inhibitor of the apoptosis protein family, is a potent tumor marker for diagnosis and prognosis. The enzyme-linked immunosorbent assay (ELISA) is one of the methods that has been used for detection of survivin. However, ELISA has several disadvantages caused by the use of conventional antibodies, and we have therefore been trying to develop a novel ELISA system using camelid single-domain antibodies (VHHs) as advantageous replacements. Here we report a supplemental approach to improve the VHH-polyclonal antibody sandwich ELISA for survivin detection. Iodoacetyl-functionalized pullulan was synthesized, and its thiol reactivity was characterized by a model reaction with l-cysteine. The thiophilic pullulan was applied to an immunoassay asan additive upon coating of standard assay plates with an anti-survivin VHH fusion protein with C-terminal cysteine. The results showed that the mole ratio of the additive to VHH had a significant effect on the consequent response. Mole ratios of 0.07, 0.7, and 7 led to 90% lower, 15% higher, and 69% lower responses, respectively, than the response of a positive control in which no additive was used. The background levels observed in any additive conditions were as low as that of a negative control lacking both VHH and the additive. These results indicate the applicability of the thiol-reactive pullulan as a response enhancer to VHH-based ELISA.
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Affiliation(s)
- Takahiko Matsushita
- Area for Molecular Function, Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan; Medical Innovation Research Unit (MiU), Advanced Institute of Innovative Technology (AIIT), Saitama University, Sakura, Saitama 338-8570, Japan
| | - Hidenao Arai
- Epsilon Molecular Engineering (EME) Inc., Saitama University Comprehensive Open Innovation Center #303, Sakura, Saitama 338-8570, Japan
| | - Tetsuo Koyama
- Area for Molecular Function, Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan
| | - Ken Hatano
- Area for Molecular Function, Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan; Medical Innovation Research Unit (MiU), Advanced Institute of Innovative Technology (AIIT), Saitama University, Sakura, Saitama 338-8570, Japan
| | - Naoto Nemoto
- Area for Molecular Function, Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan; Medical Innovation Research Unit (MiU), Advanced Institute of Innovative Technology (AIIT), Saitama University, Sakura, Saitama 338-8570, Japan; Epsilon Molecular Engineering (EME) Inc., Saitama University Comprehensive Open Innovation Center #303, Sakura, Saitama 338-8570, Japan
| | - Koji Matsuoka
- Area for Molecular Function, Division of Material Science, Graduate School of Science and Engineering, Saitama University, Sakura, Saitama 338-8570, Japan; Medical Innovation Research Unit (MiU), Advanced Institute of Innovative Technology (AIIT), Saitama University, Sakura, Saitama 338-8570, Japan.
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3
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Brofelth M, Städe LW, Ekstrand AI, Edfeldt LP, Kovačič R, Nielsen TT, Larsen KL, Duroux L, Wingren C. Site-specific photocoupling of p Bpa mutated scFv antibodies for use in affinity proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:985-996. [DOI: 10.1016/j.bbapap.2017.03.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/13/2017] [Accepted: 03/20/2017] [Indexed: 12/26/2022]
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4
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Mirzadeh A, Saadatnia G, Golkar M, Babaie J, Noordin R. Production of refolded Toxoplasma gondii recombinant SAG1-related sequence 3 (SRS3) and its use for serodiagnosis of human toxoplasmosis. Protein Expr Purif 2017; 133:66-74. [PMID: 28263855 DOI: 10.1016/j.pep.2017.03.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 03/01/2017] [Accepted: 03/01/2017] [Indexed: 11/26/2022]
Abstract
SAG1-related sequence 3 (SRS3) is one of the major Toxoplasma gondii tachyzoite surface antigens and has been shown to be potentially useful for the detection of toxoplasmosis. This protein is highly conformational due to the presence of six disulfide bonds. To achieve solubility and antigenicity, SRS3 depends on proper disulfide bond formation. The aim of this study was to over-express the SRS3 protein with correct folding for use in serodiagnosis of the disease. To achieve this, a truncated SRS3 fusion protein (rtSRS3) was produced, containing six histidyl residues at both terminals and purified by immobilized metal affinity chromatography. The refolding process was performed through three methods, namely dialysis in the presence of chemical additives along with reduced/oxidized glutathione and drop-wise dilution methods with reduced/oxidized glutathione or reduced DTT/oxidized glutathione. Ellman's assay and ELISA showed that the protein folding obtained by the dialysis method was the most favorable, probably due to the correct folding. Subsequently, serum samples from individuals with chronic infection (n = 76), probable acute infection (n = 14), and healthy controls (n = 81) were used to determine the usefulness of the refolded rtSRS3 for Toxoplasma serodiagnosis. The results of the developed IgG-ELISA showed a diagnostic specificity of 91% and a sensitivity of 82.89% and 100% for chronic and acute serum samples, respectively. In conclusion, correctly folded rtSRS3 has the potential to be used as a soluble antigen for the detection of human toxoplasmosis.
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Affiliation(s)
- Abolfazl Mirzadeh
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran; Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Geita Saadatnia
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran.
| | - Majid Golkar
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Jalal Babaie
- Molecular Parasitology Laboratory, Department of Parasitology, Pasteur Institute of Iran, Tehran, Iran
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
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5
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Shen M, Rusling J, Dixit CK. Site-selective orientated immobilization of antibodies and conjugates for immunodiagnostics development. Methods 2017; 116:95-111. [PMID: 27876681 PMCID: PMC5374010 DOI: 10.1016/j.ymeth.2016.11.010] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 01/11/2023] Open
Abstract
Immobilized antibody systems are the key to develop efficient diagnostics and separations tools. In the last decade, developments in the field of biomolecular engineering and crosslinker chemistry have greatly influenced the development of this field. With all these new approaches at our disposal, several new immobilization methods have been created to address the main challenges associated with immobilized antibodies. Few of these challenges that we have discussed in this review are mainly associated to the site-specific immobilization, appropriate orientation, and activity retention. We have discussed the effect of antibody immobilization approaches on the parameters on the performance of an immunoassay.
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Affiliation(s)
- Min Shen
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
| | - James Rusling
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
- Institute of Materials Science, University of Connecticut, Storrs, Connecticut 06269-3136
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 060
- School of Chemistry, National University of Ireland at Galway, Galway, Ireland
| | - Chandra K Dixit
- Department of Chemistry, University of Connecticut, Storrs, Connecticut 06269-3060
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6
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Scaffolds for oriented and close-packed immobilization of immunoglobulins. Biosens Bioelectron 2017; 89:810-821. [DOI: 10.1016/j.bios.2016.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 02/07/2023]
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7
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Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays. MICROARRAYS 2016; 5:microarrays5020016. [PMID: 27600082 PMCID: PMC5003492 DOI: 10.3390/microarrays5020016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Revised: 12/02/2015] [Accepted: 12/09/2015] [Indexed: 11/17/2022]
Abstract
Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the antibodies and the solid surfaces plays a central role. In this study, we have taken on the first comprehensive view and evaluated the overall impact of solid surfaces on the recombinant antibody microarray design. The results clearly demonstrated the importance of the surface-antibody interaction and showed the effect of the solid supports on the printing process, the array format of planar arrays (slide- and well-based), the assay performance (spot features, reproducibility, specificity and sensitivity) and assay processing (degree of automation). In the end, two high-end recombinant antibody microarray technology platforms were designed, based on slide-based (black polymer) and well-based (clear polymer) arrays, paving the way for future large-scale protein expression profiling efforts.
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8
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Gand M, Thöle C, Müller H, Brundiek H, Bashiri G, Höhne M. A NADH-accepting imine reductase variant: Immobilization and cofactor regeneration by oxidative deamination. J Biotechnol 2016; 230:11-8. [PMID: 27164259 DOI: 10.1016/j.jbiotec.2016.05.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 04/29/2016] [Accepted: 05/03/2016] [Indexed: 11/16/2022]
Abstract
Engineering cofactor specificity of enzymes is a promising approach that can expand the application of enzymes for biocatalytic production of industrially relevant chemicals. Until now, only NADPH-dependent imine reductases (IREDs) are known. This limits their applications to reactions employing whole cells as a cost-efficient cofactor regeneration system. For applications of IREDs as cell-free catalysts, (i) we created an IRED variant showing an improved activity for NADH. With rational design we were able to identify four residues in the (R)-selective IRED from Streptomyces GF3587 (IR-Sgf3587), which coordinate the 2'-phosphate moiety of the NADPH cofactor. From a set of 15 variants, the highest NADH activity was caused by the single amino acid exchange K40A resulting in a 3-fold increased acceptance of NADH. (ii) We showed its applicability using an immobilisate obtained either from purified enzyme or from lysate using the EziG(™) carriers. Applying the variant and NADH, we reached 88% conversion in a preparative scale biotransformation when employing 4% (w/v) 2-methylpyrroline. (iii) We demonstrated a one-enzyme cofactor regeneration approach using the achiral amine N-methyl-3-aminopentanone as a hydrogen donor co-substrate.
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Affiliation(s)
- Martin Gand
- Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Christian Thöle
- Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Hubertus Müller
- Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany
| | - Henrike Brundiek
- Enzymicals AG, Walther-Rathenau-Straße 49a, 17489 Greifswald, Germany.
| | - Ghader Bashiri
- Structural Biology Laboratory and Maurice Wilkins Centre for Molecular Biodiscovery, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand.
| | - Matthias Höhne
- Institute of Biochemistry, Greifswald University, Felix-Hausdorff-Str. 4, 17487 Greifswald, Germany.
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9
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Thatikonda N, Delfani P, Jansson R, Petersson L, Lindberg D, Wingren C, Hedhammar M. Genetic fusion of single-chain variable fragments to partial spider silk improves target detection in micro- and nanoarrays. Biotechnol J 2015; 11:437-48. [PMID: 26470853 DOI: 10.1002/biot.201500297] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Revised: 08/18/2015] [Accepted: 10/07/2015] [Indexed: 12/20/2022]
Abstract
Immobilizing biomolecules with retained functionality and stability on solid supports is crucial for generation of sensitive immunoassays. However, upon use of conventional immobilization strategies, a major portion of the biomolecules (e.g. antibodies) frequently tends to lose their bioactivity. In this study, we describe a procedure to immobilize human single-chain variable fragment (scFv) via genetic fusion to partial spider silk, which have a high tendency to adhere to solid supports. Two scFvs, directed towards serum proteins, were genetically fused to partial spider silk proteins and expressed as silk fusion proteins in E. coli. Antigen binding ability of scFvs attached to a partial silk protein denoted RC was investigated using microarray analysis, whereas scFvs fused to the NC silk variant were examined using nanoarrays. Results from micro- and nanoarrays confirmed the functionality of scFvs attached to both RC and NC silk, and also for binding of targets in crude serum. Furthermore, the same amount of added scFv gives higher signal intensity when immobilized via partial spider silk compared to when immobilized alone. Together, the results suggest that usage of scFv-silk fusion proteins in immunoassays could improve target detection, in the long run enabling novel biomarkers to be detected in crude serum proteomes.
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Affiliation(s)
- Naresh Thatikonda
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Payam Delfani
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | - Ronnie Jansson
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Linn Petersson
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden
| | | | - Christer Wingren
- Department of Immunotechnology and CREATE Health, Lund University, Lund, Sweden.
| | - My Hedhammar
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden. .,Division of Protein Technology, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden.
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10
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Molecular design of recombinant scFv antibodies for site-specific photocoupling to β-cyclodextrin in solution and onto solid support. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:2164-73. [PMID: 25172394 DOI: 10.1016/j.bbapap.2014.08.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 08/18/2014] [Accepted: 08/19/2014] [Indexed: 12/14/2022]
Abstract
The ability to design and tailor-make antibodies to meet the biophysical demands required by the vast range of current and future antibody-based applications within biotechnology and biomedicine will be essential. In this proof-of-concept study, we have for the first time tailored human recombinant scFv antibodies for site-specific photocoupling through the use of an unnatural amino acid (UAA) and the dock'n'flash technology. In more detail, we have successfully explored the possibility to expand the genetic code of E. coli and introduced the photoreactive UAA p-benzoyl-L-phenylalanine (pBpa), and showed that the mutated scFv antibody could be expressed in E. coli with retained structural and functional properties, as well as binding affinity. The pBpa group was then used for affinity capture of the mutated antibody by β-cyclodextrin (β-CD), which provided the hydrogen atoms to be abstracted in the subsequent photocoupling process upon irradiation at 365nm. The results showed that the pBpa mutated antibody could be site-specifically photocoupled to free and surface (array) immobilized β-CD. Taken together, this paves the way for novel means of tailoring recombinant scFv antibodies for site-specific photochemical-based tagging, functionalization and immobilization in numerous applications.
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11
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Tsai CW, Jheng SL, Chen WY, Ruaan RC. Strategy of Fc-Recognizable Peptide Ligand Design for Oriented Immobilization of Antibody. Anal Chem 2014; 86:2931-8. [DOI: 10.1021/ac4029467] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Ching-Wei Tsai
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Siang-Long Jheng
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Wen-Yih Chen
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
- Institute
of Biomedical Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
| | - Ruoh-Chyu Ruaan
- Department
of Chemical and Materials Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
- Institute
of Biomedical Engineering, National Central University, Chung-Li City, Taoyuan 32001, Taiwan
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12
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Borrebaeck CAK, Wingren C. High-throughput proteomics using antibody microarrays: an update. Expert Rev Mol Diagn 2014; 7:673-86. [PMID: 17892372 DOI: 10.1586/14737159.7.5.673] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Antibody-based microarrays are a rapidly emerging technology that has advanced from the first proof-of-concept studies to demanding serum protein profiling applications during recent years, displaying great promise within disease proteomics. Miniaturized micro- and nanoarrays can be fabricated with an almost infinite number of antibodies carrying the desired specificities. While consuming only minute amounts of reagents, multiplexed and ultrasensitive assays can be performed targeting high- as well as low-abundance analytes in complex nonfractionated proteomes. The microarray images generated can then be converted into protein expression profiles or protein atlases, revealing a detailed composition of the sample. The technology will provide unique opportunities for fields such as disease diagnostics, biomarker discovery, patient stratification, predicting disease recurrence and drug target discovery. This review describes an update of high-throughput proteomics, using antibody-based microarrays, focusing on key technological advances and novel applications that have emerged over the last 3 years.
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Affiliation(s)
- Carl A K Borrebaeck
- Lund University, Department of Immunotechnology & CREATE Health, BMC D13, SE-221 84 Lund, Sweden.
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13
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Wingren C. Novel type of protein chip for multiplex detection of autoantibodies. Expert Rev Proteomics 2013; 10:417-20. [PMID: 24088012 DOI: 10.1586/14789450.2013.842900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Evaluation of: Akada J, Kamei S, Ito A et al. A new type of protein chip to detect hepatocellular carcinoma-related autoimmune antibodies in the sera of hepatitis C virus-positive patients. Proteome Sci. 11(1), 33 (2013). Unlocking the proteome and delivering biomarkers to the clinic will be critical for early and improved diagnosis and prognosis. Conventional protein microarrays have evolved as a promising proteomic technology with great potential for protein expression profiling in health and disease. In this study, Akada et al. explore a new type of protein chip, interfaced with a dual-color fluorescence-based read-out, for screening of autoantibodies in serum. Uniquely, the recombinant antigens were microarray adapted by molecular design to contain a five-cysteine tag for immobilization and green fluorescent protein for detection (color 1). The engineered antigens were immobilized on in-house-designed maleimide-incorporated diamond-like carbon substrates and subsequently heat treated in a solution of denaturing and reducing agents before any specifically bound serum autoantibodies were detected (color 2). The authors used a 4-plex array targeting hepatocellular carcinoma-related autoantibodies in the sera of hepatitis C virus-positive patients as model system to demonstrate proof-of-concept.
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Affiliation(s)
- Christer Wingren
- Department of Immunotechnology, Lund University, Medicon Village, SE-22381 Lund, Sweden
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14
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Ericsson EM, Enander K, Bui L, Lundström I, Konradsson P, Liedberg B. Site-specific and covalent attachment of his-tagged proteins by chelation assisted photoimmobilization: a strategy for microarraying of protein ligands. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11687-11694. [PMID: 24007525 DOI: 10.1021/la4011778] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A novel strategy for site-specific and covalent attachment of proteins has been developed, intended for robust and controllable immobilization of histidine (His)-tagged ligands in protein microarrays. The method is termed chelation assisted photoimmobilization (CAP) and was demonstrated using human IgG-Fc modified with C-terminal hexahistidines (His-IgGFc) as the ligand and protein A as the analyte. Alkanethiols terminated with either nitrilotriacetic acid (NTA), benzophenone (BP), or oligo(ethylene glycol) were synthesized and mixed self-assembled monolayers (SAMs) were prepared on gold and thoroughly characterized by infrared reflection absorption spectroscopy (IRAS), ellipsometry, and contact angle goniometry. In the process of CAP, NTA chelates Ni(2+) and the complex coordinates the His-tagged ligand in an oriented assembly. The ligand is then photoimmobilized via BP, which forms covalent bonds upon UV light activation. In the development of affinity biosensors and protein microarrays, site-specific attachment of ligands in a fashion where analyte binding sites are available is often preferred to random coupling. Analyte binding performance of ligands immobilized either by CAP or by standard amine coupling was characterized by surface plasmon resonance in combination with IRAS. The relative analyte response with randomly coupled ligand was 2.5 times higher than when site-specific attachment was used. This is a reminder that also when immobilizing ligands via residues far from the binding site, there are many other factors influencing availability and activity. Still, CAP provides a valuable expansion of protein immobilization techniques since it offers attractive microarraying possibilities amenable to applications within proteomics.
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Affiliation(s)
- Emma M Ericsson
- Division of Molecular Physics, ‡Division of Organic Chemistry, and §Division of Applied Physics; Department of Physics, Chemistry and Biology, Linköping University , SE-581 83 Linköping, Sweden
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15
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Ierardi V, Ferrera F, Millo E, Damonte G, Filaci G, Valbusa U. Bioactive surfaces for antibody-antigen complex detection by Atomic Force Microscopy. ACTA ACUST UNITED AC 2013. [DOI: 10.1088/1742-6596/439/1/012001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Harmsen MM, Fijten HPD. Improved functional immobilization of llama single-domain antibody fragments to polystyrene surfaces using small peptides. J Immunoassay Immunochem 2012; 33:234-51. [PMID: 22738648 DOI: 10.1080/15321819.2011.634473] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We studied the effect of different fusion domains on the functional immobilization of three llama single-domain antibody fragments (VHHs) after passive adsorption to polystyrene in enzyme-linked immunosorbent assays (ELISA). Three VHHs produced without any fusion domain were efficiently adsorbed to polystyrene, which, however, resulted in inefficient antigen binding. Functional VHH immobilization was improved by VHH fusion to a consecutive myc-His6-tag and was even more improved by fusion to the llama antibody long hinge region containing an additional His6-tag (LHc-His6). The partial dimerization of VHH-LHc-His6 fusion proteins through LHc-mediated disulfide-bond formation was not essential for their improved functional immobilization. VHH fusions to specific polystyrene binding peptides, hydrophobins, or other, unrelated VHH domains were less suitable for increasing functional VHH immobilization because of reduced microbial expression levels. Thus, VHH-LHc-His6 fusion proteins are most suited for functional passive adsorption in ELISA.
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Affiliation(s)
- Michiel M Harmsen
- Central Veterinary Institute of Wageningen UR, Lelystad, The Netherlands.
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17
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Wong LS, Karthikeyan CV, Eichelsdoerfer DJ, Micklefield J, Mirkin CA. A methodology for preparing nanostructured biomolecular interfaces with high enzymatic activity. NANOSCALE 2012; 4:659-666. [PMID: 22159287 DOI: 10.1039/c1nr11443c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The development of a novel method for functionalizing nanopatterned surfaces with catalytically active proteins is reported. This method involves using dip-pen nanolithography (DPN) and polymer pen lithography (PPL) to generate nanoscale patterns of coenzyme A, followed by a phosphopantetheinyl transferase-mediated coupling between coenzyme A and proteins fused to the ybbR-tag. By exploiting the ability to generate protein features over large areas afforded by DPN and PPL, it was now possible to measure protein activity directly on these surfaces. It was found that proteins immobilized on the nanoscale features not only display higher activity per area with decreasing feature size, but are also robust and can be used for repeated catalytic cycles. The immobilization method is applicable to a variety of proteins and gives rise to superior activity compared to proteins attached in random orientations on the surface.
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Affiliation(s)
- Lu Shin Wong
- Department of Chemistry and Institute of Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208-3113, United States
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18
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Hu X, O’Connor IB, Wall JG. Antibody Immobilization on Solid Surfaces: Methods and Applications. BIOLOGICAL INTERACTIONS WITH SURFACE CHARGE IN BIOMATERIALS 2011. [DOI: 10.1039/9781849733366-00090] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The correct immobilization of the antibody component is one of the most critical steps in the development of immunoassays, immunosensors and immunochromatography matrices. Advances in hybridoma technology and protein engineering have allowed traditional limitations of polyreactivity of antibody preparations, poor device stability and random orientation of binding pockets to be largely overcome, resulting in stable, sensitive, highly specific and enormously diverse immunoplatforms with applications in diagnostics, environmental monitoring, and food and public safety. In this Chapter we introduce antibody structure and antibody-derived fragments, describe the most common methods of their immobilization and discuss ‘traditional’ applications of immobilized antibodies such as enzyme immunoassays and immunoaffinity chromatography, as well as exciting emerging uses in immunosensors, microarrays and nanomedicine.
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Affiliation(s)
- X. Hu
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
- Dalian University, Medical School Dalian Development Zone, Dalian China
| | - I. B. O’Connor
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
| | - J. G. Wall
- National University of Ireland, Galway, Microbiology and Network of Excellence in Functional Biomaterials University Road, Galway Ireland
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19
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Schmidt J, Guillaume P, Irving M, Baumgaertner P, Speiser D, Luescher IF. Reversible major histocompatibility complex I-peptide multimers containing Ni(2+)-nitrilotriacetic acid peptides and histidine tags improve analysis and sorting of CD8(+) T cells. J Biol Chem 2011; 286:41723-41735. [PMID: 21990358 DOI: 10.1074/jbc.m111.283127] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
MHC-peptide multimers containing biotinylated MHC-peptide complexes bound to phycoerythrin (PE) streptavidin (SA) are widely used for analyzing and sorting antigen-specific T cells. Here we describe alternative T cell-staining reagents that are superior to conventional reagents. They are built on reversible chelate complexes of Ni(2+)-nitrilotriacetic acid (NTA) with oligohistidines. We synthesized biotinylated linear mono-, di-, and tetra-NTA compounds using conventional solid phase peptide chemistry and studied their interaction with HLA-A*0201-peptide complexes containing a His(6), His(12), or 2×His(6) tag by surface plasmon resonance on SA-coated sensor chips and equilibrium dialysis. The binding avidity increased in the order His(6) < His(12) < 2×His(6) and NTA(1) < NTA(2) < NTA(4), respectively, depending on the configuration of the NTA moieties and increased to picomolar K(D) for the combination of a 2×His(6) tag and a 2×Ni(2+)-NTA(2). We demonstrate that HLA-A2-2×His(6)-peptide multimers containing either Ni(2+)-NTA(4)-biotin and PE-SA- or PE-NTA(4)-stained influenza and Melan A-specific CD8+ T cells equal or better than conventional multimers. Although these complexes were highly stable, they very rapidly dissociated in the presence of imidazole, which allowed sorting of bona fide antigen-specific CD8+ T cells without inducing T cell death as well as assessment of HLA-A2-peptide monomer dissociation kinetics on CD8+ T cells.
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Affiliation(s)
- Julien Schmidt
- Ludwig Center of the University of Lausanne, 1066 Epalinges, Switzerland
| | - Philippe Guillaume
- Ludwig Center of the University of Lausanne, 1066 Epalinges, Switzerland
| | - Melita Irving
- Swiss Institute of Bioinformatics, Batiment Genopode, 1015 Lausanne Switzerland
| | - Petra Baumgaertner
- Division of Clinical Onco-Immunology, Ludwig Center of the University of Lausanne, 1011 Lausanne, Switzerland
| | - Daniel Speiser
- Division of Clinical Onco-Immunology, Ludwig Center of the University of Lausanne, 1011 Lausanne, Switzerland
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Tajima N, Takai M, Ishihara K. Significance of Antibody Orientation Unraveled: Well-Oriented Antibodies Recorded High Binding Affinity. Anal Chem 2011; 83:1969-76. [DOI: 10.1021/ac1026786] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Madoka Takai
- Department of Materials Engineering,
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kazuhiko Ishihara
- Department of Materials Engineering,
- Department of Bioengineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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21
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Abstract
Protein arrays are miniaturised and highly parallelised formats of interaction-based functional protein assays. Major bottlenecks in protein microarraying are the limited availability and high cost of purified, functional proteins for immobilisation and the limited stability of immobilised proteins in their functional state. In contrast, protein-coding DNA is readily available by PCR, and DNA arrays can be stored over prolonged times without deterioration. This chapter presents a method for the rapid and economical "printing" of replicate protein microarrays directly from a single DNA array template using cell-free protein synthesis, termed "DNA array to protein array," DAPA. The procedure is a truly enabling technology, making customised protein microarrays affordable for laboratories with no access to routine microarray spotting. The experimental effort involved for the printing of a protein array from the template DNA array is comparable to the assembly of a Western blot.
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Abstract
Affinity proteomics, mainly represented by antibody microarrays, has in recent years been established as a powerful tool for high-throughput (disease) proteomics. The technology can be used to generate detailed protein expression profiles, or protein maps, of focused set of proteins in crude proteomes and potentially even high-resolution portraits of entire proteomes. The technology provides unique opportunities, for example biomarker discovery, disease diagnostics, patient stratification and monitoring of disease, and taking the next steps toward personalized medicine. However, the process of designing high-performing, high-density antibody micro- and nanoarrays has proven to be challenging, requiring truly cross-disciplinary efforts to be adopted. In this mini-review, we address one of these key technological issues, namely, the choice of probe format, and focus on the use of recombinant antibodies vs. polyclonal and monoclonal antibodies for the generation of antibody arrays.
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Abstract
The development of protein microarrays makes possible interaction-based protein assays in miniaturised, multiplexed formats. A major requirement determining their uptake and use is the availability and stability of purified, functional proteins for immobilisation. With conventional methods, involving individual expression and purification of recombinant proteins, the cost of commercial high-content protein arrays is often found to be prohibitively high. Moreover, due to the need for specialised microarray production equipment, custom-made protein arrays containing more focussed sets of proteins of interest are also in little use. In the DNA array to protein array technology described herein, repeated economical printing of protein microarrays from a reusable template DNA microarray is performed on demand by cell-free -protein synthesis. Once the template DNA microarray has been obtained, protein microarrays are made using purely macro-handling procedures, making protein arraying accessible without sophisticated microarraying apparatus.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies Ltd, Cambridge, UK.
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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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Optimisation of a multivalent Strep tag for protein detection. Biophys Chem 2010; 152:170-7. [PMID: 20970240 DOI: 10.1016/j.bpc.2010.09.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 09/20/2010] [Accepted: 09/20/2010] [Indexed: 02/05/2023]
Abstract
The Strep tag is a peptide sequence that is able to mimic biotin's ability to bind to streptavidin. Sequences of Strep tags from 0 to 5 have been appended to the N-terminus of a model protein, the Stefin A Quadruple Mutant (SQM) peptide aptamer scaffold, and the recombinant fusion proteins expressed. The affinities of the proteins for streptavidin have been assessed as a function of the number of tags inserted using a variety of labelled and label-free bioanalytical and surface based methods (Western blots, microarray assays and surface plasmon resonance spectroscopy). The binding affinity increases with the number of tags across all assays, reaching nanomolar levels with 5 inserts, an observation assigned to a progressive increase in the probability of a binding interaction occurring. In addition a novel interfacial FRET based assay has been developed for generic Strep tag interactions, which utilises a conventional microarray scanner and bypasses the requirement for expensive lifetime imaging equipment. By labelling both the tagged StrepX-SQM(2) and streptavidin targets, the conjugate is primed for label-free FRET based displacement assays.
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26
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Stoevesandt O, Vetter M, Kastelic D, Palmer EA, He M, Taussig MJ. Cell free expression put on the spot: advances in repeatable protein arraying from DNA (DAPA). N Biotechnol 2010; 28:282-90. [PMID: 20850573 DOI: 10.1016/j.nbt.2010.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2010] [Accepted: 09/01/2010] [Indexed: 11/25/2022]
Abstract
We have previously described the 'DNA array to protein array' (DAPA) method for microarraying of proteins expressed by cell-free systems in situ on the array surface. In this technique, a DNA array on one slide acts as the template for generating a protein array on a second slide, mediated by a cell free lysate between the two juxtaposed slides. Here we explore the feature of the repeatability of the technology, in which the same DNA array is reused several times, and use the method to generate a microarray of 116 diverse proteins. The capabilities of DAPA technology in comparison with other protein array methods are discussed.
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Affiliation(s)
- Oda Stoevesandt
- Protein Technology Group, Babraham Bioscience Technologies, Cambridge CB22 3AT, UK.
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27
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Ibii T, Kaieda M, Hatakeyama S, Shiotsuka H, Watanabe H, Umetsu M, Kumagai I, Imamura T. Direct immobilization of gold-binding antibody fragments for immunosensor applications. Anal Chem 2010; 82:4229-35. [PMID: 20415430 DOI: 10.1021/ac100557k] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A novel method that enables antibody fragments to be immobilized on a sensor substrate with a high binding capability using molecular recognition has been developed. Using genetic engineering, we fabricated bispecific recombinant antibody fragments, which consist of two kinds of antibody fragments: a gold antibody fragment and a target molecule antibody fragment. Surface plasmon resonance (SPR) analysis indicated that these gold-binding bispecific antibody fragments bind directly to the gold substrate with high affinity (K(D) approximately 10(-9) M). About 70% of the bispecific antibody fragments immobilized on the gold substrate retained their target protein-binding efficiency. The Sips isotherm was used to assess the heterogeneity in antibody affinity for the bispecific antibody fragments. The results showed that the immobilized bispecific antibody fragments exhibited an increased homogeneity of affinity (K(D)) to target molecules when compared with monospecific antibody fragments immobilized by conventional methods. The use of bispecific antibody fragments to directly immobilize antibody fragments on a solid-phase substrate offers a useful platform for immunosensor applications.
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Affiliation(s)
- Takahisa Ibii
- Corporate R&D Headquarters, Frontier Research Center, Canon Inc., 30-2, Shimomaruko 3-chome, Ohta-ku, Tokyo 146-8501, Japan.
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28
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Dudak FC, Boyaci IH. Rapid and label-free bacteria detection by surface plasmon resonance (SPR) biosensors. Biotechnol J 2009; 4:1003-11. [PMID: 19288516 DOI: 10.1002/biot.200800316] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Surface Plasmon Resonance (SPR) biosensor technology has been successfully used for the detection of various analytes such as proteins, drugs, DNA, and microorganisms. SPR-based immunosensors that coupled with a specific antigen-antibody reaction, have become a promising tool for the quantification of bacteria as it offers sensitive, specific, rapid, and label-free detection. In this paper, we review the important issues in the development of SPR-based immunoassays for bacteria detection, concentrating on instrumentation, surface functionalization, liquid handling, and surface regeneration. In addition, this review touches on the recent advances in SPR biosensing for sensitivity enhancement.
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Affiliation(s)
- Fahriye Ceyda Dudak
- Department of Food Engineering, Hacettepe University, Beytepe, Ankara, Turkey
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29
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High quality protein microarray using in situ protein purification. BMC Biotechnol 2009; 9:72. [PMID: 19698181 PMCID: PMC2746808 DOI: 10.1186/1472-6750-9-72] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2009] [Accepted: 08/23/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the postgenomic era, high throughput protein expression and protein microarray technologies have progressed markedly permitting screening of therapeutic reagents and discovery of novel protein functions. Hexa-histidine is one of the most commonly used fusion tags for protein expression due to its small size and convenient purification via immobilized metal ion affinity chromatography (IMAC). This purification process has been adapted to the protein microarray format, but the quality of in situ His-tagged protein purification on slides has not been systematically evaluated. We established methods to determine the level of purification of such proteins on metal chelate-modified slide surfaces. Optimized in situ purification of His-tagged recombinant proteins has the potential to become the new gold standard for cost-effective generation of high-quality and high-density protein microarrays. RESULTS Two slide surfaces were examined, chelated Cu2+ slides suspended on a polyethylene glycol (PEG) coating and chelated Ni2+ slides immobilized on a support without PEG coating. Using PEG-coated chelated Cu2+ slides, consistently higher purities of recombinant proteins were measured. An optimized wash buffer (PBST) composed of 10 mM phosphate buffer, 2.7 mM KCl, 140 mM NaCl and 0.05% Tween 20, pH 7.4, further improved protein purity levels. Using Escherichia coli cell lysates expressing 90 recombinant Streptococcus pneumoniae proteins, 73 proteins were successfully immobilized, and 66 proteins were in situ purified with greater than 90% purity. We identified several antigens among the in situ-purified proteins via assays with anti-S. pneumoniae rabbit antibodies and a human patient antiserum, as a demonstration project of large scale microarray-based immunoproteomics profiling. The methodology is compatible with higher throughput formats of in vivo protein expression, eliminates the need for resin-based purification and circumvents protein solubility and denaturation problems caused by buffer exchange steps and freeze-thaw cycles, which are associated with resin-based purification, intermittent protein storage and deposition on microarrays. CONCLUSION An optimized platform for in situ protein purification on microarray slides using His-tagged recombinant proteins is a desirable tool for the screening of novel protein functions and protein-protein interactions. In the context of immunoproteomics, such protein microarrays are complimentary to approaches using non-recombinant methods to discover and characterize bacterial antigens.
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30
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Wong LS, Khan F, Micklefield J. Selective Covalent Protein Immobilization: Strategies and Applications. Chem Rev 2009; 109:4025-53. [DOI: 10.1021/cr8004668] [Citation(s) in RCA: 387] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lu Shin Wong
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Farid Khan
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jason Micklefield
- School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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31
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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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32
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Wingren C, James P, Borrebaeck CAK. Strategy for surveying the proteome using affinity proteomics and mass spectrometry. Proteomics 2009; 9:1511-7. [PMID: 19235165 DOI: 10.1002/pmic.200800802] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Antibody-based microarrays is a rapidly evolving technology that has gone from the first proof-of-concept studies to more demanding proteome profiling applications, during the last years. Miniaturized microarrays can be printed with large number of antibodies harbouring predetermined specificities, capable of targeting high- as well as low-abundant analytes in complex, nonfractionated proteomes. Consequently, the resolution of such proteome profiling efforts correlate directly to the number of antibodies included, which today is a key limiting factor. To overcome this bottleneck and to be able to perform in-depth global proteome surveys, we propose to interface affinity proteomics with MS-based read-out, as outlined in this technical perspective. Briefly, we have defined a range of peptide motifs, each motif being present in 5-100 different proteins. In this manner, 100 antibodies, binding 100 different motifs commonly distributed among different proteins, would potentially target a protein cluster of 10(4) individual molecules, i.e. around 50% of the nonredundant human proteome. Notably, these motif-specific antibodies would be directly applicable to any proteome in a specie independent manner and not biased towards abundant proteins or certain protein classes. The biological sample is digested, exposed to these immobilized antibodies, whereby motif-containing peptides are specifically captured, enriched and subsequently detected and identified using MS.
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33
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Oriented Immobilization of Anti-Pneumolysin Tagged Recombinant Antibody Fragments. Curr Microbiol 2009; 59:81-7. [DOI: 10.1007/s00284-009-9402-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/04/2009] [Accepted: 03/05/2009] [Indexed: 10/21/2022]
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Design of high-density antibody microarrays for disease proteomics: key technological issues. J Proteomics 2009; 72:928-35. [PMID: 19457338 DOI: 10.1016/j.jprot.2009.01.027] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Revised: 01/26/2009] [Accepted: 01/27/2009] [Indexed: 01/01/2023]
Abstract
Antibody-based microarray is a novel proteomic technology setting a new standard for molecular profiling of non-fractionated complex proteomes. The first generation of antibody microarrays has already demonstrated its potential for generating detailed protein expression profiles, or protein atlases, of human body fluids in health and disease, paving the way for new discoveries within the field of disease proteomics. The process of designing highly miniaturized, high-density and high-performing antibody microarray set-ups have, however, proven to be challenging. In this mini-review we discuss key technological issues that must be addressed in a cross-disciplinary manner before true global proteome analysis can be performed using antibody microarrays.
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35
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Abstract
Antibody-based microarrays are a new powerful proteomic technology that can be used to generate rapid and detailed expression profiles of defined sets of protein analytes in complex samples as well as high-resolution portraits of entire proteomes. Miniaturized micro- and nanoarrays can be printed with numerous antibodies carrying the desired specificities. Multiplexed and ultra-sensitive assays, specifically targeting several analytes in a single experiment, can be performed, while consuming only minute amounts of the sample. The array images generated can then be converted into protein expression profiles, or maps, revealing the detailed composition of the sample. This promising proteomic research tool will thus provide unique opportunities for e.g. disease proteomics, biomarker discovery, disease diagnostics, and patient stratification. This review describes the antibody-based microarray technology and applications thereof.
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36
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Seurynck-Servoss SL, Baird CL, Miller KD, Pefaur NB, Gonzalez RM, Apiyo DO, Engelmann HE, Srivastava S, Kagan J, Rodland KD, Zangar RC. Immobilization strategies for single-chain antibody microarrays. Proteomics 2008; 8:2199-210. [PMID: 18452230 DOI: 10.1002/pmic.200701036] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Sandwich ELISA microarrays have great potential for validating disease biomarkers. Each ELISA relies on robust-affinity reagents that retain activity when immobilized on a solid surface or when labeled for detection. Single-chain antibodies (scFv) are affinity reagents that have greater potential for high-throughput production than traditional IgG. Unfortunately, scFv are typically less active than IgG following immobilization on a solid surface and not always suitable for use in sandwich ELISAs. We therefore investigated different immobilization strategies and scFv constructs to determine a more robust strategy for using scFv as ELISA reagents. Two promising strategies emerged from these studies: (i) the precapture of epitope-tagged scFv using an antiepitope antibody and (ii) the direct printing of a thioredoxin (TRX)/scFv fusion protein on glass slides. Both strategies improved the stability of immobilized scFv and increased the sensitivity of the scFv ELISA microarray assays, although the antiepitope precapture method introduced a risk of reagent transfer. Using the direct printing method, we show that scFv against prostate-specific antigen (PSA) are highly specific when tested against 21 different IgG-based assays. In addition, the scFv microarray PSA assay gave comparable quantitative results (R(2) = 0.95) to a commercial 96-well ELISA when tested using human serum samples. In addition, we find that TRX-scFv fusions against epidermal growth factor and toxin X have good LOD. Overall, these results suggest that minor modifications of the scFv construct are sufficient to produce reagents that are suitable for use in multiplex assay systems.
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37
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Saerens D, Huang L, Bonroy K, Muyldermans S. Antibody Fragments as Probe in Biosensor Development. SENSORS 2008; 8:4669-4686. [PMID: 27873779 PMCID: PMC3705465 DOI: 10.3390/s8084669] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Revised: 08/06/2008] [Accepted: 08/07/2008] [Indexed: 11/30/2022]
Abstract
Today's proteomic analyses are generating increasing numbers of biomarkers, making it essential to possess highly specific probes able to recognize those targets. Antibodies are considered to be the first choice as molecular recognition units due to their target specificity and affinity, which make them excellent probes in biosensor development. However several problems such as difficult directional immobilization, unstable behavior, loss of specificity and steric hindrance, may arise from using these large molecules. Luckily, protein engineering techniques offer designed antibody formats suitable for biomarker analysis. Minimization strategies of antibodies into Fab fragments, scFv or even single-domain antibody fragments like VH, VL or VHHs are reviewed. Not only the size of the probe but also other issues like choice of immobilization tag, type of solid support and probe stability are of critical importance in assay development for biosensing. In this respect, multiple approaches to specifically orient and couple antibody fragments in a generic one-step procedure directly on a biosensor substrate are discussed.
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Affiliation(s)
- Dirk Saerens
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium.
| | - Lieven Huang
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium
- Department of Molecular Biology, Technologiepark 927, B-9052 Zwijnaarde, Ghent University, Ghent, Belgium
- Department for Molecular Biomedical Research, VIB, Ghent, Belgium
| | | | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium
- Department of Molecular and Cellular Interactions, VIB, Brussels, Belgium
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38
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Saerens D, Ghassabeh GH, Muyldermans S. Antibody technology in proteomics. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2008; 7:275-82. [DOI: 10.1093/bfgp/eln028] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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39
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He M, Stoevesandt O, Taussig MJ. In situ synthesis of protein arrays. Curr Opin Biotechnol 2008; 19:4-9. [DOI: 10.1016/j.copbio.2007.11.009] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2007] [Accepted: 11/16/2007] [Indexed: 10/22/2022]
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40
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Jung Y, Jeong JY, Chung BH. Recent advances in immobilization methods of antibodies on solid supports. Analyst 2008; 133:697-701. [DOI: 10.1039/b800014j] [Citation(s) in RCA: 210] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Sandwich ELISA Microarrays: Generating Reliable and Reproducible Assays for High-Throughput Screens. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-59745-463-6_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/13/2023]
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42
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Dexlin L, Ingvarsson J, Frendéus B, Borrebaeck CAK, Wingren C. Design of recombinant antibody microarrays for cell surface membrane proteomics. J Proteome Res 2007; 7:319-27. [PMID: 18047267 DOI: 10.1021/pr070257x] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Generating proteomic maps of membrane proteins, common targets for therapeutic interventions and disease diagnostics, has turned out to be a major challenge. Antibody-based microarrays are among the novel rapidly evolving proteomic technologies that may enable global proteome analysis to be performed. Here, we have designed the first generation of a scaleable human recombinant scFv antibody microarray technology platform for cell surface membrane proteomics as well as glycomics targeting intact cells. The results showed that rapid and multiplexed profiling of the cell surface proteome (and glycome) could be performed in a highly specific and sensitive manner and that differential expression patterns due to external stimuli could be monitored.
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Affiliation(s)
- Linda Dexlin
- Deptartment of Immunotechnology, BMC D13, Lund University, SE-221 84 Lund, Sweden
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43
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Stoevesandt O, Taussig MJ. Affinity reagent resources for human proteome detection: initiatives and perspectives. Proteomics 2007; 7:2738-50. [PMID: 17639606 DOI: 10.1002/pmic.200700155] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Essential to the ambition of characterising fully the human proteome are systematic and comprehensive collections of specific affinity reagents directed against all human proteins, including splice variants and modifications. Although a large number of affinity reagents are available commercially, their quality is often questionable and only a fraction of the proteome is covered. In order for more targets to be examined, there is a need for broad availability of panels of affinity reagents, including binders against proteins of unknown functions. The most familiar affinity reagents are antibodies and their fragments, but engineered forms of protein scaffolds and nucleic acid aptamers with similar diversity and binding properties are becoming viable alternatives. Recent initiatives in Europe and the USA have been established to improve both the availability and quality of reagents for affinity proteomics, with the ultimate aim of creating standardised collections of well-validated binding molecules for proteome analysis. As well as coordinating affinity reagent production through existing resources and technology providers, these projects aim to benchmark key molecular entities, tools, and applications, and establish the bioinformatics framework and databases needed. The benefits of such reagent resources will be seen in basic research, medicine and the biotechnology and pharmaceutical industries.
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Affiliation(s)
- Oda Stoevesandt
- Technology Research Group, The Babraham Institute, Cambridge, UK
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Wingren C, Ingvarsson J, Dexlin L, Szul D, Borrebaeck CAK. Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support. Proteomics 2007; 7:3055-65. [PMID: 17787036 DOI: 10.1002/pmic.200700025] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Antibody-based microarray is a novel technology with great potential within high-throughput proteomics. The process of designing high-performing antibody (protein) microarrays has, however, turned out to be a challenging process. In this study, we have developed further our human recombinant single-chain variable-fragment (scFv) antibody microarray methodology by addressing two crucial technological issues, choice of sample labeling-tag and solid support. We examined the performance of a range of dyes in a one- or two-color approach on a selection of solid supports providing different surface and coupling chemistries, and surface structures. The set-ups were evaluated in terms of sensitivity, specificity, and selectivity. The results showed that a one-color approach, based on NHS-biotin (or ULS-biotin) labeling, on black polymer Maxisorb slides (or Nexterion slide H) was the superior approach for targeting low-abundant (pg/mL) analytes in nonfractionated, complex proteomes, such as human serum or crude cell supernatants. Notably, microarrays displaying adequate spot morphologies, high S/Ns, minimized nonspecific binding, and most importantly a high selectivity, specificity, and sensitivity (>or=fM range) were obtained. Taken together, we have designed the first generation of a high-performing recombinant scFv antibody microarray technology platform on black polymer Maxisorb slides for sensitive profiling of low-abundant analytes in nonfractionated biotinylated complex proteomes.
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Affiliation(s)
- Christer Wingren
- Department of Immunotechnology, BMC D13, Lund University, Lund, Sweden.
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45
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Ingvarsson J, Larsson A, Sjöholm AG, Truedsson L, Jansson B, Borrebaeck CAK, Wingren C. Design of Recombinant Antibody Microarrays for Serum Protein Profiling: Targeting of Complement Proteins. J Proteome Res 2007; 6:3527-36. [PMID: 17696517 DOI: 10.1021/pr070204f] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Antibody-based microarrays is a novel technology with great promise for high-throughput proteomics. The process of designing high-performing arrays has, however, turned out to be challenging. Here, we have designed the next generation of a human recombinant scFv antibody microarray platform for protein expression profiling of nonfractionated biotinylated human plasma and serum proteomes. The setup, based on black polymer Maxisorb slides interfaced with a fluorescent-based read-out system, was found to provide specific, sensitive (subpicomolar (pM) range) and reproducible means for protein profiling. Further, a chip-to-chip normalization protocol critical for comparing data generated on different chips was devised. Finally, the microarray data were found to correlate well with clinical laboratory data obtained using conventional methods, as demonstrated for a set of medium abundant (micromolar (microM) to nanomolar (nM) range) protein analytes in serum and plasma samples derived from healthy and complement-deficient individuals.
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Affiliation(s)
- Johan Ingvarsson
- Department of Immunotechnology, BMC D13, Lund University, SE-221 84 Lund, Sweden
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46
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Loch CM, Ramirez AB, Liu Y, Sather CL, Delrow JJ, Scholler N, Garvik BM, Urban ND, McIntosh MW, Lampe PD. Use of high density antibody arrays to validate and discover cancer serum biomarkers. Mol Oncol 2007; 1:313-20. [PMID: 19383305 DOI: 10.1016/j.molonc.2007.08.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2007] [Revised: 08/22/2007] [Accepted: 08/23/2007] [Indexed: 11/16/2022] Open
Abstract
Perhaps the greatest barrier to translation of serum biomarker discoveries is the inability to evaluate putative biomarkers in high throughput validation studies. Here we report on the development, production, and implementation of a high-density antibody microarray used to evaluate large numbers of candidate ovarian cancer serum biomarkers. The platform was shown to be useful for evaluation of individual antibodies for comparative analysis, such as with disease classification, and biomarker validation and discovery. We demonstrate its performance by showing that known tumor markers behave as expected. We also identify several promising biomarkers from a candidate list and generate hypotheses to support new discovery studies.
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Affiliation(s)
- Christian M Loch
- Molecular Diagnostics Program, Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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47
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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