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Punetha A, Kotiya D. Advancements in Oncoproteomics Technologies: Treading toward Translation into Clinical Practice. Proteomes 2023; 11:2. [PMID: 36648960 PMCID: PMC9844371 DOI: 10.3390/proteomes11010002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 01/12/2023] Open
Abstract
Proteomics continues to forge significant strides in the discovery of essential biological processes, uncovering valuable information on the identity, global protein abundance, protein modifications, proteoform levels, and signal transduction pathways. Cancer is a complicated and heterogeneous disease, and the onset and progression involve multiple dysregulated proteoforms and their downstream signaling pathways. These are modulated by various factors such as molecular, genetic, tissue, cellular, ethnic/racial, socioeconomic status, environmental, and demographic differences that vary with time. The knowledge of cancer has improved the treatment and clinical management; however, the survival rates have not increased significantly, and cancer remains a major cause of mortality. Oncoproteomics studies help to develop and validate proteomics technologies for routine application in clinical laboratories for (1) diagnostic and prognostic categorization of cancer, (2) real-time monitoring of treatment, (3) assessing drug efficacy and toxicity, (4) therapeutic modulations based on the changes with prognosis and drug resistance, and (5) personalized medication. Investigation of tumor-specific proteomic profiles in conjunction with healthy controls provides crucial information in mechanistic studies on tumorigenesis, metastasis, and drug resistance. This review provides an overview of proteomics technologies that assist the discovery of novel drug targets, biomarkers for early detection, surveillance, prognosis, drug monitoring, and tailoring therapy to the cancer patient. The information gained from such technologies has drastically improved cancer research. We further provide exemplars from recent oncoproteomics applications in the discovery of biomarkers in various cancers, drug discovery, and clinical treatment. Overall, the future of oncoproteomics holds enormous potential for translating technologies from the bench to the bedside.
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Affiliation(s)
- Ankita Punetha
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Rutgers University, 225 Warren St., Newark, NJ 07103, USA
| | - Deepak Kotiya
- Department of Pharmacology and Nutritional Sciences, University of Kentucky, 900 South Limestone St., Lexington, KY 40536, USA
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2
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Yoo CH, Yu JK, Seong Y, Choi JK. Microarrays Incorporating Gold Grid Patterns for Protein Quantification. ACS OMEGA 2020; 5:16664-16669. [PMID: 32685833 PMCID: PMC7364605 DOI: 10.1021/acsomega.0c01549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 06/18/2020] [Indexed: 06/11/2023]
Abstract
Protein microarrays are miniaturized two-dimensional arrays, incorporating thousands of immobilized proteins, typically printed in minute amounts on functionalized solid substrates, which can be analyzed in a high-throughput fashion. Irreproducibility of the printing techniques adopted, resulting in inconsistently and nonuniformly deposited microscopic spots, nonuniform signal intensities from the printed microspots, and significantly high background noise are some of the critical issues that affect protein analysis using traditional protein microarrays. To overcome such issues, in this study, we introduced a novel gold grid pattern-based protein microarray. The grid patterns incorporated in our microarray are equivalent to the spots used for protein analysis in conventional protein microarrays. We utilized the signal intensities from the grid patterns acting as spots for quantifying the protein concentration levels. To demonstrate the utility of our novel design concept, we quantified as low as 66.7 ng/mL of bovine serum albumin using our gold grid pattern-based protein microarray. Our grid pattern-based design concept for protein quantification overcame the signal nonuniformity issues and ensured that the dominance of any distorted signal from a single spot did not affect the overall protein quantification results as encountered in conventional protein microarrays.
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Affiliation(s)
- Chang-Hyuk Yoo
- Division
of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 22012, Korea
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | | | - Yeju Seong
- Small
Machines Company, Ltd., Daejeon 34012, Korea
| | - Jun-Kyu Choi
- Small
Machines Company, Ltd., Daejeon 34012, Korea
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3
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A decade of Nucleic Acid Programmable Protein Arrays (NAPPA) availability: News, actors, progress, prospects and access. J Proteomics 2018; 198:27-35. [PMID: 30553075 DOI: 10.1016/j.jprot.2018.12.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/04/2018] [Accepted: 12/10/2018] [Indexed: 12/29/2022]
Abstract
Understanding the dynamic of the proteome is a critical challenge because it requires high sensitive methodologies in high-throughput formats in order to decipher its modifications and complexity. While molecular biology provides relevant information about cell physiology that may be reflected in post-translational changes, High-Throughput (HT) experimental proteomic techniques are essential to provide valuable functional information of the proteins, peptides and the interconnections between them. Hence, many methodological developments and innovations have been reported during the last decade. To study more dynamic protein networks and fine interactions, Nucleic Acid Programmable Protein Arrays (NAPPA) was introduced a decade ago. The tool is rapidly maturing and serving as a gateway to characterize biological systems and diseases thanks primarily to its accuracy, reproducibility, throughput and flexibility. Currently, NAPPA technology has proved successful in several research areas adding valuable information towards innovative diagnostic and therapeutic applications. Here, the basic and latest advances within this modern technology in basic, translational research are reviewed, in addition to presenting its exciting new directions. Our final goal is to encourage more scientists/researchers to incorporate this method, which can help to remove bottlenecks in their particular research or biomedical projects. SIGNIFICANCE: Nucleic Acid Programmable Protein Arrays (NAPPA) is becoming an essential tool for functional proteomics and protein-protein interaction studies. The technology impacts decisively on projects aiming massive screenings and the latest innovations like the multiplexing capability or printing consistency make this a promising method to be integrated in novel and combinatorial proteomic approaches.
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4
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Zhang Y, Huang Q, Deng Z, Xu Y, Liu T. Enhancing the efficiency of cell-free protein synthesis system by systematic titration of transcription and translation components. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.07.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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5
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Contreras-Llano LE, Tan C. High-throughput screening of biomolecules using cell-free gene expression systems. Synth Biol (Oxf) 2018; 3:ysy012. [PMID: 32995520 PMCID: PMC7445777 DOI: 10.1093/synbio/ysy012] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 05/31/2018] [Accepted: 06/25/2018] [Indexed: 01/13/2023] Open
Abstract
The incorporation of cell-free transcription and translation systems into high-throughput screening applications enables the in situ and on-demand expression of peptides and proteins. Coupled with modern microfluidic technology, the cell-free methods allow the screening, directed evolution and selection of desired biomolecules in minimal volumes within a short timescale. Cell-free high-throughput screening applications are classified broadly into in vitro display and on-chip technologies. In this review, we outline the development of cell-free high-throughput screening methods. We further discuss operating principles and representative applications of each screening method. The cell-free high-throughput screening methods may be advanced by the future development of new cell-free systems, miniaturization approaches, and automation technologies.
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Affiliation(s)
| | - Cheemeng Tan
- Department of Biomedical Engineering, University of California Davis, Davis, CA, USA
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6
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Krizkova S, Heger Z, Zalewska M, Moulick A, Adam V, Kizek R. Nanotechnologies in protein microarrays. Nanomedicine (Lond) 2015; 10:2743-55. [PMID: 26039143 DOI: 10.2217/nnm.15.81] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Protein microarray technology became an important research tool for study and detection of proteins, protein-protein interactions and a number of other applications. The utilization of nanoparticle-based materials and nanotechnology-based techniques for immobilization allows us not only to extend the surface for biomolecule immobilization resulting in enhanced substrate binding properties, decreased background signals and enhanced reporter systems for more sensitive assays. Generally in contemporarily developed microarray systems, multiple nanotechnology-based techniques are combined. In this review, applications of nanoparticles and nanotechnologies in creating protein microarrays, proteins immobilization and detection are summarized. We anticipate that advanced nanotechnologies can be exploited to expand promising fields of proteins identification, monitoring of protein-protein or drug-protein interactions, or proteins structures.
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Affiliation(s)
- Sona Krizkova
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Zbynek Heger
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Marta Zalewska
- Department of Biomedical & Environmental Analysis, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211, 50-556 Wroclaw, Poland, European Union
| | - Amitava Moulick
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Vojtech Adam
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
| | - Rene Kizek
- Department of Chemistry & Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00 Brno, Czech Republic, European Union.,Central European Institute of Technology, Brno University of Technology, Technicka 3058/10, CZ-616 00 Brno, Czech Republic, European Union
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7
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Romanov V, Davidoff SN, Miles AR, Grainger DW, Gale BK, Brooks BD. A critical comparison of protein microarray fabrication technologies. Analyst 2015; 139:1303-26. [PMID: 24479125 DOI: 10.1039/c3an01577g] [Citation(s) in RCA: 91] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Of the diverse analytical tools used in proteomics, protein microarrays possess the greatest potential for providing fundamental information on protein, ligand, analyte, receptor, and antibody affinity-based interactions, binding partners and high-throughput analysis. Microarrays have been used to develop tools for drug screening, disease diagnosis, biochemical pathway mapping, protein-protein interaction analysis, vaccine development, enzyme-substrate profiling, and immuno-profiling. While the promise of the technology is intriguing, it is yet to be realized. Many challenges remain to be addressed to allow these methods to meet technical and research expectations, provide reliable assay answers, and to reliably diversify their capabilities. Critical issues include: (1) inconsistent printed microspot morphologies and uniformities, (2) low signal-to-noise ratios due to factors such as complex surface capture protocols, contamination, and static or no-flow mass transport conditions, (3) inconsistent quantification of captured signal due to spot uniformity issues, (4) non-optimal protocol conditions such as pH, temperature, drying that promote variability in assay kinetics, and lastly (5) poor protein (e.g., antibody) printing, storage, or shelf-life compatibility with common microarray assay fabrication methods, directly related to microarray protocols. Conventional printing approaches, including contact (e.g., quill and solid pin), non-contact (e.g., piezo and inkjet), microfluidics-based, microstamping, lithography, and cell-free protein expression microarrays, have all been used with varying degrees of success with figures of merit often defined arbitrarily without comparisons to standards, or analytical or fiduciary controls. Many microarray performance reports use bench top analyte preparations lacking real-world relevance, akin to "fishing in a barrel", for proof of concept and determinations of figures of merit. This review critiques current protein-based microarray preparation techniques commonly used for analytical and function-based proteomics and their effects on array-based assay performance.
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Affiliation(s)
- Valentin Romanov
- Wasatch Microfluidics, LLC, 825 N. 300 W., Suite C325, Salt Lake City, UT, USA.
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8
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Østerbye T, Buus S. Automated High-Throughput Mapping of Linear B-Cell Epitopes Using a Statistical Analysis of High-Density Peptide Microarray Data. Methods Mol Biol 2015; 1348:215-228. [PMID: 26424275 DOI: 10.1007/978-1-4939-2999-3_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Detailed information of antibodies' specificity is often missing or inadequate even for continuous (i.e., linear) epitopes. Recent developments in peptide microarray technology has enabled the synthesis of up to two million peptides per array thereby allowing linear peptide epitopes to be examined by a systematic amino acid substitution and positional scanning approach. This kind of analysis generates a very large body of data, which needs to be analyzed and interpreted in a robust and automated manner. Here, we describe a rational systematic approach to define linear antibody epitopes using ANOVA statistics to identify not only significant but also important residues involved in antibody recognition. This statistical approach can be used to perform a comprehensive linear epitope discovery. For polyclonal antibodies, this could be extended to entire proteins pinpointing critical residues for each epitope. We argue that the ANOVA analysis levels out issues of unknown peptide concentration/quality and unknown antibody titers leading to identification of epitopes that otherwise would be neglected if the evaluation was based merely on signal strength.
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Affiliation(s)
- Thomas Østerbye
- Laboraty of experimental Immunology, Faculty of Health Sciences, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.
| | - Søren Buus
- Laboraty of experimental Immunology, Faculty of Health Sciences, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
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9
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Gahoi N, Ray S, Srivastava S. Array-based proteomic approaches to study signal transduction pathways: prospects, merits and challenges. Proteomics 2014; 15:218-31. [PMID: 25266292 DOI: 10.1002/pmic.201400261] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 09/17/2014] [Accepted: 09/25/2014] [Indexed: 01/17/2023]
Abstract
Very often dysfunctional aspects of various signalling networks are found to be associated with human diseases and disorders. The major characteristics of signal transduction pathways are specificity, amplification of the signal, desensitisation and integration, which is accomplished not solely, but majorly by proteins. Array-based profiling of protein-protein and other biomolecular interactions is a versatile approach, which holds immense potential for multiplex interactome mapping and provides an inclusive representation of the signal transduction pathways and networks. Protein microarrays such as analytical protein microarrays (antigen-antibody interactions, autoantibody screening), RP microarrays (interaction of a particular ligand with all the possible targets in cell), functional protein microarrays (protein-protein or protein-ligand interactions) are implemented for various applications, including analysis of protein interactions and their significance in signalling cascades. Additionally, successful amalgamation of the array-based approaches with different label-free detection techniques allows real-time analysis of interaction kinetics of multiple interaction events simultaneously. This review discusses the prospects, merits and limitations of different variants of array-based techniques and their promising applications for studying the modifications and interactions of biomolecules, and highlights the studies associated with signal transduction pathways and their impact on disease pathobiology.
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Affiliation(s)
- Nikita Gahoi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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10
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Yu X, Woolery AR, Luong P, Hao YH, Grammel M, Westcott N, Park J, Wang J, Bian X, Demirkan G, Hang HC, Orth K, LaBaer J. Copper-catalyzed azide-alkyne cycloaddition (click chemistry)-based detection of global pathogen-host AMPylation on self-assembled human protein microarrays. Mol Cell Proteomics 2014; 13:3164-76. [PMID: 25073739 PMCID: PMC4223499 DOI: 10.1074/mcp.m114.041103] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/14/2014] [Indexed: 12/22/2022] Open
Abstract
AMPylation (adenylylation) is a recently discovered mechanism employed by infectious bacteria to regulate host cell signaling. However, despite significant effort, only a few host targets have been identified, limiting our understanding of how these pathogens exploit this mechanism to control host cells. Accordingly, we developed a novel nonradioactive AMPylation screening platform using high-density cell-free protein microarrays displaying human proteins produced by human translational machinery. We screened 10,000 unique human proteins with Vibrio parahaemolyticus VopS and Histophilus somni IbpAFic2, and identified many new AMPylation substrates. Two of these, Rac2, and Rac3, were confirmed in vivo as bona fide substrates during infection with Vibrio parahaemolyticus. We also mapped the site of AMPylation of a non-GTPase substrate, LyGDI, to threonine 51, in a region regulated by Src kinase, and demonstrated that AMPylation prevented its phosphorylation by Src. Our results greatly expanded the repertoire of potential host substrates for bacterial AMPylators, determined their recognition motif, and revealed the first pathogen-host interaction AMPylation network. This approach can be extended to identify novel substrates of AMPylators with different domains or in different species and readily adapted for other post-translational modifications.
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Affiliation(s)
- Xiaobo Yu
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Andrew R Woolery
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Phi Luong
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Yi Heng Hao
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Markus Grammel
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Nathan Westcott
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Jin Park
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Jie Wang
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Xiaofang Bian
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Gokhan Demirkan
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Howard C Hang
- ¶The Laboratory of Chemical Biology and Microbial Pathogenesis, The Rockefeller University, New York 10065, USA
| | - Kim Orth
- §Department of Molecular Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9148, USA
| | - Joshua LaBaer
- From the ‡The Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA;
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11
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Mesri M. Advances in Proteomic Technologies and Its Contribution to the Field of Cancer. Adv Med 2014; 2014:238045. [PMID: 26556407 PMCID: PMC4590950 DOI: 10.1155/2014/238045] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/30/2014] [Indexed: 12/12/2022] Open
Abstract
Systematic studies of the cancer genome have generated a wealth of knowledge in recent years. These studies have uncovered a number of new cancer genes not previously known to be causal targets in cancer. Genetic markers can be used to determine predisposition to tumor development, but molecularly targeted treatment strategies are not widely available for most cancers. Precision care plans still must be developed by understanding and implementing basic science research into clinical treatment. Proteomics is continuing to make major strides in the discovery of fundamental biological processes as well as more recent transition into an assay platform capable of measuring hundreds of proteins in any biological system. As such, proteomics can translate basic science discoveries into the clinical practice of precision medicine. The proteomic field has progressed at a fast rate over the past five years in technology, breadth and depth of applications in all areas of the bioscience. Some of the previously experimental technical approaches are considered the gold standard today, and the community is now trying to come to terms with the volume and complexity of the data generated. Here I describe contribution of proteomics in general and biological mass spectrometry in particular to cancer research, as well as related major technical and conceptual developments in the field.
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Affiliation(s)
- Mehdi Mesri
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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12
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da Costa JP, Oliveira-Silva R, Daniel-da-Silva AL, Vitorino R. Bionanoconjugation for Proteomics applications — An overview. Biotechnol Adv 2014; 32:952-70. [DOI: 10.1016/j.biotechadv.2014.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 03/15/2014] [Accepted: 04/26/2014] [Indexed: 12/29/2022]
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13
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Abel L, Kutschki S, Turewicz M, Eisenacher M, Stoutjesdijk J, Meyer HE, Woitalla D, May C. Autoimmune profiling with protein microarrays in clinical applications. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:977-87. [PMID: 24607371 DOI: 10.1016/j.bbapap.2014.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 02/18/2014] [Accepted: 02/27/2014] [Indexed: 02/05/2023]
Abstract
In recent years, knowledge about immune-related disorders has substantially increased, especially in the field of central nervous system (CNS) disorders. Recent innovations in protein-related microarray technology have enabled the analysis of interactions between numerous samples and up to 20,000 targets. Antibodies directed against ion channels, receptors and other synaptic proteins have been identified, and their causative roles in different disorders have been identified. Knowledge about immunological disorders is likely to expand further as more antibody targets are discovered. Therefore, protein microarrays may become an established tool for routine diagnostic procedures in the future. The identification of relevant target proteins requires the development of new strategies to handle and process vast quantities of data so that these data can be evaluated and correlated with relevant clinical issues, such as disease progression, clinical manifestations and prognostic factors. This review will mainly focus on new protein array technologies, which allow the processing of a large number of samples, and their various applications with a deeper insight into their potential use as diagnostic tools in neurodegenerative diseases and other diseases. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Laura Abel
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Simone Kutschki
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Michael Turewicz
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Martin Eisenacher
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Jale Stoutjesdijk
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Helmut E Meyer
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany; Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Dirk Woitalla
- S. Josef Hospital, Ruhr-University Bochum, 44780 Bochum, Germany; St. Josef-Krankenhaus Kupferdreh, Heidbergweg 22-24, 45257 Essen, Germany
| | - Caroline May
- Department of Medical Proteomics/Bioanalytics, Medizinisches Proteom-Center, Ruhr-Universität Bochum, 44801 Bochum, Germany.
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14
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Alternative fermentation conditions for improved Escherichia coli-based cell-free protein synthesis for proteins requiring supplemental components for proper synthesis. Process Biochem 2014. [DOI: 10.1016/j.procbio.2013.10.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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15
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Chandra H, Reddy PJ, Srivastava S. Protein microarrays and novel detection platforms. Expert Rev Proteomics 2014; 8:61-79. [DOI: 10.1586/epr.10.99] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Ayoglu B, Häggmark A, Neiman M, Igel U, Uhlén M, Schwenk JM, Nilsson P. Systematic antibody and antigen-based proteomic profiling with microarrays. Expert Rev Mol Diagn 2014; 11:219-34. [DOI: 10.1586/erm.10.110] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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17
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18
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Protein arrays as tool for studies at the host-pathogen interface. J Proteomics 2013; 94:387-400. [PMID: 24140974 DOI: 10.1016/j.jprot.2013.10.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 01/10/2023]
Abstract
Pathogens and parasites encode a wide spectrum of multifunctional proteins interacting to and modifying proteins in host cells. However, the current lack of a reliable method to unveil the protein-protein interactions (PPI) at the host-pathogen interface is retarding our understanding of many important pathogenic processes. Thus, the identification of proteins involved in host-pathogen interactions is important for the elucidation of virulence determinants, mechanisms of infection, host susceptibility and/or disease resistance. In this sense, proteomic technologies have experienced major improvements in recent years and protein arrays are a powerful and modern method for studying PPI in a high-throughput format. This review focuses on these techniques analyzing the state-of-the-art of proteomic technologies and their possibilities to diagnose and explore host-pathogen interactions. Major technical advancements, applications and protocol concerns are presented, so readers can appreciate the immense progress achieved and the current technical options available for studying the host-pathogen interface. Finally, future uses of this kind of array-based proteomic tools in the fight against infectious and parasitic diseases are discussed.
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19
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Hansen LB, Buus S, Schafer-Nielsen C. Identification and mapping of linear antibody epitopes in human serum albumin using high-density Peptide arrays. PLoS One 2013; 8:e68902. [PMID: 23894373 PMCID: PMC3720873 DOI: 10.1371/journal.pone.0068902] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Accepted: 06/07/2013] [Indexed: 11/19/2022] Open
Abstract
We have recently developed a high-density photolithographic, peptide array technology with a theoretical upper limit of 2 million different peptides per array of 2 cm2. Here, we have used this to perform complete and exhaustive analyses of linear B cell epitopes of a medium sized protein target using human serum albumin (HSA) as an example. All possible overlapping 15-mers from HSA were synthesized and probed with a commercially available polyclonal rabbit anti-HSA antibody preparation. To allow for identification of even the weakest epitopes and at the same time perform a detailed characterization of key residues involved in antibody binding, the array also included complete single substitution scans (i.e. including each of the 20 common amino acids) at each position of each 15-mer peptide. As specificity controls, all possible 15-mer peptides from bovine serum albumin (BSA) and from rabbit serum albumin (RSA) were included as well. The resulting layout contained more than 200.000 peptide fields and could be synthesized in a single array on a microscope slide. More than 20 linear epitope candidates were identified and characterized at high resolution i.e. identifying which amino acids in which positions were needed, or not needed, for antibody interaction. As expected, moderate cross-reaction with some peptides in BSA was identified whereas no cross-reaction was observed with peptides from RSA. We conclude that high-density peptide microarrays are a very powerful methodology to identify and characterize linear antibody epitopes, and should advance detailed description of individual specificities at the single antibody level as well as serologic analysis at the proteome-wide level.
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Affiliation(s)
- Lajla Bruntse Hansen
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
- Schafer-N, Copenhagen, Denmark
| | - Soren Buus
- Laboratory of Experimental Immunology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (SB); (CSN)
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20
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Wang X, Matei E, Deng L, Koharudin L, Gronenborn AM, Ramström O, Yan M. Sensing lectin-glycan interactions using lectin super-microarrays and glycans labeled with dye-doped silica nanoparticles. Biosens Bioelectron 2013; 47:258-64. [PMID: 23584388 DOI: 10.1016/j.bios.2013.03.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 03/07/2013] [Accepted: 03/08/2013] [Indexed: 12/12/2022]
Abstract
A new microarray platform, based on lectin super-microarrays and glycans labeled with dye-doped nanoparticles, has been developed to study glycan-lectin interactions. Glycan ligands were conjugated onto fluorescein-doped silica nanoparticles (FSNPs) using a general photocoupling chemistry to afford FSNP-labeled glycan probes. Lectins were printed on epoxy slides in duplicate sets to generate lectin super-microarrays where multiple assays could be carried out simultaneously in each lectin microarray. Thus, the lectin super-microarray was treated with FSNP-labeled glycans to screen for specific binding pairs. Furthermore, a series of ligand competition assays were carried out on a single lectin super-microarray to generate the dose-response curve for each glycan-lectin pair, from which the apparent affinity constants were obtained. Results showed 4-7 orders of magnitude increase in affinity over the free glycans with the corresponding lectins. Thus, the glycan epitope structures having weaker affinity than the parent glycans could be readily identified and analyzed from the lectin super-microarrays.
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Affiliation(s)
- Xin Wang
- Department of Chemistry, Portland State University, P.O. Box 751, Portland, OR, 97207-0751, USA
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21
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Byun JY, Lee KH, Lee KY, Kim MG, Kim DM. In-gel expression and in situ immobilization of proteins for generation of three dimensional protein arrays in a hydrogel matrix. LAB ON A CHIP 2013; 13:886-891. [PMID: 23303405 DOI: 10.1039/c2lc41137g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A method has been developed for the direct conversion of DNA arrays into three dimensional protein arrays on a hydrogel matrix. An agarose gel embedded with bacterial protein synthesis machinery was used as the DNA-programmable expression gel matrix for the in situ translation of genes on a DNA array. Upon incubation of the expression gel matrix cast on a DNA array, protein synthesis took place at the interface of the two surfaces and the cell-free synthesized proteins were deposited on the gel matrix surrounding the corresponding DNA spots. Diffusional dilution of the expressed proteins was minimized by modifying the agarose with Ni-NTA moieties. This procedure resulted in the generation of localized protein spots with confined radii. The developed approach not only simplifies the procedures typically used for the preparation of protein arrays but it also provides conditions for the loading of higher amounts of proteins on the array while retaining their structural integrity and functionality over extended time periods.
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Affiliation(s)
- Ju-Young Byun
- Department of Fine Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 305-764, Korea
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22
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Thomas F. Fmoc-based peptide thioester synthesis with self-purifying effect: heading to native chemical ligation in parallel formats. J Pept Sci 2013; 19:141-7. [DOI: 10.1002/psc.2494] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 01/22/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Franziska Thomas
- School of Chemistry; University of Bristol; Cantock's Close Bristol BS8 1TS UK
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Jia L, Lu Y, Shao J, Liang XJ, Xu Y. Nanoproteomics: a new sprout from emerging links between nanotechnology and proteomics. Trends Biotechnol 2013; 31:99-107. [DOI: 10.1016/j.tibtech.2012.11.010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2012] [Revised: 11/29/2012] [Accepted: 11/29/2012] [Indexed: 10/27/2022]
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24
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Yuk JS, Guignon EF, Lynes MA. Highly sensitive grating coupler-based surface plasmon-coupled emission (SPCE) biosensor for immunoassay. Analyst 2013; 138:2576-82. [DOI: 10.1039/c3an00135k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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25
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Casteleijn MG, Urtti A, Sarkhel S. Expression without boundaries: Cell-free protein synthesis in pharmaceutical research. Int J Pharm 2013; 440:39-47. [DOI: 10.1016/j.ijpharm.2012.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Revised: 04/01/2012] [Accepted: 04/03/2012] [Indexed: 11/15/2022]
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26
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Lab-on-a-Chip, Micro- and Nanoscale Immunoassay Systems, and Microarrays. THE IMMUNOASSAY HANDBOOK 2013. [PMCID: PMC7152144 DOI: 10.1016/b978-0-08-097037-0.00013-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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27
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Shigeta K, He Y, Sutanto E, Kang S, Le AP, Nuzzo RG, Alleyne AG, Ferreira PM, Lu Y, Rogers JA. Functional Protein Microarrays by Electrohydrodynamic Jet Printing. Anal Chem 2012; 84:10012-8. [DOI: 10.1021/ac302463p] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kazuyo Shigeta
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Ying He
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Erick Sutanto
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Somi Kang
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - An-Phong Le
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Ralph G. Nuzzo
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Andrew G. Alleyne
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Placid M. Ferreira
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - Yi Lu
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
| | - John A. Rogers
- Department
of Materials Science and Engineering, ‡Department of Mechanical Science
and Engineering, and §Department of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois
61801, United States
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28
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Diversity in genetic in vivo methods for protein-protein interaction studies: from the yeast two-hybrid system to the mammalian split-luciferase system. Microbiol Mol Biol Rev 2012; 76:331-82. [PMID: 22688816 DOI: 10.1128/mmbr.05021-11] [Citation(s) in RCA: 134] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The yeast two-hybrid system pioneered the field of in vivo protein-protein interaction methods and undisputedly gave rise to a palette of ingenious techniques that are constantly pushing further the limits of the original method. Sensitivity and selectivity have improved because of various technical tricks and experimental designs. Here we present an exhaustive overview of the genetic approaches available to study in vivo binary protein interactions, based on two-hybrid and protein fragment complementation assays. These methods have been engineered and employed successfully in microorganisms such as Saccharomyces cerevisiae and Escherichia coli, but also in higher eukaryotes. From single binary pairwise interactions to whole-genome interactome mapping, the self-reassembly concept has been employed widely. Innovative studies report the use of proteins such as ubiquitin, dihydrofolate reductase, and adenylate cyclase as reconstituted reporters. Protein fragment complementation assays have extended the possibilities in protein-protein interaction studies, with technologies that enable spatial and temporal analyses of protein complexes. In addition, one-hybrid and three-hybrid systems have broadened the types of interactions that can be studied and the findings that can be obtained. Applications of these technologies are discussed, together with the advantages and limitations of the available assays.
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Díez P, Dasilva N, González-González M, Matarraz S, Casado-Vela J, Orfao A, Fuentes M. Data Analysis Strategies for Protein Microarrays. MICROARRAYS 2012; 1:64-83. [PMID: 27605336 PMCID: PMC5003438 DOI: 10.3390/microarrays1020064] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2012] [Revised: 07/13/2012] [Accepted: 07/31/2012] [Indexed: 01/22/2023]
Abstract
Microarrays constitute a new platform which allows the discovery and characterization of proteins. According to different features, such as content, surface or detection system, there are many types of protein microarrays which can be applied for the identification of disease biomarkers and the characterization of protein expression patterns. However, the analysis and interpretation of the amount of information generated by microarrays remain a challenge. Further data analysis strategies are essential to obtain representative and reproducible results. Therefore, the experimental design is key, since the number of samples and dyes, among others aspects, would define the appropriate analysis method to be used. In this sense, several algorithms have been proposed so far to overcome analytical difficulties derived from fluorescence overlapping and/or background noise. Each kind of microarray is developed to fulfill a specific purpose. Therefore, the selection of appropriate analytical and data analysis strategies is crucial to achieve successful biological conclusions. In the present review, we focus on current algorithms and main strategies for data interpretation.
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Affiliation(s)
- Paula Díez
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Noelia Dasilva
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - María González-González
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Sergio Matarraz
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Juan Casado-Vela
- Translational Oncology Unit, Instituto de Investigaciones Biomédicas 'Alberto Sols', Spanish National Research Council (CSIC-UAM), 28029 Madrid, Spain.
| | - Alberto Orfao
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
| | - Manuel Fuentes
- Centro de Investigación del Cáncer/IBMCC (USAL/CSIC), IBSAL, Departamento de Medicina and Servicio General de Citometría, University of Salamanca, Salamanca 37007, Spain.
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30
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Seefeld TH, Halpern AR, Corn RM. On-chip synthesis of protein microarrays from DNA microarrays via coupled in vitro transcription and translation for surface plasmon resonance imaging biosensor applications. J Am Chem Soc 2012; 134:12358-61. [PMID: 22793370 DOI: 10.1021/ja304187r] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Protein microarrays are fabricated from double-stranded DNA (dsDNA) microarrays by a one-step, multiplexed enzymatic synthesis in an on-chip microfluidic format and then employed for antibody biosensing measurements with surface plasmon resonance imaging (SPRI). A microarray of dsDNA elements (denoted as generator elements) that encode either a His-tagged green fluorescent protein (GFP) or a His-tagged luciferase protein is utilized to create multiple copies of mRNA (mRNA) in a surface RNA polymerase reaction; the mRNA transcripts are then translated into proteins by cell-free protein synthesis in a microfluidic format. The His-tagged proteins diffuse to adjacent Cu(II)-NTA microarray elements (denoted as detector elements) and are specifically adsorbed. The net result is the on-chip, cell-free synthesis of a protein microarray that can be used immediately for SPRI protein biosensing. The dual element format greatly reduces any interference from the nonspecific adsorption of enzyme or proteins. SPRI measurements for the detection of the antibodies anti-GFP and antiluciferase were used to verify the formation of the protein microarray. This convenient on-chip protein microarray fabrication method can be implemented for multiplexed SPRI biosensing measurements in both clinical and research applications.
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Affiliation(s)
- Ting H Seefeld
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, United States
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31
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Gonzalez-Gonzalez M, Jara-Acevedo R, Matarraz S, Jara-Acevedo M, Paradinas S, Sayagües J, Orfao A, Fuentes M. Nanotechniques in proteomics: Protein microarrays and novel detection platforms. Eur J Pharm Sci 2012; 45:499-506. [DOI: 10.1016/j.ejps.2011.07.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 07/07/2011] [Accepted: 07/14/2011] [Indexed: 11/16/2022]
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Andreasson-Ochsner M, Fu Z, May S, Xiu LY, Nallani M, Sinner EK. Selective deposition and self-assembly of triblock copolymers into matrix arrays for membrane protein production. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:2044-2048. [PMID: 22201509 DOI: 10.1021/la2038087] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
To improve the stability of cell membrane mimics, there has been growing interest in the use of block copolymers. Here, we present an easy approach to create an array of planar polymeric matrices capable of hosting membrane proteins. The array of polymeric matrices was formed by the selective deposition of triblock copolymers onto an array of hydrophilic islands situated within a hydrophobic background. The thickness of these matrices corresponds to the length of a single polymer chain. These polymeric matrices were used to host cell-free expressed membrane proteins, and offers a prototype from which a membrane protein array can be created for diagnostics or drug discovery purposes.
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33
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Zhou WJ, Halpern AR, Seefeld TH, Corn RM. Near infrared surface plasmon resonance phase imaging and nanoparticle-enhanced surface plasmon resonance phase imaging for ultrasensitive protein and DNA biosensing with oligonucleotide and aptamer microarrays. Anal Chem 2011; 84:440-5. [PMID: 22126812 DOI: 10.1021/ac202863k] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The techniques of surface plasmon resonance-phase imaging (SPR-PI) and nanoparticle-enhanced SPR-PI have been implemented for the multiplexed bioaffinity detection of proteins and nucleic acids. The SPR-PI experiments utilized a near-infrared 860 nm light emitting diode (LED) light source and a wedge depolarizer to create a phase grating on a four-element single-stranded DNA (ssDNA) microarray; bioaffinity adsorption onto the various microarray elements was detected via multiplexed real time phase shift measurements. In a first set of demonstration experiments, an ssDNA aptamer microarray was used to directly detect thrombin at concentrations down to 100 pM with SPR-PI. Two different ssDNA aptamers were used in these experiments with two different Langmuir adsorption coefficients, K(A1) = 4.4 × 10(8) M(-1) and K(A2) = 1.2 × 10(8) M(-1). At concentrations below 1 nM, the equilibrium phase shifts observed upon thrombin adsorption vary linearly with concentration with a slope that is proportional to the appropriate Langmuir adsorption coefficient. The observed detection limit of 100 pM is approximately 20 times more sensitive than that observed previously with SPRI. In a second set of experiments, two short ssDNA oligonucleotides (38mers) were simultaneously detected at concentrations down to 25 fM using a three-sequence hybridization format that employed 120 nm DNA-modified silica nanoparticles to enhance the SPR-PI signal. In this first demonstration of nanoparticle-enhanced SPR-PI, the adsorbed silica nanoparticles provided a greatly enhanced phase shift upon bioaffinity adsorption due to a large increase in the real component of the interfacial refractive index from the adsorbed nanoparticle. As in the case of SPR-PI, the detection limit of 25 fM for nanoparticle-enhanced SPR-PI is approximately 20 times more sensitive than that observed previously with nanoparticle-enhanced SPRI.
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Affiliation(s)
- Wen-Juan Zhou
- Department of Chemistry, University of California-Irvine, Irvine, California 92697, USA
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Babel I, Barderas R, Peláez-García A, Casal JI. Antibodies on demand: a fast method for the production of human scFvs with minimal amounts of antigen. BMC Biotechnol 2011; 11:61. [PMID: 21635725 PMCID: PMC3125328 DOI: 10.1186/1472-6750-11-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Accepted: 06/02/2011] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Antibodies constitute a powerful tool to study protein function, protein localization and protein-protein interactions, as well as for diagnostic and therapeutic purposes. High-throughput antibody development requires faster methodologies with lower antigen consumption. RESULTS Here, we describe a novel methodology to select human monoclonal recombinant antibodies by combining in vitro protein expression, phage display antibody libraries and antibody microarrays. The application of this combination of methodologies permitted us to generate human single-chain variable fragments (scFvs) against two proteins: green fluorescent protein (GFP) and thioredoxin (Trx) in a short time, using as low as 5 μg of purified protein. These scFvs showed specific reactivity against their respective targets and worked well by ELISA and western blot. The scFvs were able to recognise as low as 31 ng of protein of their respective targets by western blot. CONCLUSION This work describes a novel and miniaturized methodology to obtain human monoclonal recombinant antibodies against any target in a shorter time than other methodologies using only 5 μg of protein. The protocol could be easily adapted to a high-throughput procedure for antibody production.
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Affiliation(s)
- Ingrid Babel
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Rodrigo Barderas
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - Alberto Peláez-García
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
| | - J Ignacio Casal
- Functional Proteomics Laboratory. Centro de Investigaciones Biológicas (CIB-CSIC). Ramiro de Maeztu 9, Madrid 28040, Spain
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Ray S, Reddy PJ, Choudhary S, Raghu D, Srivastava S. Emerging nanoproteomics approaches for disease biomarker detection: a current perspective. J Proteomics 2011; 74:2660-81. [PMID: 21596164 DOI: 10.1016/j.jprot.2011.04.027] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Revised: 03/15/2011] [Accepted: 04/28/2011] [Indexed: 01/29/2023]
Abstract
Availability of genome sequence of human and different pathogens has advanced proteomics research for various clinical applications. One of the prime goals of proteomics is identification and characterization of biomarkers for cancer and other fatal human diseases to aid an early diagnosis and monitor disease progression. However, rapid detection of low abundance biomarkers from the complex biological samples under clinically relevant conditions is extremely difficult, and it requires the development of ultrasensitive, robust and high-throughput technological platform. In order to overcome several technical limitations associated with sensitivity, dynamic range, detection time and multiplexing, proteomics has started integrating several emerging disciplines such as nanotechnology, which has led to the development of a novel analytical platform known as 'nanoproteomics'. Among the diverse classes of nanomaterials, the quantum dots, gold nanoparticles, carbon nanotubes and silicon nanowires are the most promising candidates for diagnostic applications. Nanoproteomics offers several advantages such as ultralow detection, short assay time, high-throughput capability and low sample consumption. In this article, we have discussed the application of nanoproteomics for biomarker discovery in various diseases with special emphasis on various types of cancer. Furthermore, we have discussed the prospects, merits and limitations of nanoproteomics.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai 400076, India
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Ray S, Reddy PJ, Jain R, Gollapalli K, Moiyadi A, Srivastava S. Proteomic technologies for the identification of disease biomarkers in serum: advances and challenges ahead. Proteomics 2011; 11:2139-61. [PMID: 21548090 DOI: 10.1002/pmic.201000460] [Citation(s) in RCA: 170] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 02/28/2011] [Accepted: 03/07/2011] [Indexed: 01/22/2023]
Abstract
Serum is an ideal biological sample that contains an archive of information due to the presence of a variety of proteins released by diseased tissue, and serum proteomics has gained considerable interest for the disease biomarker discovery. Easy accessibility and rapid protein changes in response to disease pathogenesis makes serum an attractive sample for clinical research. Despite these advantages, the analysis of serum proteome is very challenging due to the wide dynamic range of proteins, difficulty in finding low-abundance target analytes due to the presence of high-abundance serum proteins, high levels of salts and other interfering compounds, variations among individuals and paucity of reproducibility. Sample preparation introduces pre-analytical variations and poses major challenges to analyze the serum proteome. The label-free detection techniques such as surface plasmon resonance, microcantilever, few nanotechniques and different resonators are rapidly emerging for the analysis of serum proteome and they have exhibited potential to overcome few limitations of the conventional techniques. In this article, we will discuss the current status of serum proteome analysis for the biomarker discovery and address key technological advancements, with a focus on challenges and amenable solutions.
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Affiliation(s)
- Sandipan Ray
- Wadhwani Research Center for Biosciences and Bioengineering, Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
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38
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Khabibullina NF, Lyukmanova EN, Kopeina GS, Shenkarev ZO, Arsen’ev AS, Dolgikh DA, Kirpichnikov MP. Development and optimization of a coupled cell-free system for the synthesis of the transmembrane domain of the receptor tyrosine kinase ErbB3. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:654-60. [DOI: 10.1134/s1068162010050080] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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39
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He M. In vitro protein expression: an emerging alternative to cell-based approaches. N Biotechnol 2010; 28:209-10. [PMID: 20804874 DOI: 10.1016/j.nbt.2010.08.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 08/23/2010] [Indexed: 11/17/2022]
Abstract
Protein expression remains a bottleneck in the production of proteins. Owing to several advantages, cell-free translation is emerging as an alternative to cell-based methods for the generation of proteins. Recent advances have led to many novel applications of cell-free systems in biotechnology, proteomics and fundamental biological research. This special issue of New Biotechnology describes recent advances in cell-free protein expression systems and their applications.
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Affiliation(s)
- Mingyue He
- Protein Expression Facility, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK.
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