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Dowling P, Trollet C, Negroni E, Swandulla D, Ohlendieck K. How Can Proteomics Help to Elucidate the Pathophysiological Crosstalk in Muscular Dystrophy and Associated Multi-System Dysfunction? Proteomes 2024; 12:4. [PMID: 38250815 PMCID: PMC10801633 DOI: 10.3390/proteomes12010004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
This perspective article is concerned with the question of how proteomics, which is a core technique of systems biology that is deeply embedded in the multi-omics field of modern bioresearch, can help us better understand the molecular pathogenesis of complex diseases. As an illustrative example of a monogenetic disorder that primarily affects the neuromuscular system but is characterized by a plethora of multi-system pathophysiological alterations, the muscle-wasting disease Duchenne muscular dystrophy was examined. Recent achievements in the field of dystrophinopathy research are described with special reference to the proteome-wide complexity of neuromuscular changes and body-wide alterations/adaptations. Based on a description of the current applications of top-down versus bottom-up proteomic approaches and their technical challenges, future systems biological approaches are outlined. The envisaged holistic and integromic bioanalysis would encompass the integration of diverse omics-type studies including inter- and intra-proteomics as the core disciplines for systematic protein evaluations, with sophisticated biomolecular analyses, including physiology, molecular biology, biochemistry and histochemistry. Integrated proteomic findings promise to be instrumental in improving our detailed knowledge of pathogenic mechanisms and multi-system dysfunction, widening the available biomarker signature of dystrophinopathy for improved diagnostic/prognostic procedures, and advancing the identification of novel therapeutic targets to treat Duchenne muscular dystrophy.
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Affiliation(s)
- Paul Dowling
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
| | - Capucine Trollet
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Elisa Negroni
- Center for Research in Myology U974, Sorbonne Université, INSERM, Myology Institute, 75013 Paris, France; (C.T.); (E.N.)
| | - Dieter Swandulla
- Institute of Physiology, Faculty of Medicine, University of Bonn, D53115 Bonn, Germany;
| | - Kay Ohlendieck
- Department of Biology, Maynooth University, National University of Ireland, W23 F2H6 Maynooth, Co. Kildare, Ireland;
- Kathleen Lonsdale Institute for Human Health Research, Maynooth University, W23 F2H6 Maynooth, Co. Kildare, Ireland
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2
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Chen G, Yang L, Liu G, Zhu Y, Yang F, Dong X, Xu F, Zhu F, Cao C, Zhong D, Li S, Zhang H, Li B. Research progress in protein microarrays: Focussing on cancer research. Proteomics Clin Appl 2023; 17:e2200036. [PMID: 36316278 DOI: 10.1002/prca.202200036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/10/2022] [Accepted: 09/27/2022] [Indexed: 01/22/2023]
Abstract
Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.
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Affiliation(s)
- Guang Chen
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Lina Yang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Guoxiang Liu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Yunfan Zhu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Fanghao Yang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Xiaolei Dong
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Fenghua Xu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Feng Zhu
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Can Cao
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Di Zhong
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Shuang Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Huhu Zhang
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China
| | - Bing Li
- Department of Genetics and Cell Biology, Basic Medical College, Qingdao University, Qingdao, China.,Department of Hematology, The Affiliated Hospital of Qingdao University, Qingdao, China
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3
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Barber KW, Shrock E, Elledge SJ. CasPlay provides a gRNA-barcoded CRISPR-based display platform for antibody repertoire profiling. CELL REPORTS METHODS 2022; 2:100318. [PMID: 36313802 PMCID: PMC9606310 DOI: 10.1016/j.crmeth.2022.100318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/06/2022] [Accepted: 09/23/2022] [Indexed: 11/06/2022]
Abstract
Protein display technologies link proteins to distinct nucleic acid sequences (barcodes), enabling multiplexed protein assays via DNA sequencing. Here, we develop Cas9 display (CasPlay) to interrogate customized peptide libraries fused to catalytically inactive Cas9 (dCas9) by sequencing the guide RNA (gRNA) barcodes associated with each peptide. We first confirm the ability of CasPlay to characterize antibody epitopes by recovering a known binding motif for a monoclonal anti-FLAG antibody. We then use a CasPlay library tiling the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) proteome to evaluate vaccine-induced antibody reactivities. Using a peptide library representing the human virome, we demonstrate the ability of CasPlay to identify epitopes across many viruses from microliters of patient serum. Our results suggest that CasPlay is a viable strategy for customized protein interaction studies from highly complex libraries and could provide an alternative to phage display technologies.
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Affiliation(s)
- Karl W. Barber
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Shrock
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J. Elledge
- Division of Genetics, Brigham and Women’s Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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4
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Hendriks J, Schasfoort RBM, Huskens J, Saris DF, Karperien M. Kinetic characterization of SPR-based biomarker assays enables quality control, calibration free measurements and robust optimization for clinical application. Anal Biochem 2022; 658:114918. [PMID: 36170905 DOI: 10.1016/j.ab.2022.114918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 09/09/2022] [Accepted: 09/15/2022] [Indexed: 11/27/2022]
Abstract
Biomarker measurements are essential for the early diagnosis of complex diseases. However, many current biomarker assays lack sensitivity and multiplexing capacity, work in a narrow detection range and importantly lack real time quality control opportunities, which hampers clinical translation. In this paper, we demonstrate a toolbox to kinetically characterize a biomarker measurement assay using Surface Plasmon Resonance imaging (SPRi) with ample opportunities for real time quality control by exploiting quantitative descriptions of the various biomolecular interactions. We show an accurate prediction of SPRi measurements at both low and high concentrations of various analytes with deviations <5% between actual measurements and predicted measurement. The biphasic binding sites model was accurate for fitting the experimental curves and enables optimal detection of heterophilic antibodies, cross-reactivity, spotting irregularities and/or other confounders. The toolbox can also be used to create a (simulated) calibration curve, enabling calibration-free measurements with good recovery, it allows for easy assay optimizations, and could help bridge the gap to bring new biomarker assays to the clinic.
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Affiliation(s)
- Jan Hendriks
- Department of Developmental BioEngineering, Technical Medical Centre, University of Twente, the Netherlands
| | - Richard B M Schasfoort
- Medical Cell Biophysics, Technical Medical Centre, University of Twente, the Netherlands
| | - Jurriaan Huskens
- Molecular Nanofabrication, MESA+ Institute for Nanotechnology, University of Twente, the Netherlands
| | - DaniëlB F Saris
- Department of Orthopedics, Mayo Clinic, Rochester, MN, USA; Department of Orthopedics, UMC Utrecht, the Netherlands
| | - Marcel Karperien
- Department of Developmental BioEngineering, Technical Medical Centre, University of Twente, the Netherlands.
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5
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Beck S, Nakajima R, Jasinskas A, Abram TJ, Kim SJ, Bigdeli N, Tifrea DF, Hernandez-Davies J, Huw Davies D, Hedde PN, Felgner PL, Zhao W. A Protein Microarray-Based Respiratory Viral Antigen Testing Platform for COVID-19 Surveillance. Biomedicines 2022; 10:biomedicines10092238. [PMID: 36140339 PMCID: PMC9496200 DOI: 10.3390/biomedicines10092238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 09/03/2022] [Accepted: 09/06/2022] [Indexed: 11/16/2022] Open
Abstract
High-throughput and rapid screening testing is highly desirable to effectively combat the rapidly evolving COVID-19 pandemic co-presents with influenza and seasonal common cold epidemics. Here, we present a general workflow for iterative development and validation of an antibody-based microarray assay for the detection of a respiratory viral panel: (a) antibody screening to quickly identify optimal reagents and assay conditions, (b) immunofluorescence assay design including signal amplification for low viral titers, (c) assay characterization with recombinant proteins, inactivated viral samples and clinical samples, and (d) multiplexing to detect a panel of common respiratory viruses. Using RT-PCR-confirmed SARS-CoV-2 positive and negative pharyngeal swab samples, we demonstrated that the antibody microarray assay exhibited a clinical sensitivity and specificity of 77.2% and 100%, respectively, which are comparable to existing FDA-authorized antigen tests. Moreover, the microarray assay is correlated with RT-PCR cycle threshold (Ct) values and is particularly effective in identifying high viral titers. The multiplexed assay can selectively detect SARS-CoV-2 and influenza virus, which can be used to discriminate these viral infections that share similar symptoms. Such protein microarray technology is amenable for scale-up and automation and can be broadly applied as a both diagnostic and research tool.
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Affiliation(s)
- Sungjun Beck
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
| | - Rie Nakajima
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - Algis Jasinskas
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | | | - Sun Jin Kim
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Nader Bigdeli
- Student Health Center, University of California, Irvine, CA 92697, USA
| | - Delia F. Tifrea
- Department of Pathology and Laboratory Medicine, University of California, Irvine, CA 92697, USA
| | - Jenny Hernandez-Davies
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
| | - D. Huw Davies
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
- Institute for Immunology, University of California, Irvine, CA 92697, USA
| | - Per Niklas Hedde
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
- Laboratory for Fluorescence Dynamics, University of California, Irvine, CA 92697, USA
- Beckman Laser Institute and Medical Clinic, University of California, Irvine, CA 92697, USA
- Correspondence: (P.N.H.); (P.L.F.); (W.Z.)
| | - Philip L. Felgner
- Department of Physiology and Biophysics, University of California, Irvine, CA 92697, USA
- Institute for Immunology, University of California, Irvine, CA 92697, USA
- Correspondence: (P.N.H.); (P.L.F.); (W.Z.)
| | - Weian Zhao
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
- Institute for Immunology, University of California, Irvine, CA 92697, USA
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, CA 92697, USA
- Chao Family Comprehensive Cancer Center, University of California, Irvine, CA 92697, USA
- Edwards Life Sciences Center for Advanced Cardiovascular Technology, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
- Correspondence: (P.N.H.); (P.L.F.); (W.Z.)
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6
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Preparation of substrates for microarray protein chips with different ending functional groups. J Immunol Methods 2022; 502:113218. [PMID: 35026296 DOI: 10.1016/j.jim.2022.113218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 08/26/2021] [Accepted: 01/03/2022] [Indexed: 11/20/2022]
Abstract
Protein microarray chips are composed of three components, these are pre-treatment substrates, surface chemical modification, and immobilizing protein on substrate surfaces. In this study, self-assembly monolayers are used for surface chemical modification. Using this method, silanization on a glass and silicon chip is achieved, forming the terminal group substrates. Modification of the substrate surface to provide COOH and NH2 terminal functional groups provides a mechanism to proteins to immobilize on the substrate surface. To observe immobilized proteins on the substrate surface, they are first labeled with Cy5 fluorescent dye before analysis using a GenePix 4000B Microarray Scanner. The scanner induces fluorescence in the labelling dye and the resulting light is analyzed to provide information concerning both the quantity of immobilized protein, and the orientation of attachment. The antigen of the HSV-1 virus, a common human virus, was used in this study, performing an antigen-antibody analysis to determine the efficacy of the method under test for clinical diagnosis.
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7
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Fomitcheva-Khartchenko A, Rapsomaniki MA, Sobottka B, Schraml P, Kaigala GV. Spatial protein heterogeneity analysis in frozen tissues to evaluate tumor heterogeneity. PLoS One 2021; 16:e0259332. [PMID: 34797831 PMCID: PMC8604290 DOI: 10.1371/journal.pone.0259332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 10/19/2021] [Indexed: 11/19/2022] Open
Abstract
A new workflow for protein-based tumor heterogeneity probing in tissues is here presented. Tumor heterogeneity is believed to be key for therapy failure and differences in prognosis in cancer patients. Comprehending tumor heterogeneity, especially at the protein level, is critical for tracking tumor evolution, and showing the presence of different phenotypical variants and their location with respect to tissue architecture. Although a variety of techniques is available for quantifying protein expression, the heterogeneity observed in the tissue is rarely addressed. The proposed method is validated in breast cancer fresh-frozen tissues derived from five patients. Protein expression is quantified on the tissue regions of interest (ROI) with a resolution of up to 100 μm in diameter. High heterogeneity values across the analyzed patients in proteins such as cytokeratin 7, β-actin and epidermal growth factor receptor (EGFR) using a Shannon entropy analysis are observed. Additionally, ROIs are clustered according to their expression levels, showing their location in the tissue section, and highlighting that similar phenotypical variants are not always located in neighboring regions. Interestingly, a patient with a phenotype related to increased aggressiveness of the tumor presents a unique protein expression pattern. In summary, a workflow for the localized extraction and protein analysis of regions of interest from frozen tissues, enabling the evaluation of tumor heterogeneity at the protein level is presented.
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Affiliation(s)
| | | | - Bettina Sobottka
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
| | - Peter Schraml
- Department of Pathology and Molecular Pathology, University Hospital Zurich and University Zurich, Zurich, Switzerland
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8
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Secretome Analysis of Rabbit and Human Mesenchymal Stem and Endothelial Progenitor Cells: A Comparative Study. Int J Mol Sci 2021; 22:ijms222212283. [PMID: 34830165 PMCID: PMC8625496 DOI: 10.3390/ijms222212283] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/05/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022] Open
Abstract
Human adipose tissue-derived mesenchymal stem cells (AT-MSCs) have been studied several years for their immunomodulatory effect through the paracrine mechanism and cytokine secretion. In combination with endothelial progenitor cells (EPCs), MSCs have great therapeutical potential for the repair of endothelium and wound healing. However, little is known about the cytokine profile of rabbit AT-MSCs or even EPCs. The aim of this study was to analyze the secretomes of these rabbit stem/progenitor cells. A large-scale human cytokine array (up to 80 cytokines) was used to identify and compare cytokines secreted into conditioned media of human and rabbit AT-MSCs as well as HUVECs and rabbit EPCs. Few cytokines were highly expressed by human AT-MSCs (TIMP-2, TIMP-1), HUVECs (MCP-1, TIMP-2, GRO, Angiogenin, IL-8, TIMP-1), or by rabbit EPCs (TIMP-2). Several cytokines have moderate expression by human (MCP-1, GRO, Angiogenin, TGF-β 2, IL-8, LIF, IL-6, Osteopontin, Osteoprotegerin) and rabbit AT-MSCs (TIMP-2, TGF-β 2, LIF, Osteopontin, IL-8, IL-5, IL-3) or by HUVECs (IL-6, MIF, TGF-β 2, GCP-2, IGFBP-2, Osteoprotegerin, EGF, LIF, PDGF-BB, MCP-3, Osteopontin, Leptin, IL-5, ENA-78, TNF-β) and rabbit EPCs (TGF-β 2, Osteopontin, GRO, LIF, IL-8, IL-5, IL-3). In conclusion, the proposed method seems to be useful for the secretome analysis of rabbit stem/progenitor cells.
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9
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Barber KW, Shrock E, Elledge SJ. CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays. Mol Cell 2021; 81:3650-3658.e5. [PMID: 34390675 DOI: 10.1016/j.molcel.2021.07.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/25/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023]
Abstract
CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.
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Affiliation(s)
- Karl W Barber
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Shrock
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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10
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Shlyapnikov YM, Malakhova EA, Shlyapnikova EA. Improving Immunoassay Performance with Cleavable Blocking of Microarrays. Anal Chem 2021; 93:1126-1134. [PMID: 33305941 DOI: 10.1021/acs.analchem.0c04175] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among the key issues that are commonly associated with the development of microarray-based assays are nonspecific binding and diffusion constraints. Here we present a novel strategy addressing both of these challenges simultaneously. The essence of the method consists in blocking the microarray surface with a blocking agent containing a perfluoroalkyl chain and a disulfide linker. The resulting surface is hydrophobic, and no immiscible liquid layer remains on it upon cyclically draining and replenishing the sample solution, ensuring an efficient mass transfer of an analyte onto a microarray. Prior to the signal detection procedure, disulfide bonds are chemically cleaved, and the perfluoroalkyl chains are removed from the microarray surface along with nonspecifically adsorbed proteins, resulting in extremely low background. Using conventional fluorescent detection, we show a 30-fold increase in signal/background ratio compared to a common epoxy-modified glass substrate. The combination of this technique with magnetic beads detection results in a simple and ultrasensitive cholera toxin (CT) immunoassay. The limit of detection (LOD) is 1 fM, which is achieved with an analyte binding time of 1 h. Efficient mass transfer provides highly sensitive detection of whole virus particles despite their low diffusion coefficient. The achieved LOD for vaccinia virus is 104 particles in 1 mL of sample. Finally, we have performed for the first time the simultaneous detection of whole virus and CT protein biomarker in a single assay. The developed technique can be used for multiplex detection of trace amounts of pathogens of various natures.
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Affiliation(s)
- Yuri M Shlyapnikov
- Institute of Theoretical and Experimental Biophysics Russian Academy of Sciences, Pushchino 142290, Russia
| | - Ekaterina A Malakhova
- Institute of Theoretical and Experimental Biophysics Russian Academy of Sciences, Pushchino 142290, Russia
| | - Elena A Shlyapnikova
- Institute of Theoretical and Experimental Biophysics Russian Academy of Sciences, Pushchino 142290, Russia
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11
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Abstract
Recent advances in biosensing analytical platforms have brought relevant outcomes for novel diagnostic and therapy-oriented applications. In this context, hydrogels have emerged as appealing matrices to locally confine biomolecules onto sensing surfaces under solution mimetic conditions, preserving their structural integrity and function. Here, we describe the application of a self-assembling peptide hydrogel as a suitable matrix for 3D microarray bioassays. The hydrogel is printable and self-adhesive and allows for fast analyte diffusion. As a showcase example, we describe its application in a diagnostic immunoassay for the detection of arbovirus infection.
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12
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Li BW, Zhang Y, Wang YC, Xue Y, Nie XY. Rapid Fabrication of Protein Microarrays via Autogeneration and on-Chip Purification of Biotinylated Probes. ACS Synth Biol 2020; 9:2267-2273. [PMID: 32810400 DOI: 10.1021/acssynbio.0c00343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A streamlined approach toward the rapid fabrication of streptavidin-biotin-based protein microarrays was investigated. First, using our engineered versatile plasmid (pBADcM-tBirA) and an optimal coexpression strategy for biotin ligase and biotin acceptor peptide (BAP) chimeric recombinant protein, an autogeneration system for biotinylated probes was developed. This system permitted an advantageous biotinylation of BAP chimeric recombinant proteins, providing a strategy for the high-throughput synthesis of biotinylated probes. Then, to bypass the conventional rate-limiting steps, we employed an on-chip purification process to immobilize the biotinylated probes with high-throughput recombinant lysates. The integration of the autogeneration of probes and on-chip purification not only contributed to the effective and reliable fabrication of the protein microarray, but also enabled simplification of the process and an automated throughput format. This labor- and cost-effective approach may facilitate the use of protein microarrays for diagnosis, pharmacology, proteomics, and other laboratory initiatives.
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Affiliation(s)
- Bo-Wen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, 350002, P. R. China
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yi Zhang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yin-Chun Wang
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Yang Xue
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
| | - Xin-Yi Nie
- Key Laboratory of Biopesticide and Chemical Biology of Education Ministry, Key Laboratory of Pathogenic Fungi and Mycotoxins of Fujian Province, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, P. R. China
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13
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Uzdensky AB. Apoptosis regulation in the penumbra after ischemic stroke: expression of pro- and antiapoptotic proteins. Apoptosis 2020; 24:687-702. [PMID: 31256300 DOI: 10.1007/s10495-019-01556-6] [Citation(s) in RCA: 179] [Impact Index Per Article: 44.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Ischemic stroke is the leading cause of human disability and mortality in the world. The main problem in stroke therapy is the search of efficient neuroprotector capable to rescue neurons in the potentially salvageable transition zone (penumbra), which is expanding after brain damage. The data on molecular mechanisms of penumbra formation and expression of diverse signaling proteins in the penumbra during first 24 h after ischemic stroke are discussed. Two basic features of cell death regulation in the ischemic penumbra were observed: (1) both apoptotic and anti-apoptotic proteins are simultaneously over-expressed in the penumbra, so that the fate of individual cells is determined by the balance between these opposite tendencies. (2) Similtaneous and concerted up-regulation in the ischemic penumbra of proteins that execute apoptosis (caspases 3, 6, 7; Bcl-10, SMAC/DIABLO, AIF, PSR), signaling proteins that regulate different apoptosis pathways (p38, JNK, DYRK1A, neurotrophin receptor p75); transcription factors that control expression of various apoptosis regulation proteins (E2F1, p53, c-Myc, GADD153); and proteins, which are normally involved in diverse cellular functions, but stimulate apoptosis in specific situations (NMDAR2a, Par4, GAD65/67, caspase 11). Hence, diverse apoptosis initiation and regulation pathways are induced simultaneously in penumbra from very different initial positions. Similarly, various anti-apoptotic proteins (Bcl-x, p21/WAF-1, MDM2, p63, PKBα, ERK1, RAF1, ERK5, MAKAPK2, protein phosphatases 1α and MKP-1, estrogen and EGF receptors, calmodulin, CaMKII, CaMKIV) are upregulated. These data provide an integral view of neurodegeneration and neuroprotection in penumbra. Some discussed proteins may serve as potential targets for anti-stroke therapy.
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Affiliation(s)
- Anatoly B Uzdensky
- Laboratory of Molecular Neurobiology, Academy of Biology and Biotechnology, Southern Federal University, 194/1 Stachky Prospect, Rostov-on-Don, Russia, 344090.
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14
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Identification of tumor-associated antigens with diagnostic ability of colorectal cancer by in-depth immunomic and seroproteomic analysis. J Proteomics 2020; 214:103635. [PMID: 31918032 DOI: 10.1016/j.jprot.2020.103635] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/02/2020] [Accepted: 01/05/2020] [Indexed: 12/18/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second leading cause of cancer related death worldwide. Its diagnosis at early stages would significantly improve the survival of CRC patients. The humoral immune response has been demonstrated useful for cancer diagnosis, predating clinical symptoms up to 3 years. Here, we employed an in-depth seroproteomic approach to identify proteins that elicit a humoral immune response in CRC patients. The seroproteomic approach relied on the immunoprecipitation with patient-derived autoantibodies of proteins from CRC cell lines with different metastatic properties followed by LC-MS/MS. After bioinformatics, we focused on 31 targets of CRC autoantibodies. After WB and IHC validation, ERP44 and TALDO1 showed potential to discriminate disease-free and metastatic CRC patients, and time to recurrence of CRC patients in stage II. Using plasma samples of 30 healthy individuals, 28 premalignant individuals, and 32 CRC patients, nine out of 13 selected targets for seroreactive analysis showed significant diagnostic ability to discriminate either CRC patients or premalignant subjects from controls. Our results suggest that the here defined panel of CRC autoantibodies and their target proteins should be included in CRC blood-based biomarker panels to get a clinically useful blood-based diagnostic signature for CRC detection. SIGNIFICANCE: Colorectal cancer is one of the deadliest cancer types mainly due to its late diagnosis. Its early diagnosis, therefore, is of great importance since it would significantly improve the survival of CRC patients. In our work, the in-depth seroproteomic analysis of colorectal cancer using isolated IgGs from colorectal cancer patients and controls and protein extract of colorectal cancer cells provide the identification of valuable biomarkers with diagnostic and prognostic ability of the disease.
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15
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Bandaru P, Chu D, Sun W, Lasli S, Zhao C, Hou S, Zhang S, Ni J, Cefaloni G, Ahadian S, Dokmeci MR, Sengupta S, Lee J, Khademhosseini A. A Microfabricated Sandwiching Assay for Nanoliter and High-Throughput Biomarker Screening. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1900300. [PMID: 30884183 DOI: 10.1002/smll.201900300] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/14/2019] [Indexed: 05/03/2023]
Abstract
Cells secrete substances that are essential to the understanding of numerous immunological phenomena and are extensively used in clinical diagnoses. Countless techniques for screening of biomarker secretion in living cells have generated valuable information on cell function and physiology, but low volume and real-time analysis is a bottleneck for a range of approaches. Here, a simple, highly sensitive assay using a high-throughput micropillar and microwell array chip (MIMIC) platform is presented for monitoring of biomarkers secreted by cancer cells. The sensing element is a micropillar array that uses the enzyme-linked immunosorbent assay (ELISA) mechanism to detect captured biomolecules. When integrated with a microwell array where few cells are localized, interleukin 8 (IL-8) secretion can be monitored with nanoliter volume using multiple micropillar arrays. The trend of cell secretions measured using MIMICs matches the results from conventional ELISA well while it requires orders of magnitude less cells and volumes. Moreover, the proposed MIMIC is examined to be used as a drug screening platform by delivering drugs using micropillar arrays in combination with a microfluidic system and then detecting biomolecules from cells as exposed to drugs.
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Affiliation(s)
- Praveen Bandaru
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Dafeng Chu
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Wujin Sun
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Soufian Lasli
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Chuanzhen Zhao
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shuang Hou
- Department of Molecular and Medical Pharmacology, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shiming Zhang
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Jiahua Ni
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Giorgia Cefaloni
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Samad Ahadian
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Mehmet Remzi Dokmeci
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Shiladitya Sengupta
- Department of Medicine, Division of Engineering in Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA
- Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Junmin Lee
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
| | - Ali Khademhosseini
- Department of Bioengineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Center for Minimally Invasive Therapeutics (C-MIT), University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Radiology, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, 90095, USA
- Department of Chemical and Biomolecular Engineering, Henry Samueli School of Engineering and Applied Sciences, University of California-Los Angeles, Los Angeles, CA, 90095, USA
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16
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Walder B, Berk C, Liao WC, Rossini AJ, Schwarzwälder M, Pradere U, Hall J, Lesage A, Copéret C, Emsley L. One- and Two-Dimensional High-Resolution NMR from Flat Surfaces. ACS CENTRAL SCIENCE 2019; 5:515-523. [PMID: 30937379 PMCID: PMC6439530 DOI: 10.1021/acscentsci.8b00916] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Indexed: 05/02/2023]
Abstract
Determining atomic-level characteristics of molecules on two-dimensional surfaces is one of the fundamental challenges in chemistry. High-resolution nuclear magnetic resonance (NMR) could deliver rich structural information, but its application to two-dimensional materials has been prevented by intrinsically low sensitivity. Here we obtain high-resolution one- and two-dimensional 31P NMR spectra from as little as 160 picomoles of oligonucleotide functionalities deposited onto silicate glass and sapphire wafers. This is enabled by a factor >105 improvement in sensitivity compared to typical NMR approaches from combining dynamic nuclear polarization methods, multiple-echo acquisition, and optimized sample formulation. We demonstrate that, with this ultrahigh NMR sensitivity, 31P NMR can be used to observe DNA bound to miRNA, to sense conformational changes due to ion binding, and to follow photochemical degradation reactions.
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Affiliation(s)
- Brennan
J. Walder
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Christian Berk
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Wei-Chih Liao
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Aaron J. Rossini
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Chemistry, Iowa State University, Ames, Iowa 50011-3020, United States
| | - Martin Schwarzwälder
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Ugo Pradere
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Jonathan Hall
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Anne Lesage
- Institut
de Sciences Analytiques, Centre de RMN à Très Hauts
Champs, Université de Lyon (CNRS/ENS
Lyon/UCB Lyon 1), 69100 Villeurbanne, France
| | - Christophe Copéret
- Department
of Chemistry and Applied Biosciences, ETH
Zürich, Vladimir Prelog Weg 1-5, CH−8093 Zürich, Switzerland
| | - Lyndon Emsley
- Institut
des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- E-mail:
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17
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Succinylated Jeffamine ED-2003 coated polycarbonate chips for low-cost analytical microarrays. Anal Bioanal Chem 2019; 411:1943-1955. [DOI: 10.1007/s00216-019-01594-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Revised: 12/03/2018] [Accepted: 01/09/2019] [Indexed: 10/27/2022]
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18
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Brambilla D, Chiari M, Gori A, Cretich M. Towards precision medicine: the role and potential of protein and peptide microarrays. Analyst 2019; 144:5353-5367. [DOI: 10.1039/c9an01142k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Techniques to comprehensively analyze protein signatures are pivotal to unravel disease mechanisms, develop novel biomarkers and targeted therapies. In this frame, protein and peptide microarrays can play a major role in fuelling precision medicine.
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Affiliation(s)
- Dario Brambilla
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Alessandro Gori
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche
- Istituto di Chimica del Riconoscimento Molecolare (ICRM)
- Milano
- Italy
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19
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Pearson AJ, Gallagher ES. Overview of Characterizing Cancer Glycans with Lectin-Based Analytical Methods. Methods Mol Biol 2019; 1928:389-408. [PMID: 30725466 DOI: 10.1007/978-1-4939-9027-6_20] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Glycosylation is a post-translational modification that is often altered in disease development and progression, including cancer. In cancerous patients, the abnormal expression of glycosylation enzymes leads to aberrant glycosylation, which has been linked to malignant tissues. Due to aberrant glycosylation, the presence of specific glycans can be used as biomarkers for identifying the type and stage of cancer. Glycan structures are heterogeneous, with different protein glycoforms having different functional activities. Lectins are an important tool in glycan analysis due to their specificity in binding to unique glycan linkages and monosaccharide units, which allows for the identification of unique glycan structural properties. In this review, we will discuss the use of lectins in microarrays and chromatography for characterizing glycan structures.
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Affiliation(s)
- Amanda J Pearson
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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20
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Carvalho AM, Montes CV, Schneider RJ, Madder A. An Anticaffeine Antibody-Oligonucleotide Conjugate for DNA-Directed Immobilization in Environmental Immunoarrays. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:14834-14841. [PMID: 30089211 DOI: 10.1021/acs.langmuir.8b01347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The development of fast and cheap high-throughput platforms for the detection of environmental contaminants is of particular importance to understand the human-related impact on the environment. The application of DNA-directed immobilization (DDI) of IgG molecules is currently limited to the clinical diagnostics scenario, possibly because of the high costs of production of such addressable platforms. We here describe the efficient and specific hybridization of an antibody-oligonucleotide conjugate to a short 12-mer capture probe. The specific antibody used is a monoclonal antibody against caffeine, a stimulant and important anthropogenic marker. With this work, we hope to contribute to broadening the application potential of DDI to environmental markers in order to develop cheaper and more stable high-throughput screening platforms for standard routine analysis of pollutants in a variety of complex matrices.
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Affiliation(s)
- Ana Margarida Carvalho
- Ghent University , Faculty of Sciences, Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group , Krijgslaan 281 (S4) , 9000 Ghent , Belgium
- BAM Federal Institute for Materials Research and Testing , Department of Analytical Chemistry; Reference Materials , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Cinthya Véliz Montes
- BAM Federal Institute for Materials Research and Testing , Department of Analytical Chemistry; Reference Materials , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Rudolf J Schneider
- BAM Federal Institute for Materials Research and Testing , Department of Analytical Chemistry; Reference Materials , Richard-Willstätter-Str. 11 , D-12489 Berlin , Germany
| | - Annemieke Madder
- Ghent University , Faculty of Sciences, Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group , Krijgslaan 281 (S4) , 9000 Ghent , Belgium
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21
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Bush DB, Knotts TA. The effects of antigen size, binding site valency, and flexibility on fab-antigen binding near solid surfaces. J Chem Phys 2018; 149:165102. [PMID: 30384722 DOI: 10.1063/1.5045356] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Next generation antibody microarray devices have the potential to outperform current molecular detection methods and realize new applications in medicine, scientific research, and national defense. However, antibody microarrays, or arrays of antibody fragments ("fabs"), continue to evade mainstream use in part due to persistent reliability problems despite improvements to substrate design and protein immobilization strategies. Other factors could be disrupting microarray performance, including effects resulting from antigen characteristics. Target molecules embody a wide range of sizes, shapes, number of epitopes, epitope accessibility, and other physical and chemical properties. As a result, it may not be ideal for microarray designs to utilize the same substrate or immobilization strategy for all of the capture molecules. This study investigates how three antigen properties, such as size, binding site valency, and molecular flexibility, affect fab binding. The work uses an advanced, experimentally validated, coarse-grain model and umbrella sampling to calculate the free energy of ligand binding and how this energy landscape is different on the surface compared to in the bulk. The results confirm that large antigens interact differently with immobilized fabs compared to smaller antigens. Analysis of the results shows that despite these differences, tethering fabs in an upright orientation on hydrophilic surfaces is the best configuration for antibody microarrays.
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Affiliation(s)
- Derek B Bush
- Department of Chemical Engineering, Brigham Young University Provo, Provo, Utah 84602, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University Provo, Provo, Utah 84602, USA
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22
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Affiliation(s)
- Limor Cohen
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - David R. Walt
- Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States
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23
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Quantification of uPA in breast tumour tissue extracts by microarray immunoassay: Comparison with ELISA technology. J Appl Biomed 2018. [DOI: 10.1016/j.jab.2018.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Grawe RW, Knotts TA. The effects of tether placement on antibody stability on surfaces. J Chem Phys 2018; 146:215102. [PMID: 28576081 DOI: 10.1063/1.4983705] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Despite their potential benefits, antibody microarrays have fallen short of performing reliably and have not found widespread use outside of the research setting. Experimental techniques have been unable to determine what is occurring on the surface of an atomic level, so molecular simulation has emerged as the primary method of investigating protein/surface interactions. Simulations of small proteins have indicated that the stability of the protein is a function of the residue on the protein where a tether is placed. The purpose of this research is to see whether these findings also apply to antibodies, with their greater size and complexity. To determine this, 24 tethering locations were selected on the antibody Protein Data Bank (PDB) ID: 1IGT. Replica exchange simulations were run on two different surfaces, one hydrophobic and one hydrophilic, to determine the degree to which these tethering sites stabilize or destabilize the antibody. Results showed that antibodies tethered to hydrophobic surfaces were in general less stable than antibodies tethered to hydrophilic surfaces. Moreover, the stability of the antibody was a function of the tether location on hydrophobic surfaces but not hydrophilic surfaces.
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Affiliation(s)
- Rebecca W Grawe
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
| | - Thomas A Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84606, USA
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25
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Hendriks J, Stojanovic I, Schasfoort RBM, Saris DBF, Karperien M. Nanoparticle Enhancement Cascade for Sensitive Multiplex Measurements of Biomarkers in Complex Fluids with Surface Plasmon Resonance Imaging. Anal Chem 2018; 90:6563-6571. [PMID: 29732889 PMCID: PMC5990928 DOI: 10.1021/acs.analchem.8b00260] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
![]()
There is a large
unmet need for reliable biomarker measurement
systems for clinical application. Such systems should meet challenging
requirements for large scale use, including a large dynamic detection
range, multiplexing capacity, and both high specificity and sensitivity.
More importantly, these requirements need to apply to complex biological
samples, which require extensive quality control. In this paper, we
present the development of an enhancement detection cascade for surface
plasmon resonance imaging (SPRi). The cascade applies an antibody
sandwich assay, followed by neutravidin and a gold nanoparticle enhancement
for quantitative biomarker measurements in small volumes of complex
fluids. We present a feasibility study both in simple buffers and
in spiked equine synovial fluid with four cytokines, IL-1β,
IL-6, IFN-γ, and TNF-α. Our enhancement cascade leads
to an antibody dependent improvement in sensitivity up to 40 000
times, resulting in a limit of detection as low as 50 fg/mL and a
dynamic detection range of more than 7 logs. Additionally, measurements
at these low concentrations are highly reliable with intra- and interassay
CVs between 2% and 20%. We subsequently showed this assay is suitable
for multiplex measurements with good specificity and limited cross-reactivity.
Moreover, we demonstrated robust detection of IL-6 and IL-1β
in spiked undiluted equine synovial fluid with small variation compared
to buffer controls. In addition, the availability of real time measurements
provides extensive quality control opportunities, essential for clinical
applications. Therefore, we consider this method is suitable for broad
application in SPRi for multiplex biomarker detection in both research
and clinical settings.
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Affiliation(s)
- Jan Hendriks
- Department of Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , Enschede , 7522 NB , The Netherlands
| | - Ivan Stojanovic
- Medical Cell Biophysics, MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , Enschede , 7522 NB , The Netherlands
| | - Richard B M Schasfoort
- Medical Cell Biophysics, MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , Enschede , 7522 NB , The Netherlands
| | - Daniël B F Saris
- Department of Orthopedics , UMC Utrecht , Utrecht , 3584 CX , The Netherlands.,Department of Reconstructive Medicine, MIRA Institute for Biomedical Technology and Technical Medicine, Faculty of Science and Technology , University of Twente , Enschede , 7522 NB , The Netherlands
| | - Marcel Karperien
- Department of Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine , University of Twente , Enschede , 7522 NB , The Netherlands
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26
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Zhan W, Qu Y, Wei T, Hu C, Pan Y, Yu Q, Chen H. Sweet Switch: Sugar-Responsive Bioactive Surfaces Based on Dynamic Covalent Bonding. ACS APPLIED MATERIALS & INTERFACES 2018; 10:10647-10655. [PMID: 29533581 DOI: 10.1021/acsami.7b18166] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Smart bioactive surfaces that can modulate interactions with biological systems are of great interest. In this work, a surface with switchable bioactivity in response to sugars has been developed. It is based on dynamic covalent bonding between phenylboronic acid (PBA) and secondary hydroxyls on the "wide" rim of β-cyclodextrin (β-CD). The system reported consists of gold surface modified with PBA-containing polymer brushes and a series of functional β-CD derivatives conjugated to diverse bioactive ligands (CD-X). CD-X molecules are attached to the surface to give specified bioactivity such as capture of a specific protein or killing of attached bacteria. Subsequent treatment with cis-diol containing biomolecules having high affinity for PBA (e.g. fructose) leads to the release of CD-X together with the captured proteins, killed bacteria, and so forth from the surface. The surface bioactivity is thereby "turned off". Effectively, this constitutes an on-off bioactivity switch in a mild and noninvasive way, which has the potential in the design of dynamic bioactive surfaces for biomedical applications.
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Affiliation(s)
- Wenjun Zhan
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Yangcui Qu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Ting Wei
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Changming Hu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Yue Pan
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Qian Yu
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
| | - Hong Chen
- State and Local Joint Engineering Laboratory for Novel Functional Polymeric Materials, College of Chemistry, Chemical Engineering and Materials Science , Soochow University , 199 Ren'ai Road , Suzhou 215123 , P. R. China
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27
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Da Gama Duarte J, Goosen RW, Lawry PJ, Blackburn JM. PMA: Protein Microarray Analyser, a user-friendly tool for data processing and normalization. BMC Res Notes 2018; 11:156. [PMID: 29482592 PMCID: PMC5828362 DOI: 10.1186/s13104-018-3266-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 02/22/2018] [Indexed: 12/12/2022] Open
Abstract
Objective Protein microarrays provide a high-throughput platform to measure protein interactions and associated functions, and can aid in the discovery of cancer biomarkers. The resulting protein microarray data can however be subject to systematic bias and noise, thus requiring a robust data processing, normalization and analysis pipeline to ensure high quality and robust results. To date, a comprehensive data processing pipeline is yet to be developed. Furthermore, a lack of analysis consistency is evident amongst different research groups, thereby impeding collaborative data consolidation and comparison. Thus, we sought to develop an accessible data processing tool using methods that are generalizable to the protein microarray field and which can be adapted to individual array layouts with minimal software engineering expertise. Results We developed an improved version of a previously developed pipeline of protein microarray data processing and implemented it as an open source software tool, with particular focus on widening its use and applicability. The Protein Microarray Analyser software presented here includes the following tools: (1) neighbourhood background correction, (2) net intensity correction, (3) user-defined noise threshold, (4) user-defined CV threshold amongst replicates and (5) assay controls, (6) composite ‘pin-to-pin’ normalization amongst sub-arrays, and (7) ‘array-to-array’ normalization amongst whole arrays. Electronic supplementary material The online version of this article (10.1186/s13104-018-3266-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jessica Da Gama Duarte
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa. .,Tumour Immunology Laboratory, Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia.
| | - Ryan W Goosen
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Peter J Lawry
- Olivia Newton-John Cancer Research Institute/School of Cancer Medicine, La Trobe University, Level 5, ONJCWC, 145 Studley Road, Heidelberg, VIC, 3084, Australia
| | - Jonathan M Blackburn
- Department of Integrative Biomedical Sciences & Institute for Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Blackburn Laboratory, N3.03, Wernher & Beit Building North, Institute of Infectious Disease & Molecular Medicine, UCT Faculty of Health Sciences, Observatory, Cape Town, 7925, South Africa
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28
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Seo J, Shin JY, Leijten J, Jeon O, Camci-Unal G, Dikina AD, Brinegar K, Ghaemmaghami AM, Alsberg E, Khademhosseini A. High-throughput approaches for screening and analysis of cell behaviors. Biomaterials 2018; 153:85-101. [PMID: 29079207 PMCID: PMC5702937 DOI: 10.1016/j.biomaterials.2017.06.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 06/17/2017] [Accepted: 06/19/2017] [Indexed: 02/06/2023]
Abstract
The rapid development of new biomaterials and techniques to modify them challenge our capability to characterize them using conventional methods. In response, numerous high-throughput (HT) strategies are being developed to analyze biomaterials and their interactions with cells using combinatorial approaches. Moreover, these systematic analyses have the power to uncover effects of delivered soluble bioactive molecules on cell responses. In this review, we describe the recent developments in HT approaches that help identify cellular microenvironments affecting cell behaviors and highlight HT screening of biochemical libraries for gene delivery, drug discovery, and toxicological studies. We also discuss HT techniques for the analyses of cell secreted biomolecules and provide perspectives on the future utility of HT approaches in biomedical engineering.
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Affiliation(s)
- Jungmok Seo
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Center for Biomaterials, Korea Institute of Science and Technology, 14 Hwarang-ro, Seongbuk-gu, Seoul, 02792, South Korea
| | - Jung-Youn Shin
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Jeroen Leijten
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Department of Developmental BioEngineering, MIRA Institute for Biomedical Technology and Technical Medicine, University of Twente, Enschede, The Netherlands
| | - Oju Jeon
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Gulden Camci-Unal
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Department of Chemical Engineering, University of Massachusetts Lowell, 1 University Ave, Lowell, MA, 01854-2827, USA
| | - Anna D Dikina
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Katelyn Brinegar
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Amir M Ghaemmaghami
- Division of Immunology, School of Life Sciences, Faculty of Medicine and Health Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Eben Alsberg
- Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH, 44106, USA; Department of Orthopaedic Surgery, Case Western Reserve University, Cleveland, OH, 44106, USA; National Center for Regenerative Medicine, Division of General Medical Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA.
| | - Ali Khademhosseini
- Biomaterials Innovation Research Center, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA, 02139, USA; Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA; Department of Bioindustrial Technologies, College of Animal Bioscience and Technology, Konkuk University, Hwayang-dong, Gwangjin-gu, Seoul, 143-701, Republic of Korea; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA; Department of Physics, King Abdulaziz University, Jeddah, 21569, Saudi Arabia.
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29
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Lederhose P, Abt D, Welle A, Müller R, Barner‐Kowollik C, Blinco JP. Exploiting λ‐Orthogonal Photoligation for Layered Surface Patterning. Chemistry 2017; 24:576-580. [DOI: 10.1002/chem.201705393] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Paul Lederhose
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QLD) 2 George St Brisbane Queensland 4001 Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
| | - Doris Abt
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Alexander Welle
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Rouven Müller
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Christopher Barner‐Kowollik
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QLD) 2 George St Brisbane Queensland 4001 Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - James P. Blinco
- School of Chemistry, Physics and Mechanical Engineering Queensland University of Technology (QLD) 2 George St Brisbane Queensland 4001 Australia
- Macromolecular Architectures, Institut für Technische Chemie und Polymerchemie Karlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
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30
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Aygun U, Avci O, Seymour E, Urey H, Ünlü MS, Ozkumur AY. Label-Free and High-Throughput Detection of Biomolecular Interactions Using a Flatbed Scanner Biosensor. ACS Sens 2017; 2:1424-1429. [PMID: 28929734 DOI: 10.1021/acssensors.7b00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence based microarray detection systems provide sensitive measurements; however, variation of probe immobilization and poor repeatability negatively affect the final readout, and thus quantification capability of these systems. Here, we demonstrate a label-free and high-throughput optical biosensor that can be utilized for calibration of fluorescence microarrays. The sensor employs a commercial flatbed scanner, and we demonstrate transformation of this low cost (∼100 USD) system into an Interferometric Reflectance Imaging Sensor through hardware and software modifications. Using this sensor, we report detection of DNA hybridization and DNA directed antibody immobilization on label-free microarrays with a noise floor of ∼30 pg/mm2, and a scan speed of 5 s (50 s for 10 frames averaged) for a 2 mm × 2 mm area. This novel system may be used as a standalone label-free sensor especially in low-resource settings, as well as for quality control and calibration of microarrays in existing fluorescence-based DNA and protein detection platforms.
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Affiliation(s)
- Ugur Aygun
- Electrical
and Electronics Engineering Department, Koç University, 34450, Sariyer, Istanbul, Turkey
| | | | - Elif Seymour
- Biotechnology
Research Program Department, ASELSAN Research Center, Ankara, 06370, Turkey
| | - Hakan Urey
- Electrical
and Electronics Engineering Department, Koç University, 34450, Sariyer, Istanbul, Turkey
| | | | - Ayca Yalcin Ozkumur
- Department
of Electrical and Electronics Engineering, Bahcesehir University, Istanbul, 34349, Turkey
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31
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Multiple epitope presentation and surface density control enabled by chemoselective immobilization lead to enhanced performance in IgE-binding fingerprinting on peptide microarrays. Anal Chim Acta 2017; 983:189-197. [DOI: 10.1016/j.aca.2017.06.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 06/09/2017] [Accepted: 06/16/2017] [Indexed: 11/17/2022]
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32
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Gourlay L, Peri C, Bolognesi M, Colombo G. Structure and Computation in Immunoreagent Design: From Diagnostics to Vaccines. Trends Biotechnol 2017; 35:1208-1220. [PMID: 28739221 DOI: 10.1016/j.tibtech.2017.06.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 06/28/2017] [Accepted: 06/30/2017] [Indexed: 11/26/2022]
Abstract
Novel immunological tools for efficient diagnosis and treatment of emerging infections are urgently required. Advances in the diagnostic and vaccine development fields are continuously progressing, with reverse vaccinology and structural vaccinology (SV) methods for antigen identification and structure-based antigen (re)design playing increasingly relevant roles. SV, in particular, is predicted to be the front-runner in the future development of diagnostics and vaccines targeting challenging diseases such as AIDS and cancer. We review state-of-the-art methodologies for structure-based epitope identification and antigen design, with specific applicative examples. We highlight the implications of such methods for the engineering of biomolecules with improved immunological properties, potential diagnostic and/or therapeutic uses, and discuss the perspectives of structure-based rational design for the production of advanced immunoreagents.
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Affiliation(s)
- Louise Gourlay
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Claudio Peri
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy
| | - Martino Bolognesi
- Dipartimento di Bioscienze, Università di Milano, Via Celoria 26, 20133, Milan, Italy; Centro di Ricerca Pediatrica Romeo ed Enrica Invernizzi, Università di Milano, Milan, Italy.
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Via Mario Bianco, 9, 20131, Milan, Italy.
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33
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Qiu X, Guo J, Jin Z, Petreto A, Medintz IL, Hildebrandt N. Multiplexed Nucleic Acid Hybridization Assays Using Single-FRET-Pair Distance-Tuning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13. [PMID: 28371153 DOI: 10.1002/smll.201700332] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Indexed: 05/04/2023]
Abstract
Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time-gated (TG) detection of a single terbium-donor-based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single-TG-FRET-pair multiplexing for molecular (Tb-to-dye) and nanoparticle (Tb-to-quantum-dot) biosensing. Both systems use acceptor-sensitization and donor-quenching for quantifying biomolecular recognition and modification of the donor-acceptor distance for tuning the PL decays. TG intensity detection provides extremely low background noise and a quick and simple one-step assay format. Single-TG-FRET-pair multiplexing can be combined with spectral and spatial resolution, paving the way for biosensing with unprecedented high-order multiplexing capabilities.
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Affiliation(s)
- Xue Qiu
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Jiajia Guo
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Zongwen Jin
- CAS/CUHK Research Centre for Biosensing and Medical Instrumentation, SIAT/CAS, Shenzhen, 518055, P. R. China
| | - Alexandra Petreto
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, DC, 20375, USA
| | - Niko Hildebrandt
- NanoBioPhotonics (nanofret.com), Institute for Integrative Biology of the Cell (I2BC), Université Paris-Saclay, Université Paris-Sud, CNRS, CEA, 91405, Orsay Cedex, France
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34
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Bush DB, Knotts TA. Probing the effects of surface hydrophobicity and tether orientation on antibody-antigen binding. J Chem Phys 2017; 146:155103. [DOI: 10.1063/1.4980083] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Derek B. Bush
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
| | - Thomas A. Knotts
- Department of Chemical Engineering, Brigham Young University, Provo, Utah 84602, USA
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35
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Svedberg G, Jeong Y, Na H, Jang J, Nilsson P, Kwon S, Gantelius J, Svahn HA. Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection. LAB ON A CHIP 2017; 17:549-556. [PMID: 28102419 DOI: 10.1039/c6lc01358a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Highly multiplexed point of care tests could improve diagnostic accuracy and differential diagnostic capacity in for instance emergency medicine and low resource environments. Available technology platforms for POC biomarker detection are typically simplex or low-plexed, whereas common lab-based microarray systems allow for the simultaneous detection of thousands of DNA or protein biomarkers. In this study, we demonstrate a novel suspension particle array platform that utilizes 900 μm bricks for POC amenable colorimetric biomarker detection with an encoding capacity of over two million. Due to the mm-scale size, both the lithographic codes and colorimetric signals of individual particles can be visualized using a consumer grade office flatbed scanner, with a potential for simultaneous imaging of around 19 000 particles per scan. The analytical sensitivity of the assay was determined to be 4 ng ml-1 using an antibody model system. As a proof of concept, autoantibodies toward anoctamin 2 were detected in order to discriminate between multiple sclerosis plasma samples and healthy controls with p < 0.0001 and an inter-assay % CV of 9.44%.
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Affiliation(s)
- Gustav Svedberg
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
| | - Yunjin Jeong
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and Institutes of Entrepreneurial BioConvergence, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea
| | - Hunjong Na
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Jisung Jang
- QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Peter Nilsson
- Affinity Proteomics, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden
| | - Sunghoon Kwon
- Department of Electrical and Computer Science, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea. and Institutes of Entrepreneurial BioConvergence, Seoul National University, Daehak-dong, Gwanak-gu, Seoul 151-742, Republic of Korea and QuantaMatrix Inc. 105, B1, Center for medical innovation, Seoul National University Hospital, Daehak-ro, Jongno-gu, Seoul, Republic of Korea
| | - Jesper Gantelius
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
| | - Helene Andersson Svahn
- Division of Proteomics and Nanobiotechnology, Science for Life Laboratory, School of Biotechnology, KTH Royal Institute of Technology, SE-17165 Stockholm, Sweden.
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36
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Longitudinal Analysis of Serum Autoantibody-Reactivities in Patients with Primary Open Angle Glaucoma and Optic Disc Hemorrhage. PLoS One 2016; 11:e0166813. [PMID: 28030545 PMCID: PMC5193360 DOI: 10.1371/journal.pone.0166813] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/04/2016] [Indexed: 11/06/2022] Open
Abstract
Background The aim of our current investigation was to analyze the autoantibody-reactivities of primary open angle glaucoma patients with optic disc hemorrhage as possibly correlated to disease progression by means of a protein microarray approach. Methods Sera of patients with primary open angle glaucoma and optic disc hemorrhage (n = 16) were collected directly after study inclusion (0 weeks) and after 2 weeks, 4 weeks and 12 weeks. As a control group patients with primary open angle glaucoma (n = 18) were used (0 weeks and 12 weeks). Microarrays were incubated and occurring antibody-antigen-reactions were visualized with fluorescence labeled anti-human-IgG secondary antibodies. To detect changes in autoantibodies spot intensities were digitized and compared. Results With respect to the immunoreactivity at 0 weeks level increment of anti-adaptor protein 1 complex subunit mu-1 antibodies and anti-SPRY domain-containing SOCS box protein 3 antibodies in sera of primary open angle patients with optic disc hemorrhage was detected. Linear trend analysis revealed a positive correlation with r ≥ 0.8 between antibody-level and time course. Control group show no relevant changes in the same period. Significant changes were found in time point 4 comparison between patient groups in anti-adaptor protein 1 complex subunit mu-1-level (p = 0.01). No significant changes in visual acuity were found. Conclusion With this approach we were able to detect autoimmune reactivities in sera of patients with primary open angle glaucoma and optic disc hemorrhage compared to patients without optic disc hemorrhage. These antibodies could give further insights into the pathogenesis and the autoimmune component of glaucomatous optic neuropathy.
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37
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Pan L, Aguilar HA, Wang L, Iliuk A, Tao WA. Three-Dimensionally Functionalized Reverse Phase Glycoprotein Array for Cancer Biomarker Discovery and Validation. J Am Chem Soc 2016; 138:15311-15314. [PMID: 27933927 DOI: 10.1021/jacs.6b10239] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Glycoproteins have vast structural diversity that plays an important role in many biological processes and have great potential as disease biomarkers. Here, we report a novel functionalized reverse phase protein array (RPPA), termed polymer-based reverse phase glycoprotein array (polyGPA), to capture and profile glycoproteomes specifically, and validate glycoproteins. Nitrocellulose membrane functionalized with globular hydroxyaminodendrimers was used to covalently capture preoxidized glycans on glycoproteins from complex protein samples such as biofluids. The captured glycoproteins were subsequently detected using the same validated antibodies as in RPPA. We demonstrated the outstanding specificity, sensitivity, and quantitative capabilities of polyGPA by capturing and detecting purified as well as endogenous α-1-acid glycoprotein (AGP) in human plasma. We further applied quantitative N-glycoproteomics and the strategy to validate a panel of glycoproteins identified as potential biomarkers for bladder cancer by analyzing urine glycoproteins from bladder cancer patients or matched healthy individuals.
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Affiliation(s)
| | | | | | - Anton Iliuk
- Tymora Analytical Operations , West Lafayette, Indiana 47906, United States
| | - W Andy Tao
- Tymora Analytical Operations , West Lafayette, Indiana 47906, United States.,Center for Cancer Research, Purdue University , West Lafayette, Indiana 47907, United States
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38
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Zou C, Wang P, Xu Y. Bulked sample analysis in genetics, genomics and crop improvement. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:1941-55. [PMID: 26990124 PMCID: PMC5043468 DOI: 10.1111/pbi.12559] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/09/2016] [Accepted: 03/12/2016] [Indexed: 05/18/2023]
Abstract
Biological assay has been based on analysis of all individuals collected from sample populations. Bulked sample analysis (BSA), which works with selected and pooled individuals, has been extensively used in gene mapping through bulked segregant analysis with biparental populations, mapping by sequencing with major gene mutants and pooled genomewide association study using extreme variants. Compared to conventional entire population analysis, BSA significantly reduces the scale and cost by simplifying the procedure. The bulks can be built by selection of extremes or representative samples from any populations and all types of segregants and variants that represent wide ranges of phenotypic variation for the target trait. Methods and procedures for sampling, bulking and multiplexing are described. The samples can be analysed using individual markers, microarrays and high-throughput sequencing at all levels of DNA, RNA and protein. The power of BSA is affected by population size, selection of extreme individuals, sequencing strategies, genetic architecture of the trait and marker density. BSA will facilitate plant breeding through development of diagnostic and constitutive markers, agronomic genomics, marker-assisted selection and selective phenotyping. Applications of BSA in genetics, genomics and crop improvement are discussed with their future perspectives.
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Affiliation(s)
- Cheng Zou
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Pingxi Wang
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yunbi Xu
- Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, China.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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39
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Decrop D, Brans T, Gijsenbergh P, Lu J, Spasic D, Kokalj T, Beunis F, Goos P, Puers R, Lammertyn J. Optical Manipulation of Single Magnetic Beads in a Microwell Array on a Digital Microfluidic Chip. Anal Chem 2016; 88:8596-603. [PMID: 27448015 DOI: 10.1021/acs.analchem.6b01734] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The detection of single molecules in magnetic microbead microwell array formats revolutionized the development of digital bioassays. However, retrieval of individual magnetic beads from these arrays has not been realized until now despite having great potential for studying captured targets at the individual level. In this paper, optical tweezers were implemented on a digital microfluidic platform for accurate manipulation of single magnetic beads seeded in a microwell array. Successful optical trapping of magnetic beads was found to be dependent on Brownian motion of the beads, suggesting a 99% chance of trapping a vibrating bead. A tailor-made experimental design was used to screen the effect of bead type, ionic buffer strength, surfactant type, and concentration on the Brownian activity of beads in microwells. With the optimal conditions, the manipulation of magnetic beads was demonstrated by their trapping, retrieving, transporting, and repositioning to a desired microwell on the array. The presented platform combines the strengths of digital microfluidics, digital bioassays, and optical tweezers, resulting in a powerful dynamic microwell array system for single molecule and single cell studies.
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Affiliation(s)
- Deborah Decrop
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Toon Brans
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Pieter Gijsenbergh
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jiadi Lu
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Dragana Spasic
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Tadej Kokalj
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
| | - Filip Beunis
- Department of Electronics and Information Systems (ELIS) and Center for Nano and Biophotonics (NB-Photonics), UGent , Sint-Pietersnieuwstraat 41, 9000 Gent, Belgium
| | - Peter Goos
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium.,Faculty of Applied Economics, University of Antwerp, Stadscampus , Prinsstraat 13, 2000 Antwerp, Belgium
| | - Robert Puers
- Department of Electrotechnical Engineering (ESAT-MICAS), KU Leuven , Kasteelpark Arenberg 10 Postbus 2440, 3001 Leuven, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, MEBIOS-Biosensors, KU Leuven , Willem de Croylaan 42, 3001 Leuven, Belgium
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40
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Pla-Roca M, Altay G, Giralt X, Casals A, Samitier J. Design and development of a microarray processing station (MPS) for automated miniaturized immunoassays. Biomed Microdevices 2016; 18:64. [PMID: 27405464 DOI: 10.1007/s10544-016-0087-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Here we describe the design and evaluation of a fluidic device for the automatic processing of microarrays, called microarray processing station or MPS. The microarray processing station once installed on a commercial microarrayer allows automating the washing, and drying steps, which are often performed manually. The substrate where the assay occurs remains on place during the microarray printing, incubation and processing steps, therefore the addressing of nL volumes of the distinct immunoassay reagents such as capture and detection antibodies and samples can be performed on the same coordinate of the substrate with a perfect alignment without requiring any additional mechanical or optical re-alignment methods. This allows the performance of independent immunoassays in a single microarray spot.
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Affiliation(s)
- Mateu Pla-Roca
- Nanobioengineering Laboratory, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac, 10-12, 08028, Barcelona, Spain.
| | - Gizem Altay
- Nanobioengineering Laboratory, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac, 10-12, 08028, Barcelona, Spain
| | - Xavier Giralt
- Robotics Laboratory, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac, 10-12, 08028, Barcelona, Spain
| | - Alícia Casals
- Robotics Laboratory, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac, 10-12, 08028, Barcelona, Spain.,Center of Research in Biomedical Engineering, Universitat Politècnica de Catalunya, Jordi Girona, 1-3, 08034, Barcelona, Spain
| | - Josep Samitier
- Nanobioengineering Laboratory, Institute for Bioengineering of Catalonia (IBEC), Baldiri Reixac, 10-12, 08028, Barcelona, Spain.,The Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Maria de Luna, 11, 50018, Zaragoza, Spain.,Department of Engineering: Electronics, University of Barcelona (UB), Martí i Franquès, 1, 08028, Barcelona, Spain
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Katchman BA, Smith JT, Obahiagbon U, Kesiraju S, Lee YK, O'Brien B, Kaftanoglu K, Blain Christen J, Anderson KS. Application of flat panel OLED display technology for the point-of-care detection of circulating cancer biomarkers. Sci Rep 2016; 6:29057. [PMID: 27374875 PMCID: PMC4931450 DOI: 10.1038/srep29057] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 06/10/2016] [Indexed: 01/07/2023] Open
Abstract
Point-of-care molecular diagnostics can provide efficient and cost-effective medical care, and they have the potential to fundamentally change our approach to global health. However, most existing approaches are not scalable to include multiple biomarkers. As a solution, we have combined commercial flat panel OLED display technology with protein microarray technology to enable high-density fluorescent, programmable, multiplexed biorecognition in a compact and disposable configuration with clinical-level sensitivity. Our approach leverages advances in commercial display technology to reduce pre-functionalized biosensor substrate costs to pennies per cm2. Here, we demonstrate quantitative detection of IgG antibodies to multiple viral antigens in patient serum samples with detection limits for human IgG in the 10 pg/mL range. We also demonstrate multiplexed detection of antibodies to the HPV16 proteins E2, E6, and E7, which are circulating biomarkers for cervical as well as head and neck cancers.
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Affiliation(s)
- Benjamin A Katchman
- Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281 USA
| | - Joseph T Smith
- Flexible Electronics and Display Center at Arizona State University, Tempe, AZ 85284 USA
| | - Uwadiae Obahiagbon
- School of Electrical Engineering at Arizona State University, Tempe, AZ 85281 USA
| | - Sailaja Kesiraju
- Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281 USA
| | - Yong-Kyun Lee
- Flexible Electronics and Display Center at Arizona State University, Tempe, AZ 85284 USA
| | - Barry O'Brien
- Flexible Electronics and Display Center at Arizona State University, Tempe, AZ 85284 USA
| | - Korhan Kaftanoglu
- Flexible Electronics and Display Center at Arizona State University, Tempe, AZ 85284 USA
| | | | - Karen S Anderson
- Center for Personalized Diagnostics, Biodesign Institute at Arizona State University, Tempe, AZ 85281 USA
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Schumacher S, Seitz H. Quality control of antibodies for assay development. N Biotechnol 2016; 33:544-50. [PMID: 26873787 DOI: 10.1016/j.nbt.2016.02.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 01/12/2016] [Accepted: 02/03/2016] [Indexed: 01/19/2023]
Abstract
Antibodies are used as powerful tools in basic research, for example, in biomarker identification, and in various forms for diagnostics, for example, identification of allergies or autoimmune diseases. Due to their robustness and ease of handling, immunoassays are favourite methods for investigation of various biological or medical questions. Nevertheless in many cases, additional analyses such as mass spectrometry are used to validate or confirm the results of immunoassays. To minimize the workload and to increase confidence in immunoassays, there are urgent needs for antibodies which are both highly specific and well validated. Unfortunately many commercially available antibodies are neither well characterized nor fully tested for cross-reactivities. Adequate quality control and validation of an antibody is time-consuming and can be frustrating. Such validation needs to be performed for every assay/application. However, where an antibody validation is successful, a highly specific and stable reagent will be on hand. This article describes the validation processes of antibodies, including some often neglected factors, as well as unspecific binding to other sample compounds in a multiparameter diagnostic assay. The validation consists of different immunological methods, with important assay controls, and is performed in relation to the development of a diagnostic test.
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Affiliation(s)
- Sarah Schumacher
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics und Bioprocesses, Am Mühlenberg 13, 14476 Potsdam, Germany; Humboldt University Berlin, Department of Biology, Invalidenstr. 110, 10115 Berlin, Germany
| | - Harald Seitz
- Fraunhofer Institute for Cell Therapy and Immunology - Bioanalytics und Bioprocesses, Am Mühlenberg 13, 14476 Potsdam, Germany.
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De-Simone SG, Napoleão-Pêgo P, De-Simone TS. Spot Synthesis: An Optimized Microarray to Detect IgE Epitopes. Methods Mol Biol 2016; 1352:263-77. [PMID: 26490482 DOI: 10.1007/978-1-4939-3037-1_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Peptide microarrays have become increasingly more affordable in recent years with the SPOT technique being one of the most frequently used methods for synthesis and screening of peptides in arrays. Here, a protocol is presented for the identification of the amino acid sites involved in the conversion of human IgG to IgE response during the passive administration of therapeutic, anti-snake venom sera. Similarly, the minimal region of both the IgG and IgE binding epitopes, important for its interaction with ligand, were identified. As the ratio of concentrations for IgG to IgE in human serum is 1:10,000, also presented is a reproductive protocol of chemiluminescence-scanning for the detection of both immunoglobulins.
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Affiliation(s)
- Salvatore G De-Simone
- FIOCRUZ, Center of Technological Development in Health (CDTS) / National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN), FIOCRUZ, Rio de Janeiro, Brazil.
| | - Paloma Napoleão-Pêgo
- Department of Cellular andMolecularBiology, Federal FluminenseUniversity,Biology Institute, Niterói, Rio de Janeiro, Brazil
| | - Thatiane S De-Simone
- IOCRUZ, Center of Technological Development in Health (CDTS) / National Institute of Science and Technology for Innovation on Neglected Diseases (INCT-IDN) FIOCRUZ, Rio de Janeiro, Brazil
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Shi L, Gehin T, Chevolot Y, Souteyrand E, Mangé A, Solassol J, Laurenceau E. Anti-heat shock protein autoantibody profiling in breast cancer using customized protein microarray. Anal Bioanal Chem 2015; 408:1497-506. [DOI: 10.1007/s00216-015-9257-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/30/2015] [Accepted: 12/07/2015] [Indexed: 10/22/2022]
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46
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Gagni P, Cretich M, Benussi L, Tonoli E, Ciani M, Ghidoni R, Santini B, Galbiati E, Prosperi D, Chiari M. Combined mass quantitation and phenotyping of intact extracellular vesicles by a microarray platform. Anal Chim Acta 2015; 902:160-167. [PMID: 26703266 DOI: 10.1016/j.aca.2015.10.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 10/08/2015] [Accepted: 10/14/2015] [Indexed: 12/25/2022]
Abstract
The interest towards extracellular vesicles (EVs) has grown exponentially over the last few years; being involved in intercellular communication and serving as reservoirs for biomarkers for tumors, they have a great potential for liquid biopsy development, possibly replacing many costly and invasive tissue biopsies. Here we propose, for the first time, the use of a Si/SiO2 interferometric, microarray platform for multiparametric intact EVs analysis combining label-free EVs mass quantitation and high sensitivity fluorescence based phenotyping. Label free interferometric measurement allows to quantify the amount of vesicles captured by printed antibodies while, on the same chip, EVs are also detected by fluorescence in a sandwich immunoassay. The proposed method simultaneously detects, quantify and phenotype intact EVs in a microarray format.
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Affiliation(s)
- Paola Gagni
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Italy
| | - Marina Cretich
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Italy.
| | - Luisa Benussi
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Elisa Tonoli
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Miriam Ciani
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Roberta Ghidoni
- Molecular Markers Laboratory, IRCCS Istituto Centro San Giovanni di Dio Fatebenefratelli, Brescia, Italy
| | - Benedetta Santini
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Elisabetta Galbiati
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Davide Prosperi
- NanoBioLab, Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milano, Italy
| | - Marcella Chiari
- Consiglio Nazionale delle Ricerche, Istituto di Chimica del Riconoscimento Molecolare (ICRM), Italy
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Chimeric peptide constructs comprising linear B-cell epitopes: application to the serodiagnosis of infectious diseases. Sci Rep 2015; 5:13364. [PMID: 26293607 PMCID: PMC4543967 DOI: 10.1038/srep13364] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 07/27/2015] [Indexed: 01/07/2023] Open
Abstract
Linear B-cell epitopes are ideal biomarkers for the serodiagnosis of infectious diseases. However, the long-predicted diagnostic value of epitopes has not been realized. Here, we demonstrated a method, diagnostic epitopes in four steps (DEIFS), that delivers a combination of epitopes for the serodiagnosis of infectious diseases with a high success rate. Using DEIFS for malaria, we identified 6 epitopes from 8 peptides and combined them into 3 chimeric peptide constructs. Along with 4 other peptides, we developed a rapid diagnostic test (RDT), which is able to differentiate Plasmodium falciparum (P. falciparum) from Plasmodium vivax (P. vivax) infections with 95.6% overall sensitivity and 99.1% overall specificity. In addition to applications in diagnosis, DEIFS could also be used in the diagnosis of virus and bacterium infections, discovery of vaccine candidates, evaluation of vaccine potency, and study of disease progression.
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Díaz-González M, Salvador JP, Bonilla D, Marco MP, Fernández-Sánchez C, Baldi A. A microfluidic device for the automated electrical readout of low-density glass-slide microarrays. Biosens Bioelectron 2015. [PMID: 26210466 DOI: 10.1016/j.bios.2015.07.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microarrays are a powerful platform for rapid and multiplexed analysis in a wide range of research fields. Electrical readout systems have emerged as an alternative to conventional optical methods for microarray analysis thanks to its potential advantages like low-cost, low-power and easy miniaturization of the required instrumentation. In this work an automated electrical readout system for low-cost glass-slide microarrays is described. The system enables the simultaneous conductimetric detection of up to 36 biorecognition events by incorporating an array of interdigitated electrode transducers. A polydimethylsiloxane microfluidic structure has been designed that creates microwells over the transducers and incorporates the microfluidic channels required for filling and draining them with readout and cleaning solutions, thus making the readout process fully automated. Since the capture biomolecules are not immobilized on the transducer surface this readout system is reusable, in contrast to previously reported electrochemical microarrays. A low-density microarray based on a competitive enzymatic immunoassay for atrazine detection was used to test the performance of the readout system. The electrical assay shows a detection limit of 0.22±0.03 μg L(-1) similar to that obtained with fluorescent detection and allows the direct determination of the pesticide in polluted water samples. These results proved that an electrical readout system such as the one presented in this work is a reliable and cost-effective alternative to fluorescence scanners for the analysis of low-density microarrays.
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Affiliation(s)
- María Díaz-González
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Spain.
| | - J Pablo Salvador
- Nanobiotechnology for Diagnostics (Nb4D) Group, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - Diana Bonilla
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - M Pilar Marco
- Nanobiotechnology for Diagnostics (Nb4D) Group, IQAC-CSIC, Jordi Girona 18-26, 08034 Barcelona, Spain
| | - César Fernández-Sánchez
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Antoni Baldi
- Instituto de Microelectrónica de Barcelona, IMB-CNM (CSIC), Campus UAB, 08193 Bellaterra, Barcelona, Spain
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Huang M, Ma Q, Liu X, Li B, Ma H. Initiator Integrated Poly(dimethysiloxane)-Based Microarray as a Tool for Revealing the Relationship between Nonspecific Interactions and Irreproducibility. Anal Chem 2015; 87:7085-91. [PMID: 26095857 DOI: 10.1021/acs.analchem.5b00694] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nonspecific interactions (NSIs) and irreproducibility greatly reduce the accuracy of antigen-antibody screening, which is key to the discovery of monoclonal antibody drugs and biomarkers identification. We previously developed a solid supporting material, polymer-coated initiator integrated poly(dimethysiloxane) (iPDMS), which is able to provide near-zero background for microarray screening. Here, we applied two monoclonal antibodies (mAbs), namely, anti-FLAG and HM1, to screen an iPDMS-based peptide microarray with 2083 peptides from 62 proteins to evaluate NSIs and irreproducibility. In addition to recognizing their cognate epitopes, the two mAbs also cross-reacted with random sequences, especially when they were used at high concentrations. At 50 μg mL(-1), 295 peptides (14.2% of the peptide library) had positive reactions to anti-FLAG and only 39 peptides (1.9%) reacted positively to HM1. Virtually all cross-reactions disappeared when the [mAbs] reached 0.01 μg mL(-1). Reproducible experiments of 404 peptides at various [mAbs] showed that only specific interactions, molecular mimicry, and mimotope were reproducible between different experiments. These findings suggest that irreproducibility was at least partially caused by NSIs. We also demonstrated that repeating tests and mAb dilution could effectively avoid NSI-related irreproducibility in serological screening. This will not only largely simplify the data analysis, but will also make immunoassays more reliable for clinical research.
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Affiliation(s)
- Mo Huang
- †Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, People's Republic of China.,‡University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Qing Ma
- †Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, People's Republic of China.,‡University of Chinese Academy of Sciences, Beijing, 100039, People's Republic of China
| | - Xing Liu
- †Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, People's Republic of China
| | - Boan Li
- §Center of Lab Test, 302 Military Hospital, Beijing, 100039, People's Republic of China
| | - Hongwei Ma
- †Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, 215123, People's Republic of China
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50
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Yeat NC, Lin C, Sager M, Lin J. Cancer proteomics: developments in technology, clinical use and commercialization. Expert Rev Proteomics 2015; 12:391-405. [PMID: 26145529 DOI: 10.1586/14789450.2015.1051969] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In the last two decades, advances in genomic, transcriptomic and proteomic methods have enabled us to identify and classify cancers by their molecular profiles. Many anticipate that a molecular taxonomy of cancer will not only lead to more effective subtyping of cancers but also earlier diagnoses, more informative prognoses and more targeted treatments. This article reviews recent technological developments in the field of proteomics, recent discoveries in proteomic cancer biomarker research and trends in clinical use. Readers are also informed of examples of successful commercialization, and the future of proteomics in cancer diagnostics.
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Affiliation(s)
- Nai Chien Yeat
- Rare Genomics Institute, 4100 Forest Park, St. Louis, MO 63108, USA
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