1
|
Martínez-Botas J, Fernández-Lozano C, Vaquero-Rey A, de la Hoz B. IgE and IgG4 Epitope Mapping of Food Allergens with a Peptide Microarray Immunoassay. Methods Mol Biol 2023; 2578:219-236. [PMID: 36152291 DOI: 10.1007/978-1-0716-2732-7_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Peptide microarrays are a powerful tool to identify linear epitopes of food allergens in a high-throughput manner. The main advantages of the microarray-based immunoassay are as follows: the possibility to assay thousands of targets simultaneously, the requirement of a low volume of serum, the more robust statistical analysis, and the possibility to test simultaneously several immunoglobulin subclasses. Among them, the last one has a special interest in the field of food allergy, because the development of tolerance to food allergens has been associated with a decrease in IgE and an increase in IgG4 levels against linear epitopes. However, the main limitation to the clinical use of microarray is the automated analysis of the data. Recent studies mapping the linear epitopes of food allergens with peptide microarray immunoassays have identified peptide biomarkers that can be used for early diagnosis of food allergies and to predict their severity or the self-development of tolerance. Using this approach, we have worked on epitope mapping of the two most important food allergens in the Spanish population, cow's milk, and chicken eggs. The final aim of these studies is to define subsets of peptides that could be used as biomarkers to improve the diagnosis and prognosis of food allergies. This chapter describes the protocol to produce microarrays using a library of overlapping peptides corresponding to the primary sequences of food allergens and data acquisition and analysis of IgE and IgG4 binding epitopes.
Collapse
Affiliation(s)
- Javier Martínez-Botas
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - Unidad de Microarray IRYCIS, Madrid, Spain.
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN) - Instituto de la Salud Carlos III, Madrid, Spain.
| | - Carlos Fernández-Lozano
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - Unidad de Microarray IRYCIS, Madrid, Spain
| | - Aida Vaquero-Rey
- Servicio de Alergología, Hospital Universitario Ramón y Cajal - Unidad de Microarray IRYCIS, Madrid, Spain
| | - Belén de la Hoz
- Servicio de Alergología, Hospital Universitario Ramón y Cajal - Unidad de Microarray IRYCIS, Madrid, Spain
- Red de Alergia ARADyAL (RD16/0006/0009) - Instituto de la Salud Carlos III, Madrid, Spain
| |
Collapse
|
2
|
Martínez-Botas J, Fernández-Lozano C, Rodríguez-Alonso A, Sánchez-Ruano L, de la Hoz B. Epitope Mapping of Food Allergens Using Noncontact Piezoelectric Microarray Printer. Methods Mol Biol 2021; 2344:119-135. [PMID: 34115356 DOI: 10.1007/978-1-0716-1562-1_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Peptide microarrays have been used to study protein-protein interaction, enzyme-substrate profiling, epitope mapping, vaccine development, and immuno-profiling. Unlike proteins, peptides are cheap to produce, and can be produced in a high-throughput manner, in a reliable and consistent procedure that reduces batch-to-batch variability. All this provides the peptide microarrays a great potential in the development of new diagnostic tools. Noncontact printing, such as piezoelectric systems, results in a considerable advance in protein and peptide microarray production. In particular, they improve drop deposition, sample distribution, quality control, and flexibility in substrate deposition and eliminate cross-contamination and carryover. These features contribute to creating reproducible assays and generating more reliable data. Here we describe the methods and materials for epitope mapping of food allergens using peptide microarrays produced with a noncontact piezoelectric microarray printer.
Collapse
Affiliation(s)
- Javier Martínez-Botas
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - IRYCIS, Madrid, Spain.
- CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN), Instituto de Salud Carlos III, Madrid, Spain.
| | - Carlos Fernández-Lozano
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - IRYCIS, Madrid, Spain
| | - Alberto Rodríguez-Alonso
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - IRYCIS, Madrid, Spain
| | - Laura Sánchez-Ruano
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal - IRYCIS, Madrid, Spain
| | - Belén de la Hoz
- Servicio de Alergología, Hospital Universitario Ramón y Cajal - IRYCIS, Madrid, Spain
| |
Collapse
|
3
|
Mizuno S, Ogishima S, Kitatani K, Kikuchi M, Tanaka H, Yaegashi N, Nakaya J. Network Analysis of a Comprehensive Knowledge Repository Reveals a Dual Role for Ceramide in Alzheimer's Disease. PLoS One 2016; 11:e0148431. [PMID: 26849355 PMCID: PMC4752297 DOI: 10.1371/journal.pone.0148431] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/18/2016] [Indexed: 12/13/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common cause of senile dementia. Many inflammatory factors such as amyloid-β and pro-inflammatory cytokines are known to contribute to the inflammatory response in the AD brain. Sphingolipids are widely known to have roles in the pathogenesis of inflammatory diseases, where the precise roles for sphingolipids in inflammation-associated pathogenesis of AD are not well understood. Here we performed a network analysis to clarify the importance of sphingolipids and to model relationships among inflammatory factors and sphingolipids in AD. In this study, we have updated sphingolipid signaling and metabolic cascades in a map of AD signaling networks that we named “AlzPathway,” a comprehensive knowledge repository of signaling pathways in AD. Our network analysis of the updated AlzPathway indicates that the pathways related to ceramide are one of the primary pathways and that ceramide is one of the important players in the pathogenesis of AD. The results of our analysis suggest the following two prospects about inflammation in AD: (1) ceramide could play important roles in both inflammatory and anti-inflammatory pathways of AD, and (2) several factors such as Sphingomyelinase and Siglec-11 may be associated with ceramide related inflammation and anti-inflammation pathways in AD. In this study, network analysis of comprehensive knowledge repository reveals a dual role for ceramide in AD. This result provides a clue to clarify sphingolipids related inflammatory and anti-inflammatory pathways in AD.
Collapse
Affiliation(s)
- Satoshi Mizuno
- Department of Clinical Informatics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
- Department of Clinical Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- * E-mail: (SM); (SO)
| | - Soichi Ogishima
- Department of Clinical Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
- * E-mail: (SM); (SO)
| | - Kazuyuki Kitatani
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Masataka Kikuchi
- Department of Genome Informatics, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Hiroshi Tanaka
- Department of Clinical Record Informatics, Tohoku Medical Megabank Organization, Tohoku University, Sendai, Miyagi, Japan
| | - Nobuo Yaegashi
- Department of Gynecology and Obstetrics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Jun Nakaya
- Department of Clinical Informatics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| |
Collapse
|
4
|
Martínez-Botas J, de la Hoz B. IgE and IgG4 Epitope Mapping of Food Allergens with a Peptide Microarray Immunoassay. Methods Mol Biol 2016; 1352:235-249. [PMID: 26490480 DOI: 10.1007/978-1-4939-3037-1_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Peptide microarrays are a powerful tool to identify linear epitopes of food allergens in a high-throughput manner. The main advantages of the microarray-based immunoassay are the possibility to assay thousands of targets simultaneously, the requirement of a low volume of serum, the more robust statistical analysis, and the possibility to test simultaneously several immunoglobulin subclasses. Among them, the last one has a special interest in the field of food allergy, because the development of tolerance to food allergens has been associated with a decrease in IgE and an increase in IgG4 levels against linear epitopes. However, the main limitation to the clinical use of microarray is the automated analysis of the data. Recent studies mapping the linear epitopes of food allergens with peptide microarray immunoassays have identified peptide biomarkers that can be used for early diagnosis of food allergies and to predict their severity or the self-development of tolerance. Using this approach, we have worked on epitope mapping of the two most important food allergens in the Spanish population, cow's milk and chicken eggs. The final aim of these studies is to define subsets of peptides that could be used as biomarkers to improve the diagnosis and prognosis of food allergies. This chapter describes the protocol to produce microarrays using a library of overlapping peptides corresponding to the primary sequences of food allergens and data acquisition and analysis of IgE- and IgG4-binding epitopes.
Collapse
Affiliation(s)
- Javier Martínez-Botas
- Servicio de Bioquímica-Investigación, Hospital Universitario Ramón y Cajal-IRYCIS and CIBER de Fisiopatología de la Obesidad y Nutrición (CIBEROBN)-Instituto de Salud Carlos III, Carretera de Colmenar Km 9, Madrid, 28034, Spain.
| | - Belén de la Hoz
- Servicio de Alergología, Hospital Universitario Ramón y Cajal-IRYCIS, Madrid, Spain
| |
Collapse
|
5
|
Sanghavi BJ, Moore JA, Chávez JL, Hagen JA, Kelley-Loughnane N, Chou CF, Swami NS. Aptamer-functionalized nanoparticles for surface immobilization-free electrochemical detection of cortisol in a microfluidic device. Biosens Bioelectron 2015; 78:244-252. [PMID: 26618642 DOI: 10.1016/j.bios.2015.11.044] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 10/21/2015] [Accepted: 11/14/2015] [Indexed: 12/26/2022]
Abstract
Monitoring the periodic diurnal variations in cortisol from small volume samples of serum or saliva is of great interest, due to the regulatory role of cortisol within various physiological functions and stress symptoms. Current detection assays are immunologically based and require cumbersome antibody immobilization chemistries, thereby limiting the assay versatility, kinetics, and reproducibility. We present a quantitative aptamer-based detection methodology for cortisol that does not require target labeling, capture probe immobilization on the detection surface or wash steps prior to readout. Using a recognition system of aptamer functionalized gold nanoparticles pre-bound with electro-active triamcinolone, the cortisol level is detected based on its competitive binding to the aptamer by following signal from the displaced triamcinolone using square wave voltammetry at patterned graphene-modified electrodes in a microfluidic or nanoslit device. Due to the 3D analyte diffusion profile at the aptamer interface and the ability to enhance the surface area for cortisol capture, this assay shows signal linearity over a five-log analyte concentration range (10 μg/mL to 30 pg/mL) and exhibits rapid binding kinetics with cortisol versus other glucocorticoids, as apparent from the absence of interferences from estradiol, testosterone and progesterone. The assay is carried out within the biologically relevant range for glucocorticoids in serum and saliva matrices, and benchmarked versus ELISA and radioimmunoassays. Based on absence of cumbersome surface immobilization and wash steps for carrying out this assay, its quantitative signal characteristics and its ability to resist interferences from other glucocorticoids, we envision its application towards routine monitoring of cortisol within bio-fluids.
Collapse
Affiliation(s)
- Bankim J Sanghavi
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - John A Moore
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA
| | - Jorge L Chávez
- Air Force Research Laboratory, Human Effectiveness Directorate, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Joshua A Hagen
- Air Force Research Laboratory, Human Effectiveness Directorate, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Nancy Kelley-Loughnane
- Air Force Research Laboratory, Human Effectiveness Directorate, 711th Human Performance Wing, Wright-Patterson Air Force Base, Dayton, OH 45433, USA
| | - Chia-Fu Chou
- Institute of Physics, Academia Sinica, Taipei-11529, Taiwan
| | - Nathan S Swami
- Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904, USA.
| |
Collapse
|