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Srisuwatchari W, Suárez-Fariñas M, Delgado AD, Grishina G, Suprun M, Sang Eun Lee A, Vichyanond P, Pacharn P, Sampson HA. Utility of epitope-specific IgE, IgG4, and IgG1 antibodies for the diagnosis of wheat allergy. J Allergy Clin Immunol 2024:S0091-6749(24)00821-2. [PMID: 39154658 DOI: 10.1016/j.jaci.2024.08.003] [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: 03/31/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
BACKGROUND The bead-based epitope assay has been used to identify epitope-specific (es) antibodies and successfully used to diagnose clinical allergy to milk, egg, and peanut. OBJECTIVE We sought to identify es-IgE, es-IgG4, and es-IgG1 of wheat proteins and determine the optimal peptides to differentiate wheat-allergic from wheat-tolerant using the bead-based epitope assay. METHODS Children and adolescents who underwent an oral food challenge to confirm their wheat allergy status were enrolled. Seventy-nine peptides from α-/β-gliadin, γ-gliadin, ω-5-gliadin, and high- and low-molecular-weight glutenin were commercially synthesized and coupled to LumAvidin beads (Luminex Corporation, Austin, Tex). Machine learning methods were used to identify diagnostic epitopes, and performance was evaluated using the DeLong test. RESULTS The analysis included 122 children (83 wheat-allergic and 39 wheat-tolerant; 57.4% male). Machine learning coupled with simulations identified wheat es-IgE, but not es-IgG4 or es-IgG1, to be the most informative for diagnosing wheat allergy. Higher es-IgE binding intensity correlated with the severity of allergy phenotypes, with wheat anaphylaxis exhibiting the highest es-IgE binding intensity. In contrast, wheat-dependent exercise-induced anaphylaxis showed lower es-IgG1 binding intensity than did all the other groups. A set of 4 informative epitopes from ω-5-gliadin and γ-gliadin were the best predictors of wheat allergy, with an area under the curve of 0.908 (sensitivity, 83.4%; specificity, 88.4%), higher than the performance exhibited by wheat-specific IgE (area under the curve = 0.646; P < .001). The predictive ability of our model was confirmed in an external cohort of 71 patients (29 allergic, 42 nonallergic), with an area under the curve of 0.908 (sensitivity, 75.9%; specificity, 90.5%). CONCLUSIONS The wheat bead-based epitope assay demonstrated greater diagnostic accuracy compared with existing specific IgE tests for wheat allergy.
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Affiliation(s)
- Witchaya Srisuwatchari
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Mayte Suárez-Fariñas
- Department of Population Health Science & Policy, Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Andrew D Delgado
- Department of Population Health Science & Policy, Center for Biostatistics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Galina Grishina
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Maria Suprun
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Ashley Sang Eun Lee
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Pakit Vichyanond
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand; Samitivej Allergy Institute, Samitivej Thonburi Hospital, Bangkok, Thailand
| | - Punchama Pacharn
- Division of Allergy and Immunology, Department of Pediatrics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Hugh A Sampson
- Division of Allergy and Immunology, Department of Pediatrics, Jaffe Food Allergy Institute, Icahn School of Medicine at Mount Sinai, New York, NY.
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Lu M, Jiang H, Wang R, An S, Wang J, Yu C. Injectiondesign: web service of plate design with optimized stratified block randomization for modern GC/LC-MS-based sample preparation. BMC Bioinformatics 2023; 24:489. [PMID: 38124029 PMCID: PMC10734102 DOI: 10.1186/s12859-023-05598-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Plate design is a necessary and time-consuming operation for GC/LC-MS-based sample preparation. The implementation of the inter-batch balancing algorithm and the intra-batch randomization algorithm can have a significant impact on the final results. For researchers without programming skills, a stable and efficient online service for plate design is necessary. RESULTS Here we describe InjectionDesign, a free online plate design service focused on GC/LC-MS-based multi-omics experiment design. It offers the ability to separate the position design from the sequence design, making the output more compatible with the requirements of a modern mass spectrometer-based laboratory. In addition, it has implemented an optimized block randomization algorithm, which can be better applied to sample stratification with block randomization for an unbalanced distribution. It is easy to use, with built-in support for common instrument models and quick export to a worksheet. CONCLUSIONS InjectionDesign is an open-source project based on Java. Researchers can get the source code for the project from Github: https://github.com/CSi-Studio/InjectionDesign . A free web service is also provided: http://www.injection.design .
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Affiliation(s)
- Miaoshan Lu
- Zhejiang University, Hangzhou, Zhejiang, China
- School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Hengxuan Jiang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Ruimin Wang
- School of Engineering, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Institute of Advanced Technology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Fudan University, Shanghai, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Shaowei An
- School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Institute of Biology, Westlake Institute for Advanced Study, 18 Shilongshan Road, Hangzhou, 310024, Zhejiang, China
- Fudan University, Shanghai, China
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Jiawei Wang
- Carbon Silicon (Hangzhou) Biotechnology Co., Ltd, Hangzhou, China
| | - Changbin Yu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China.
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Suprun M, Kearney P, Hayward C, Butler H, Getts R, Sicherer SH, Turner PJ, Campbell DE, Sampson HA. Predicting probability of tolerating discrete amounts of peanut protein in allergic children using epitope-specific IgE antibody profiling. Allergy 2022; 77:3061-3069. [PMID: 35960650 DOI: 10.1111/all.15477] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 06/14/2022] [Accepted: 06/17/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND IgE-epitope profiling can accurately diagnose clinical peanut allergy. OBJECTIVE We sought to determine whether sequential (linear) epitope-specific IgE (ses-IgE) profiling can provide probabilities of tolerating discrete doses of peanut protein in allergic subjects undergoing double-blind, placebo-controlled food challenges utilizing PRACTALL dosing. METHODS Sixty four ses-IgE antibodies were quantified in blood samples using a bead-based epitope assay. A pair of ses-IgEs that predicts Cumulative Tolerated Dose (CTD) was determined using regression in 75 subjects from the discovery cohort. This epitope-based predictor was validated on 331 subjects from five independent cohorts (ages 4-25 years). Subjects were grouped based on their predicted values and probabilities of reactions at each CTD threshold were calculated. RESULTS In discovery, an algorithm using two ses-IgE antibodies was correlated with CTDs (rho = 0.61, p < .05); this correlation was 0.51 (p < .05) in validation. Using the ses-IgE-based predictor, subjects were assigned into "high," "moderate," or "low" dose-reactivity groups. On average, subjects in the "high" group were four times more likely to tolerate a specific dose, compared with the "low" group. For example, predicted probabilities of tolerating 4, 14, 44, and 144 or 444 mg in the "low" group were 92%, 77%, 53%, 29%, and 10% compared with 98%, 95%, 94%, 88%, and 73% in the "high" group. CONCLUSIONS Accurate predictions of food challenge thresholds are complex due to factors including limited responder sample sizes at each dose and variations in study-specific challenge protocols. Despite these limitations, an epitope-based predictor was able to accurately identify CTDs and may provide a useful surrogate for peanut challenges.
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Affiliation(s)
- Maria Suprun
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | | | | | | | | | - Scott H Sicherer
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Paul J Turner
- National Heart & Lung Institute, Imperial College London, England, UK
| | | | - Hugh A Sampson
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
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Suárez‐Fariñas M, Suprun M, Kearney P, Getts R, Grishina G, Hayward C, Luta D, Porter A, Witmer M, du Toit G, Lack G, Chinthrajah RS, Galli SJ, Nadeau K, Sampson HA. Accurate and reproducible diagnosis of peanut allergy using epitope mapping. Allergy 2021; 76:3789-3797. [PMID: 33991353 PMCID: PMC8607840 DOI: 10.1111/all.14905] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 04/19/2021] [Accepted: 04/25/2021] [Indexed: 01/18/2023]
Abstract
BACKGROUND Accurate diagnosis of peanut allergy is a significant clinical challenge. Here, a novel diagnostic blood test using the peanut bead-based epitope assay ("peanut BBEA") was developed utilizing the LEAP cohort and then validated using two independent cohorts. METHODS The development of the peanut BBEA diagnostic test followed the National Academy of Medicine's established guidelines with discovery performed on 133 subjects from the non-interventional arm of the LEAP trial and an independent validation performed on 82 subjects from the CoFAR2 and 84 subjects from the POISED study. All samples were analyzed using the peanut BBEA methodology, which measures levels of IgE to two Ara h 2 sequential (linear) epitopes and compares their combination to a threshold pre-specified in the model development phase. When a patient has an inconclusive outcome by skin prick testing (or sIgE), IgE antibody levels to this combination of two epitopes can distinguish whether the patient is "Allergic" or "Not Allergic." Diagnoses of peanut allergy in all subjects were confirmed by double-blind placebo-controlled food challenge and subjects' ages were 7-55 years. RESULTS In the validation using CoFAR2 and POISED cohorts, the peanut BBEA diagnostic test correctly diagnosed 93% of the subjects, with a sensitivity of 92%, specificity of 94%, a positive predictive value of 91%, and negative predictive value of 95%. CONCLUSIONS In validation of the peanut BBEA diagnostic test, the overall accuracy was found to be superior to existing diagnostic tests for peanut allergy including skin prick testing, peanut sIgE, and peanut component sIgE testing.
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Affiliation(s)
- Mayte Suárez‐Fariñas
- Department of Population Health Science and Policy and Department of Genetics and GenomicsIcahn School of MedicineNew YorkNYUSA
| | - Maria Suprun
- Department of Pediatrics, Allergy and ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | - Paul Kearney
- AllerGenis LLCHatfieldPAUSA
- Data Incites LLCSeattleWAUSA
| | | | - Galina Grishina
- Department of Pediatrics, Allergy and ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
| | | | | | | | | | | | | | | | - Stephen J. Galli
- Sean N. Parker Center for Allergy and Asthma ResearchStanford UniversityStanfordCAUSA
- Departments of Pathology and Microbiology & ImmunologyStanford UniversityStanfordCAUSA
| | - Kari Nadeau
- Sean N. Parker Center for Allergy and Asthma ResearchStanford UniversityStanfordCAUSA
| | - Hugh A. Sampson
- Department of Pediatrics, Allergy and ImmunologyIcahn School of Medicine at Mount SinaiNew YorkNYUSA
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Suprun M, Ellis RJ, Sampson HA, Suárez-Fariñas M. bbeaR: an R package and framework for epitope-specific antibody profiling. Bioinformatics 2021; 37:131-133. [PMID: 33471075 PMCID: PMC8034521 DOI: 10.1093/bioinformatics/btaa1064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/13/2020] [Accepted: 01/16/2021] [Indexed: 11/13/2022] Open
Abstract
SUMMARY Analysis of epitope-specific antibody repertoires has provided novel insights into the pathogenesis of inflammatory disorders, especially allergies. A novel multiplex immunoassay, termed Bead-Based Epitope Assay (BBEA), was developed to quantify levels of epitope-specific immunoglobulins, including IgE, IgG, IgA and IgD isotypes. bbeaR is an open-source R package, developed for the BBEA, provides a framework to import, process and normalize .csv data files exported from the Luminex reader, evaluate various quality control metrics, analyze differential epitope-binding antibodies with linear modelling, visualize results, and map epitopes' amino acid sequences to their respective primary protein structures. bbeaR enables streamlined and reproducible analysis of epitope-specific antibody profiles. AVAILABILITY AND IMPLEMENTATION bbeaR is open-source and freely available from GitHub as an R package: https://github.com/msuprun/bbeaR; vignettes included. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Maria Suprun
- Department of Pediatrics, Allergy and Immunology
| | | | | | - Mayte Suárez-Fariñas
- Department of Population Health Science and Policy.,Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Suprun M, Sicherer SH, Wood RA, Jones SM, Leung DYM, Henning AK, Dawson P, Burks AW, Lindblad R, Getts R, Suárez-Fariñas M, Sampson HA. Early epitope-specific IgE antibodies are predictive of childhood peanut allergy. J Allergy Clin Immunol 2020; 146:1080-1088. [PMID: 32795587 PMCID: PMC8095129 DOI: 10.1016/j.jaci.2020.08.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Peanut allergy is characterized by the development of IgE against peanut antigen. OBJECTIVE We sought to evaluate the evolution of epitope-specific (es)IgE and esIgG4 in a prospective cohort of high-risk infants to determine whether antibody profiles can predict peanut allergy after age 4 years. METHODS The end point was allergy status at age 4+ years; samples from 293 children were collected at age 3 to 15 months and 2 to 3 and 4+ years. Levels of specific (s)IgE and sIgG4 to peanut and component proteins, and 50 esIgE and esIgG4 were quantified. Changes were analyzed with mixed-effects models. Machine learning algorithms were developed to identify a combination of antigen- and epitope-specific antibodies that using 3- to 15-month or 2- to 3-year samples can predict allergy status at age 4+ years. RESULTS At age 4+ years, 38% of children were Tolerant or 14% had Possible, 8% Convincing, 24% Serologic, and 16% Confirmed allergy. At age 3 to 15 months, esIgE profiles were similar among groups, whereas marked increases were evident at age 2 and 4+ years only in Confirmed and Serologic groups. In contrast, peanut sIgE level was significantly lower in the Tolerant group at age 3 to 15 months, increased in Confirmed and Serologic groups but decreased in Convincing and Possibly Allergic groups over time. An algorithm combining esIgEs with peanut sIgE outperformed different clinically relevant IgE cutoffs, predicting allergy status on an "unseen" set of patients with area under the curves of 0.84 at age 3 to 15 months and 0.87 at age 2 to 3 years. CONCLUSIONS Early epitope-specific plus peanut-specific IgE is predictive of allergy status at age 4+ years.
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Affiliation(s)
- Maria Suprun
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Robert A Wood
- Johns Hopkins University School of Medicine, Baltimore, Md
| | - Stacie M Jones
- University of Arkansas for Medical Sciences and Arkansas Children's Hospital, Little Rock, Ark
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Suprun M, Getts R, Grishina G, Tsuang A, Suárez‐Fariñas M, Sampson HA. Ovomucoid epitope-specific repertoire of IgE, IgG 4 , IgG 1 , IgA 1 , and IgD antibodies in egg-allergic children. Allergy 2020; 75:2633-2643. [PMID: 32391917 DOI: 10.1111/all.14357] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/24/2020] [Accepted: 04/08/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND Egg-white ovomucoid, that is, Gal d 1, is associated with IgE-mediated allergic reactions in most egg-allergic children. Epitope-specific IgE levels have been correlated with the severity of egg allergy, while emerging evidence suggests that other antibody isotypes (IgG1 , IgG4 , IgA, and IgD) may have a protective function; yet, their epitope-specific repertoires and associations with atopic comorbidities have not been studied. METHODS Bead-based epitope assay (BBEA) was used to quantitate the levels of epitope-specific (es)IgA, esIgE, esIgD, esIgG1 , and esIgG4 antibodies directed at 58 (15-mer) overlapping peptides, covering the entire sequence of ovomucoid, in plasma of 38 egg-allergic and 6 atopic children. Intraclass correlation (ICC) and coefficient of variation (CV) were used for the reliability assessment. The relationships across esIgs were evaluated using network analysis; linear and logistic regressions were used to compare groups based on egg allergy status and comorbidities. RESULTS BBEA had high reliability (ICC >0.75) and low variability (CV <20%) and could detect known IgE-binding epitopes. Egg-allergic children had lower esIgA1 (P = .010) and esIgG1 (P = .016) and higher esIgE (P < .001) and esIgD (P = .015) levels compared to the atopic controls. Interestingly, within the allergic group, children with higher esIgD had decreased odds of anaphylactic reactions (OR =0.48, P = .038). Network analysis identified most associations between esIgE with either esIgG4 or esIgD; indicating that IgE-secreting plasma cells could originate from either sequential isotype switch from antigen-experienced intermediate isotypes or directly from the IgD+ B cells. CONCLUSIONS Collectively, these data point toward a contribution of epitope-specific antibody repertoires to the pathogenesis of egg allergy.
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Affiliation(s)
- Maria Suprun
- Icahn School of Medicine at Mount Sinai New Yok NY USA
| | | | | | - Angela Tsuang
- Icahn School of Medicine at Mount Sinai New Yok NY USA
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Michlmayr D, Kim EY, Rahman AH, Raghunathan R, Kim-Schulze S, Che Y, Kalayci S, Gümüş ZH, Kuan G, Balmaseda A, Kasarskis A, Wolinsky SM, Suaréz-Fariñas M, Harris E. Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. Cell Rep 2020; 31:107569. [PMID: 32348760 PMCID: PMC7308490 DOI: 10.1016/j.celrep.2020.107569] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 11/18/2019] [Accepted: 04/03/2020] [Indexed: 01/02/2023] Open
Abstract
Zika virus (ZIKV) is an emerging, mosquito-borne flavivirus responsible for recent epidemics across the Americas, and it is closely related to dengue virus (DENV). Here, we study samples from 46 DENV-naive and 43 DENV-immune patients with RT-PCR-confirmed ZIKV infection at early-acute, late-acute, and convalescent time points from our pediatric cohort study in Nicaragua. We analyze the samples via RNA sequencing (RNA-seq), CyTOF, and multiplex cytokine/chemokine Luminex to generate a comprehensive, innate immune profile during ZIKV infection. Immunophenotyping and analysis of cytokines/chemokines reveal that CD14+ monocytes play a key role during ZIKV infection. Further, we identify CD169 (Siglec-1) on CD14+ monocytes as a potential biomarker of acute ZIKV infection. Strikingly distinct transcriptomic and immunophenotypic signatures are observed at all three time points. Interestingly, pre-existing dengue immunity has minimal impact on the innate immune response to Zika. Finally, this comprehensive immune profiling and network analysis of ZIKV infection in children serves as a valuable resource.
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Affiliation(s)
- Daniela Michlmayr
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Eun-Young Kim
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Adeeb H Rahman
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rohit Raghunathan
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Seunghee Kim-Schulze
- Human Immune Monitoring Center, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Oncological Sciences, Tisch Cancer Institute and the Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yan Che
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Selim Kalayci
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Guillermina Kuan
- Centro de Salud Sócrates Flores Vivas, Ministry of Health, Managua, Nicaragua; Sustainable Sciences Institute, Managua, Nicaragua
| | - Angel Balmaseda
- Sustainable Sciences Institute, Managua, Nicaragua; Laboratorio Nacional de Virología, Centro Nacional de Diagnóstico y Referencia, Ministry of Health, Managua, Nicaragua
| | - Andrew Kasarskis
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Steven M Wolinsky
- Division of Infectious Diseases, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mayte Suaréz-Fariñas
- Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Eva Harris
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, Berkeley, CA, USA.
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Novel Bead-Based Epitope Assay is a sensitive and reliable tool for profiling epitope-specific antibody repertoire in food allergy. Sci Rep 2019; 9:18425. [PMID: 31804555 PMCID: PMC6895130 DOI: 10.1038/s41598-019-54868-7] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/09/2019] [Indexed: 12/16/2022] Open
Abstract
Identification of allergenic IgE epitopes is instrumental for the development of novel diagnostic and prognostic methods in food allergy. In this work, we present the quantification and validation of a Bead-Based Epitope Assay (BBEA) that through multiplexing of epitopes and multiple sample processing enables completion of large experiments in a short period of time, using minimal quantities of patients’ blood. Peptides that are uniquely coupled to beads are incubated with serum or plasma samples, and after a secondary fluorophore-labeled antibody is added, the level of fluorescence is quantified with a Luminex reader. The signal is then normalized and converted to epitope-specific antibody binding values. We show that the effect of technical artifacts, i.e. well position or reading order, is minimal; and batch effects - different individual microplate runs - can be easily estimated and eliminated from the data. Epitope-specific antibody binding quantified with BBEA is highly reliable, reproducible and has greater sensitivity of epitope detection compared to peptide microarrays. IgE directed at allergenic epitopes is a sensitive biomarker of food allergy and can be used to predict allergy severity and phenotypes; and quantification of the relationship between epitope-specific IgE and IgG4 can further improve our understanding of the immune mechanisms behind allergic sensitization.
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