1
|
da Silva Antunes R, Weiskopf D, Sidney J, Rubiro P, Peters B, Arlehamn CSL, Grifoni A, Sette A. The MegaPool Approach to Characterize Adaptive CD4+ and CD8+ T Cell Responses. Curr Protoc 2023; 3:e934. [PMID: 37966108 PMCID: PMC10662678 DOI: 10.1002/cpz1.934] [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] [Indexed: 11/16/2023]
Abstract
Epitopes recognized by T cells are a collection of short peptide fragments derived from specific antigens or proteins. Immunological research to study T cell responses is hindered by the extreme degree of heterogeneity of epitope targets, which are usually derived from multiple antigens; within a given antigen, hundreds of different T cell epitopes can be recognized, differing from one individual to the next because T cell epitope recognition is restricted by the epitopes' ability to bind to MHC molecules, which are extremely polymorphic in different individuals. Testing large pools encompassing hundreds of peptides is technically challenging because of logistical considerations regarding solvent-induced toxicity. To address this issue, we developed the MegaPool (MP) approach based on sequential lyophilization of large numbers of peptides that can be used in a variety of assays to measure T cell responses, including ELISPOT, intracellular cytokine staining, and activation-induced marker assays, and that has been validated in the study of infectious diseases, allergies, and autoimmunity. Here, we describe the procedures for generating and testing MPs, starting with peptide synthesis and lyophilization, as well as a step-by-step guide and recommendations for their handling and experimental usage. Overall, the MP approach is a powerful strategy for studying T cell responses and understanding the immune system's role in health and disease. © 2023 Wiley Periodicals LLC. Basic Protocol 1: Generation of peptide pools ("MegaPools") Basic Protocol 2: MegaPool testing and quantitation of antigen-specific T cell responses.
Collapse
Affiliation(s)
- Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | | | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology (LJI); La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| |
Collapse
|
2
|
Liu B, Yang Z, Liu Q, Zhang Y, Ding H, Lai H, Li Q. Computational prediction of allergenic proteins based on multi-feature fusion. Front Genet 2023; 14:1294159. [PMID: 37928245 PMCID: PMC10622758 DOI: 10.3389/fgene.2023.1294159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023] Open
Abstract
Allergy is an autoimmune disorder described as an undesirable response of the immune system to typically innocuous substance in the environment. Studies have shown that the ability of proteins to trigger allergic reactions in susceptible individuals can be evaluated by bioinformatics tools. However, developing computational methods to accurately identify new allergenic proteins remains a vital challenge. This work aims to propose a machine learning model based on multi-feature fusion for predicting allergenic proteins efficiently. Firstly, we prepared a benchmark dataset of allergenic and non-allergenic protein sequences and pretested on it with a machine-learning platform. Then, three preferable feature extraction methods, including amino acid composition (AAC), dipeptide composition (DPC) and composition of k-spaced amino acid pairs (CKSAAP) were chosen to extract protein sequence features. Subsequently, these features were fused and optimized by Pearson correlation coefficient (PCC) and principal component analysis (PCA). Finally, the most representative features were picked out to build the optimal predictor based on random forest (RF) algorithm. Performance evaluation results via 5-fold cross-validation showed that the final model, called iAller (https://github.com/laihongyan/iAller), could precisely distinguish allergenic proteins from non-allergenic proteins. The prediction accuracy and AUC value for validation dataset achieved 91.4% and 0.97%, respectively. This model will provide guide for users to identify more allergenic proteins.
Collapse
Affiliation(s)
- Bin Liu
- Department of Anesthesiology, The Fourth People's Hospital of Sichuan Province, Chengdu, Sichuan, China
| | - Ziman Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Liu
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Ying Zhang
- Department of Anesthesiology, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Hui Ding
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Hongyan Lai
- Chongqing Key Laboratory of Big Data for Bio Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Qun Li
- Department of Pain, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
- Research Center of Integrated Traditional Chinese and Western Medicine, The Affiliated Traditional Chinese Medicine Hospital of Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|
3
|
Pomés A, Arruda LK. Cockroach allergy: Understanding complex immune responses to develop novel therapies. Mol Immunol 2023; 156:157-169. [PMID: 36930991 PMCID: PMC10134214 DOI: 10.1016/j.molimm.2023.03.001] [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: 10/31/2022] [Revised: 01/24/2023] [Accepted: 03/01/2023] [Indexed: 03/17/2023]
Abstract
Cockroach allergy is associated with the development of asthma. The identification of cockroach allergens, which began in the 1990 s, is an ongoing process that has led to the current listing of 20 official allergen groups in the WHO/IUIS Allergen Nomenclature database. The function and structure of some of these allergens has been determined and define their natural delivery into the environment and their allergenicity. Analysis of antigenic determinants by X-ray crystallography and rational design of site-directed mutagenesis led to the identification of IgE binding sites for the design of molecules with reduced IgE reactivity and T cell modulatory capacity. New developments in recent years include component analyses of B and T cell reactivity and a recent cockroach immunotherapy trial, CRITICAL, that will contribute to understand the immune response to cockroach and to define future directions for cockroach allergy diagnosis and immunotherapy.
Collapse
Affiliation(s)
- Anna Pomés
- Director of Basic Research, InBio, 700 Harris Street, Charlottesville, VA 22903, USA.
| | - L Karla Arruda
- Professor of Medicine, Ribeirão Preto Medical School, University of São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
| |
Collapse
|
4
|
Bianco M, Ventura G, Calvano CD, Losito I, Cataldi TRI. A new paradigm to search for allergenic proteins in novel foods by integrating proteomics analysis and in silico sequence homology prediction: Focus on spirulina and chlorella microalgae. Talanta 2022; 240:123188. [PMID: 34990986 DOI: 10.1016/j.talanta.2021.123188] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 10/19/2022]
Abstract
Since novel nutrient sources with high protein content, such as yeast, fungi, bacteria, algae, and insects, are increasingly introduced in the consumer market, safety evaluation studies on their potentially allergenic proteins are required. A pipeline for in silico establishing the sequence-based homology between proteins of spirulina (Arthrospira platensis) and chlorella (Chlorella vulgaris) micro-algae and those included in the AllergenOnline (AO) database (AllergenOnline.org) is described. The extracted proteins were first identified through tryptic peptides analysis by reversed-phase liquid chromatography and high resolution/accuracy Fourier-transform tandem mass spectrometry (RPLC-ESI-FTMS/MS), followed by a quest on the UniProt database. The AO database was subsequently interrogated to assess sequence similarity between identified microalgal proteins and known allergens, based on criteria established by the World Health Organization (WHO) and Food and Agriculture Organization (FAO). A direct search for microalgal proteins already included in allergen databases was also performed using the Allergome database. Six proteins exhibiting a significant homology with food allergens were identified in spirulina extracts. Five of them, i.e., two thioredoxins (D4ZSU6, K1VP15), a superoxide dismutase (C3V3P3), a glyceraldehyde-3-phosphate dehydrogenase (K1W168), and a triosephosphate isomerase (D5A635), resulted from the search on AO. The sixth protein, C-phycocyanin beta subunit (P72508), was directly obtained after examining the Allergome database. Two proteins exhibiting significant sequence homology with food allergens were retrieved in chlorella extracts, viz. calmodulin (A0A2P6TFR8), which is related to troponin c (D7F1Q2), and fructose-bisphosphate aldolase (A0A2P6TDD0). Specific serum screenings based on immunochemical tests should be undertaken to confirm or rule out the allergenicity of the identified proteins.
Collapse
Affiliation(s)
- Mariachiara Bianco
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Giovanni Ventura
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| | - Cosima Damiana Calvano
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Ilario Losito
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy
| | - Tommaso R I Cataldi
- Department of Chemistry, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy; Interdepartmental Research Center SMART, University of Bari Aldo Moro, Via Orabona 4, 70126, Bari, Italy.
| |
Collapse
|
5
|
Abstract
The enzyme-linked immunospot (ELISpot) is a highly sensitive immunoassay that measures the frequency of cytokine-secreting cells at the single-cell level. The secreted molecules are detected by using a detection antibody system similar to that used in the enzyme-linked immunosorbent assay (ELISA). The ELISpot assay is carried out in a 96-well plate and an automated ELISpot reader is used for analysis. The assay is easy to perform, robust and allows rapid analysis of a large number of samples and is not limited to measurement of cytokines; it is suitable for almost any secreted protein where single-cell analysis is of interest.
Collapse
|
6
|
Detection and Enumeration of Cytokine-Secreting Cells by FluoroSpot. Methods Mol Biol 2021; 2386:81-99. [PMID: 34766266 DOI: 10.1007/978-1-0716-1771-7_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: 05/12/2023]
Abstract
The FluoroSpot assay is a development of the highly sensitive enzyme-linked immunospot (ELISpot) assay which enables functional measurement of immunity at the single-cell level. Both assays are performed in a 96-well format and measures the frequency of analyte-secreting cells, in ELISpot usually limited to one analyte per well due to the use of enzymes and precipitating substrates for detection. FluoroSpot, performed in a similar way as ELISpot, overcomes this limitation by detecting each analyte with an assigned fluorophore instead of an enzyme. By using readers equipped with fluorophore-specific filters, cells producing single or multiple cytokines can be identified simultaneously in the same well. This greatly facilitates the analysis of functionally distinct subpopulations in heterogenous cell samples, for example, the frequency of polyfunctional T cells, suggested to be of importance in various disease states. FluoroSpot maintains the simplicity and sensitivity of the ELISpot while taking the assay a step further towards a multiplex analysis and an in-depth understanding of the quality of an immune response. We describe here a 96-well plate method to analyze cells that have secreted up to four different cytokines simultaneously (Four-color Fluorospot).
Collapse
|
7
|
da Silva Antunes R, Sutherland A, Frazier A, Schulten V, Pomés A, Glesner J, Calatroni A, Altman MC, Wood RA, O'Connor GT, Pongracic JA, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill M, Liu AH, Zoratti E, Kattan M, Busse PJ, Bacharier LB, Teach SJ, Wheatley LM, Togias A, Busse WW, Jackson DJ, Sette A. Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen-specific T cell responses in allergic sensitized children. Clin Transl Allergy 2021; 11:e12073. [PMID: 34691392 PMCID: PMC8514843 DOI: 10.1002/clt2.12073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 09/13/2021] [Accepted: 10/03/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Characterization of allergic responses to cockroach (CR), a common aeroallergen associated with asthma, has focused mainly on IgE reactivity, but little is known about T cell responses, particularly in children. We conducted a functional evaluation of CR allergen-specific T cell reactivity in a cohort of CR allergic children with asthma. METHODS Peripheral blood mononuclear cells (PBMCs) were obtained from 71 children, with mild-to-moderate asthma who were enrolled in a CR immunotherapy (IT) clinical trial, prior to treatment initiation. PBMC were stimulated with peptide pools derived from 11 CR allergens, and CD4+ T cell responses assessed by intracellular cytokine staining. RESULTS Highly heterogeneous responses in T cell reactivity were observed among participants, both in terms of the magnitude of cytokine response and allergen immunodominance. Reactivity against Bla g 9 and Bla g 5 was most frequent. The phenotype of the T cell response was dominated by IL-4 production and a Th2 polarized profile in 54.9% of participants, but IFNγ production and Th1 polarization was observed in 25.3% of the participants. The numbers of regulatory CD4+ T cells were also highly variable and the magnitude of effector responses and Th2 polarization were positively correlated with serum IgE levels specific to a clinical CR extract. CONCLUSIONS Our results demonstrate that in children with mild-to-moderate asthma, CR-specific T cell responses display a wide range of magnitude, allergen dominance, and polarization. These results will enable examination of whether any of the variables measured are affected by IT and/or are predictive of clinical outcomes.
Collapse
Affiliation(s)
| | - Aaron Sutherland
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - April Frazier
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Veronique Schulten
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
| | - Anna Pomés
- Basic ResearchIndoor Biotechnologies, Inc.CharlottesvilleVirginiaUSA
| | - Jill Glesner
- Basic ResearchIndoor Biotechnologies, Inc.CharlottesvilleVirginiaUSA
| | | | - Matthew C. Altman
- Benaroya Research Institute Systems Immunology DivisionDepartment of MedicineUniversity of WashingtonSeattleWashingtonUSA
| | - Robert A. Wood
- Division of Pediatric Allergy, Immunology and RheumatologyDepartment of PediatricsJohns Hopkins University School of MedicineBaltimoreMarylandUSA
| | - George T. O'Connor
- Boston University School of MedicinePulmonary CenterBostonMassachusettsUSA
| | - Jacqueline A. Pongracic
- Advanced General Pediatrics and Primary CareAnn & Robert H. Lurie Children's Hospital of ChicagoChicagoIllinoisUSA
| | | | - Carolyn M. Kercsmar
- Division of Pulmonary MedicineCincinnati Children's HospitalCincinnatiOhioUSA
| | - Rebecca S. Gruchalla
- Divisions of Infectious Diseases and Pulmonary Vascular BiologyDepartment of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Michelle Gill
- Divisions of Infectious Diseases and Pulmonary Vascular BiologyDepartment of PediatricsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Andrew H. Liu
- Department of PediatricsChildren's Hospital ColoradoUniversity of Colorado School of MedicineAuroraColoradoUSA
| | - Edward Zoratti
- Henry Ford Health System and Wayne State University School of MedicineDetroitMichiganUSA
| | - Meyer Kattan
- College of Physicians and SurgeonsColumbia UniversityNew YorkNew YorkUSA
| | - Paula J. Busse
- Division of Clinical Immunology and AllergyIcahn School of Medicine at Mount SinaiNew YorkNew YorkUSA
| | - Leonard B. Bacharier
- Department of PediatricsMonroe Carell Jr Children's Hospital at Vanderbilt University Medical CenterNashvilleTennesseeUSA
| | - Stephen J. Teach
- Center for Translational ResearchChildren's National HospitalWashingtonDCUSA
| | - Lisa M. Wheatley
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMarylandUSA
| | - Alkis Togias
- Division of Allergy, Immunology, and TransplantationNational Institute of Allergy and Infectious DiseasesNational Institutes of HealthRockvilleMarylandUSA
| | - William W. Busse
- Departments of Pediatrics and MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Daniel J. Jackson
- Departments of Pediatrics and MedicineUniversity of Wisconsin School of Medicine and Public HealthMadisonWisconsinUSA
| | - Alessandro Sette
- Division of Vaccine DiscoveryLa Jolla Institute for ImmunologyLa JollaCaliforniaUSA
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| |
Collapse
|
8
|
Pomés A, Schulten V, Glesner J, da Silva Antunes R, Sutherland A, Bacharier LB, Beigelman A, Busse P, Frazier A, Sette A. IgE and T Cell Reactivity to a Comprehensive Panel of Cockroach Allergens in Relation to Disease. Front Immunol 2021; 11:621700. [PMID: 33643303 PMCID: PMC7902920 DOI: 10.3389/fimmu.2020.621700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/22/2020] [Indexed: 02/04/2023] Open
Abstract
IgE sensitization to cockroach allergens is associated with development of allergic diseases, such as asthma. To understand the relevance of different cockroach allergens for diagnosis and immunotherapy, a comprehensive analysis of IgE antibody levels and T cell reactivity to an expanded set of cockroach allergens and their relationship to disease was performed in a cohort of USA cockroach sensitized patients. IgE antibody levels to recombinant chitinase and hemocyanin were measured for 23 subjects by custom-made ImmunoCAPs and compared with IgE levels to eight cockroach allergens we previously reported for the same cohort. Ex vivo T cell activation (Ox40/PDL-1 expression) of PBMCs stimulated with peptide pools derived from 11 German cockroach proteins, including nine official cockroach allergens, plus chitinase and vitellogenin, was determined by flow cytometry. IgE prevalences to chitinase (17%) and hemocyanin (44%) were comparable to values for the other eight allergens that we previously reported (21-57%). Hemocyanin (Bla g 3), was a major allergen (one to which more than 50% of patients with an allergy to its source react) for a sub-group of 15 highly cockroach-sensitized subjects (IgE > 3.5 kUA/L: 53%). Chitinase was officially named as new allergen Bla g 12. Cockroach-specific IgE levels in plasma showed excellent correlation with the sum of 10 allergen-specific IgE (r = 0.94, p < 0.001). T cell reactivity to 11 proteins was highly variable among subjects, the highest being for vitellogenin, followed by Bla g 3. The main finding was that cockroach allergen-specific IgE and T cell reactivity patterns were unique per subject, and lacked immunodominant allergens and correlation with clinical phenotype/disease severity in the studied cohort. Knowing the subject-specific B/T cell reactivity profiles to a comprehensive panel of cockroach allergens will contribute to diagnosis of cockroach allergy and will be important for planning and assessing allergen immunotherapy outcomes, according to the allergen content in therapeutic cockroach extracts.
Collapse
Affiliation(s)
- Anna Pomés
- Basic Research, Indoor Biotechnologies, Inc., Charlottesville, VA, United States
| | - Véronique Schulten
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Jill Glesner
- Basic Research, Indoor Biotechnologies, Inc., Charlottesville, VA, United States
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Leonard B Bacharier
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, United States
| | - Avraham Beigelman
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, United States.,Kipper Institute of Allergy and Immunology, Schneider Children's Medical Center of Israel, Tel Aviv University, Tel Aviv, Israel
| | - Paula Busse
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
9
|
Current insights into the genetics of food allergy. J Allergy Clin Immunol 2021; 147:15-28. [PMID: 33436162 DOI: 10.1016/j.jaci.2020.10.039] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/02/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022]
Abstract
Food allergy (FA), a growing public health burden in the United States, and familial aggregation studies support strong roles for both genes and environment in FA risk. Deepening our understanding of the molecular and cellular mechanisms driving FAs is paramount to improving its prevention, diagnosis, and clinical management. In this review, we document lessons learned from the genetics of FA that have aided our understanding of these mechanisms. Although current genetic association studies suffer from low power, heterogeneity in definition of FA, and difficulty in our ability to truly disentangle FA from food sensitization (FS) and general atopy genetics, they reveal a set of genetic loci, genes, and variants that continue to implicate the importance of barrier and immune function genes across the atopic march, and FA in particular. The largest reported effects on FA are from MALT1 (odds ratio, 10.99), FLG (average odds ratio, ∼2.9), and HLA (average odds ratio, ∼2.03). The biggest challenge in the field of FA genetics is to elucidate the specific mechanism of action on FA risk and pathogenesis for these loci, and integrative approaches including genetics/genomics with transcriptomics, proteomics, and metabolomics will be critical next steps to translating these genetic insights into practice.
Collapse
|
10
|
Identification and Characterization of CD4 + T Cell Epitopes after Shingrix Vaccination. J Virol 2020; 94:JVI.01641-20. [PMID: 32999027 DOI: 10.1128/jvi.01641-20] [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: 08/19/2020] [Accepted: 09/24/2020] [Indexed: 12/27/2022] Open
Abstract
Infections with varicella-zoster virus (VZV) are associated with a range of clinical manifestations. Primary infection with VZV causes chicken pox. The virus remains latent in neurons, and it can reactivate later in life, causing herpes zoster (HZ). Two different vaccines have been developed to prevent HZ; one is based on a live attenuated VZV strain (Zostavax), and the other is based on adjuvanted gE recombinant protein (Shingrix). While Zostavax efficacy wanes with age, Shingrix protection retains its efficacy in elderly subjects (individuals 80 years of age and older). In this context, it is of much interest to understand if there is a role for T cell immunity in the differential clinical outcome and if there is a correlate of protection between T cell immunity and Shingrix efficacy. In this study, we characterized the Shingrix-specific ex vivo CD4 T cell responses in the context of natural exposure and HZ vaccination using pools of predicted epitopes. We show that T cell reactivity following natural infection and Zostavax vaccination dominantly targets nonstructural (NS) proteins, while Shingrix vaccination redirects dominant reactivity to target gE. We mapped the gE-specific responses following Shingrix vaccination to 89 different gE epitopes, 34 of which accounted for 80% of the response. Using antigen presentation assays and single HLA molecule-transfected lines, we experimentally determined HLA restrictions for 94 different donor/peptide combinations. Finally, we used our results as a training set to assess strategies to predict restrictions based on measured or predicted HLA binding and the corresponding HLA types of the responding subjects.IMPORTANCE Understanding the T cell profile associated with the protection observed in elderly vaccinees following Shingrix vaccination is relevant to the general definition of correlates of vaccine efficacy. Our study enables these future studies by clarifying the patterns of immunodominance associated with Shingrix vaccination, as opposed to natural infection or Zostavax vaccination. Identification of epitopes recognized by Shingrix-induced CD4 T cells and their associated HLA restrictions enables the generation of tetrameric staining reagents and, more broadly, the capability to characterize the specificity, magnitude, and phenotype of VZV-specific T cells.
Collapse
|
11
|
Sidney J, Peters B, Sette A. Epitope prediction and identification- adaptive T cell responses in humans. Semin Immunol 2020; 50:101418. [PMID: 33131981 DOI: 10.1016/j.smim.2020.101418] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/24/2020] [Accepted: 10/22/2020] [Indexed: 12/16/2022]
Abstract
Epitopes, in the context of T cell recognition, are short peptides typically derived by antigen processing, and presented on the cell surface bound to MHC molecules (HLA molecules in humans) for TCR scrutiny. The identification of epitopes is a context-dependent process, with consideration given to, for example, the source pathogen and protein, the host organism, and state of the immune reaction (e.g., following natural infection, vaccination, etc.). In the following review, we consider the various approaches used to define T cell epitopes, including both bioinformatic and experimental approaches, and discuss the concepts of immunodominance and immunoprevalence. We also discuss HLA polymorphism and epitope restriction, and the resulting impact on the identification of, and potential population coverage afforded by, epitopes or epitope-based vaccines. Finally, some examples of the practical application of T cell epitope identification are provided, showing how epitopes have been valuable for deriving novel immunological insights in the context of the immune response to various pathogens and allergens.
Collapse
Affiliation(s)
- John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 9420 Athena Circle, La Jolla, CA, 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA, 92037, USA.
| |
Collapse
|
12
|
Maurer-Stroh S, Krutz NL, Kern PS, Gunalan V, Nguyen MN, Limviphuvadh V, Eisenhaber F, Gerberick GF. AllerCatPro-prediction of protein allergenicity potential from the protein sequence. Bioinformatics 2020; 35:3020-3027. [PMID: 30657872 PMCID: PMC6736023 DOI: 10.1093/bioinformatics/btz029] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 12/18/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
Motivation Due to the risk of inducing an immediate Type I (IgE-mediated) allergic response, proteins intended for use in consumer products must be investigated for their allergenic potential before introduction into the marketplace. The FAO/WHO guidelines for computational assessment of allergenic potential of proteins based on short peptide hits and linear sequence window identity thresholds misclassify many proteins as allergens. Results We developed AllerCatPro which predicts the allergenic potential of proteins based on similarity of their 3D protein structure as well as their amino acid sequence compared with a data set of known protein allergens comprising of 4180 unique allergenic protein sequences derived from the union of the major databases Food Allergy Research and Resource Program, Comprehensive Protein Allergen Resource, WHO/International Union of Immunological Societies, UniProtKB and Allergome. We extended the hexamer hit rule by removing peptides with high probability of random occurrence measured by sequence entropy as well as requiring 3 or more hexamer hits consistent with natural linear epitope patterns in known allergens. This is complemented with a Gluten-like repeat pattern detection. We also switched from a linear sequence window similarity to a B-cell epitope-like 3D surface similarity window which became possible through extensive 3D structure modeling covering the majority (74%) of allergens. In case no structure similarity is found, the decision workflow reverts to the old linear sequence window rule. The overall accuracy of AllerCatPro is 84% compared with other current methods which range from 51 to 73%. Both the FAO/WHO rules and AllerCatPro achieve highest sensitivity but AllerCatPro provides a 37-fold increase in specificity. Availability and implementation https://allercatpro.bii.a-star.edu.sg/ Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Sebastian Maurer-Stroh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | - Nora L Krutz
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Petra S Kern
- The Procter & Gamble Services Company, Strombeek-Bever, Belgium
| | - Vithiagaran Gunalan
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Minh N Nguyen
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Vachiranee Limviphuvadh
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore
| | - Frank Eisenhaber
- Biomolecular Function Discovery Division, Bioinformatics Institute, Agency for Science, Technology and Research, Singapore.,Department of Biological Sciences, National University of Singapore, Singapore
| | | |
Collapse
|
13
|
Gong JJ, Margolis DJ, Monos DS. Predictive in silico binding algorithms reveal HLA specificities and autoallergen peptides associated with atopic dermatitis. Arch Dermatol Res 2020; 312:647-656. [PMID: 32152724 DOI: 10.1007/s00403-020-02059-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 02/26/2020] [Indexed: 12/18/2022]
Abstract
Atopic dermatitis (AD) is a skin disease that results from a combination of skin barrier dysfunction and immune dysregulation. The immune dysregulation is often associated with IgE sensitivity. There is also evidence that autoallergens Hom s 1, 2, 3, and 4 play a role in AD; it is possible that patients with specific HLA subtypes are predisposed to autoreactivity due to increased presentation of autoallergen peptides. The goal of our study was to use in silico epitope prediction platforms as an approach to identify HLA subtypes that may preferentially bind autoallergen peptides and are thus candidates for further study. Considering the previously described association of DRB1 alleles with AD and progression of disease, emphasis was placed on DRB1. Certain DRB1 alleles (08:04, 11:01, and 11:04) were identified by both algorithms to bind a significant percent of the generated autoallergen peptides. Conversely, autoallergen core peptide sequences FRQLSHRFH and IRAKLRLQA (Hom s 1), IRKSKNILF (Hom s 2), FKWVPVTDS and MAAIEKVRK (Hom s 3), and FRYFATLKV (Hom s 4) were predicted to bind many DRB1 alleles and, thus, may play a role in the pathogenesis of AD. Our findings provide candidate DRB1 alleles and autoallergen epitopes that will guide future studies exploring the relationship between DRB1 subtype and autoreactivity in AD. A similar approach can be used for any antigen that has been associated with an IgE response and AD.
Collapse
Affiliation(s)
- Jan J Gong
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - David J Margolis
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Dermatology, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biostatistics and Epidemiology, University of Pennsylvania, Philadelphia, PA, USA.
| | - Dimitrios S Monos
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| |
Collapse
|
14
|
Jadoon MH, Rehman Z, Khan A, Rizwan M, Khan S, Mehmood A, Munir A. In silico T-cell and B-cell Epitope Based Vaccine Design Against Alphavirus Strain of Chikungunya. Infect Disord Drug Targets 2020; 20:523-530. [PMID: 31109281 DOI: 10.2174/1871526519666190521100521] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 03/08/2019] [Accepted: 04/22/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Chikungunya an arbovirus, is transmitted to humans by the bite of Aedes mosquito. The virus occurrences have been reported in Southeast Asian countries including Pakistan. Its symptoms include typical febrile illness and arthralgic syndrome. The virus has not decisively proved to be life-threatening. METHODS The attempt was to design T-cell and B-cell epitope-based vaccine for Chikungunya. The proteome of chikungunya was retrieved, antigenic proteins were identified and T-cell epitopes and B-cell epitopes were predicted. Interacting HLA alleles were also identified. The final analysis was done to confirm that predicted T-cell epitopes and B-cell epitopes can be used as a vaccine. RESULTS About 32 T-cell epitopes and a 10mer B-cell epitope were identified. Both T-cell and Bcell epitopes demonstrated strong interactions with HLA alleles. The predicted T-cell and B-cell epitopes were docked with respective HLA alleles. The docking analysis showed that the predicted respective epitopes best fit into the binding pockets of the alleles. CONCLUSION On the basis of this computational analysis, it is suggested that these predicted epitopes can be used as a remedy against Alphavirus strain of chikungunya. Further laboratory experiments can be conducted to determine the efficacy and stability of this work.
Collapse
Affiliation(s)
- Maharij Haroon Jadoon
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Zainab Rehman
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Areeba Khan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Muhammad Rizwan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Sajid Khan
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Azhar Mehmood
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
| | - Anum Munir
- Department of Bioinformatics, Government Post Graduate College, Mandian, Abbottabad, Pakistan
- Department of Bioinformatics, Capital University of Science and Technology, Islamabad, Pakistan
| |
Collapse
|
15
|
Pomés A, Schulten V. Cross-reactivity in allergy: A double-edged sword. Allergy 2020; 75:9-11. [PMID: 31325165 PMCID: PMC6952562 DOI: 10.1111/all.13993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 07/09/2019] [Accepted: 07/14/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, USA
| | | |
Collapse
|
16
|
Wu DM, Zheng ZH, Wang S, Wen X, Han XR, Wang YJ, Shen M, Fan SH, Zhang ZF, Shan Q, Li MQ, Hu B, Zheng YL, Chen GQ, Lu J. Retracted: The role of HOTAIR-induced downregulation of microRNA-126 and interleukin-13 in the development of bronchial hyperresponsiveness in neonates. J Cell Physiol 2019; 234:16400-16411. [PMID: 30790266 DOI: 10.1002/jcp.28309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 01/18/2019] [Accepted: 01/24/2019] [Indexed: 01/24/2023]
Abstract
Long noncoding RNAs, including HOTAIR, are involved in the pathogenesis of a wide range of diseases. This study aimed to explore the mechanism underlying the involvement of HOTAIR in neonatal bronchial hyperresponsiveness (BHR). A total of 105 newborns were recruited in this study to collect their peripheral blood mononuclear cell and serum samples, which were then divided into different genotype groups based on the genotypes of rs4759314, rs874945, and rs7958904. The real-time polymerase chain reaction, western blot analysis, computational analyses, and luciferase assays were performed to establish the regulatory relationships between the HOTAIR, microRNA-126 (miR-126), and interleukin-13 (IL-13). The level of HOTAIR, miR-126, and IL-13 among rs4759314 AA, AG, and GG groups, as well as among rs874945 GG, AG, and AA groups was similar. However, the level of HOTAIR was increased in the rs7958904 GG group, accompanied by a decreased level of miR-126 and IL-13. In addition, the level of airway responsiveness was comparable among rs4759314 AA, AG, and GG groups, as well as among rs874945 GG, AG, and AA groups. However, the airway responsiveness in the groups rs7958904 CG and CC was much stronger than that of the GG group. We also demonstrated that, by directly binding to miR-126, HOTAIR reduced the expression of miR-126, which in turn decreased the expression of IL-13. In summary, we demonstrated the role of HOTAIR-induced downregulation of miR-126 and IL-13 in the development of BHR in neonates.
Collapse
Affiliation(s)
- Dong-Mei Wu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zi-Hui Zheng
- State Key Laboratory Cultivation Base for TCM Quality and Efficacy, School of Medicine and Life Science, Nanjing University of Chinese Medicine, Nanjing, China
| | - Shan Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xin Wen
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xin-Rui Han
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yong-Jian Wang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Min Shen
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Shao-Hua Fan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Zi-Feng Zhang
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Qun Shan
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Meng-Qiu Li
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Bin Hu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Yuan-Lin Zheng
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Gui-Quan Chen
- State Key Laboratory of Pharmaceutical Biotechnology, MOE Key Laboratory of Model Animal for Disease Study, Model Animal Research Center, Nanjing University, Nanjing, China
| | - Jun Lu
- Key Laboratory for Biotechnology on Medicinal Plants of Jiangsu, School of Life Science, College of Health Sciences, Jiangsu Normal University, Xuzhou, China.,College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| |
Collapse
|
17
|
Characterization and epitope identification of the T cell response in non-allergic individuals exposed to mouse allergen. World Allergy Organ J 2019; 12:100026. [PMID: 31044023 PMCID: PMC6479169 DOI: 10.1016/j.waojou.2019.100026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 03/05/2019] [Accepted: 03/18/2019] [Indexed: 01/11/2023] Open
Abstract
Background Exposure to airborne allergens is a frequent trigger of respiratory allergy and asthma in atopic individuals. While allergic patients suffer hypersensitivity reactions to these allergens, non-allergic individuals do not exhibit clinical symptoms despite environmental exposure to these ubiquitous allergen sources. The aim of this study was to characterize T cell responses in non-allergic laboratory workers, who are heavily exposed to mice allergens (Exposed Non-Allergics, ENA) and compare this data to previously published T cell responses measured in mouse (MO)-allergic patients. METHODS: Peripheral mononuclear cells (PBMC) from ENA subjects were expanded for 2 weeks in vitro with mouse urine extract and screened for IFNγ and IL-5 cytokine production in response to mouse antigen-derived peptides by ELISPOT. Ex vivo T cell reactivity in the ENA cohort was performed after 6hr stimulation with peptide pools by intracellular staining of CD154. Results Vigorous responses were detected, associated with 147 epitopes derived from 16 mouse antigens. As expected, responses in ENA subjects were somewhat lower than those observed in MO-allergics for both responder frequency and overall response magnitude. While responses in allergics were polarized towards IL-5 production and associated with low IFNγ production, ENA responses were not polarized. The composition of targeted antigens and epitopes was overall similar between the two cohorts, with the majority of T cell reactivity directed against Mus m 1 and other major urinary proteins. However, kappa-casein precursor and odorant binding protein Ib were more abundantly recognized in MO-allergics compared to ENA subjects. Additionally, T cell responses against oligopeptides derived from the low molecular weight fraction of mouse urine were also assessed. Interestingly, no difference in the response frequency, magnitude or polarization between MO-allergic and ENA individuals was observed. Finally, assessment of ex vivo T cell activation also revealed T cell reactivity in the ENA cohort, with a non-significant trend for lower responses compared to MO-allergics. Conclusion Exposure to mouse induces potent T cell responses in non-allergic individuals, targeting similar epitopes as seen in allergic patients.
Collapse
|
18
|
Tian Y, da Silva Antunes R, Sidney J, Lindestam Arlehamn CS, Grifoni A, Dhanda SK, Paul S, Peters B, Weiskopf D, Sette A. A Review on T Cell Epitopes Identified Using Prediction and Cell-Mediated Immune Models for Mycobacterium tuberculosis and Bordetella pertussis. Front Immunol 2018; 9:2778. [PMID: 30555469 PMCID: PMC6281829 DOI: 10.3389/fimmu.2018.02778] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/12/2018] [Indexed: 01/01/2023] Open
Abstract
In the present review, we summarize work from our as well as other groups related to the characterization of bacterial T cell epitopes, with a specific focus on two important pathogens, namely, Mycobacterium tuberculosis (Mtb), the bacterium that causes tuberculosis (TB), and Bordetella pertussis (BP), the bacterium that causes whooping cough. Both bacteria and their associated diseases are of large societal significance. Although vaccines exist for both pathogens, their efficacy is incomplete. It is widely thought that defects and/or alteration in T cell compartments are associated with limited vaccine effectiveness. As discussed below, a full genome-wide map was performed in the case of Mtb. For BP, our focus has thus far been on the antigens contained in the acellular vaccine; a full genome-wide screen is in the planning stage. Nevertheless, the sum-total of the results in the two different bacterial systems allows us to exemplify approaches and techniques that we believe are generally applicable to the mapping and characterization of human immune responses to bacterial pathogens. Finally, we add, as a disclaimer, that this review by design is focused on the work produced by our laboratory as an illustration of approaches to the study of T cell responses to Mtb and BP, and is not meant to be comprehensive, nor to detract from the excellent work performed by many other groups.
Collapse
Affiliation(s)
- Yuan Tian
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | | | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| |
Collapse
|
19
|
Cantillo JF, Puerta L, Fernandez-Caldas E, Subiza JL, Soria I, Wöhrl S, Ebner C, Keller W, Resch-Marat Y, Vrtala S, Bohle B. Tropomyosins in mosquito and house dust mite cross-react at the humoral and cellular level. Clin Exp Allergy 2018; 48:1354-1363. [DOI: 10.1111/cea.13229] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/01/2018] [Accepted: 07/02/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jose F. Cantillo
- Complutense University of Madrid; Madrid Spain
- Institute for Immunological Research/University of Cartagena; Cartagena Colombia
| | - Leonardo Puerta
- Institute for Immunological Research/University of Cartagena; Cartagena Colombia
| | - Enrique Fernandez-Caldas
- Inmunotek S.L.; Alcalá de Henares Spain
- University of South Florida College of Medicine; Tampa Florida
| | | | | | - Stefan Wöhrl
- Floridsdorf Allergy Center (FAZ); Vienna Austria
| | | | - Walter Keller
- Division of Structural Biology; Institute of Molecular Biosciences; BioTechMed University of Graz; Graz Austria
| | - Yvonne Resch-Marat
- Department of Pathophysiology and Allergy Research; Medical University of Vienna; Vienna Austria
| | - Susanne Vrtala
- Department of Pathophysiology and Allergy Research; Medical University of Vienna; Vienna Austria
| | - Barbara Bohle
- Department of Pathophysiology and Allergy Research; Medical University of Vienna; Vienna Austria
| |
Collapse
|
20
|
Zobayer N, Hossain ABM. B and T-cell Epitopes Based Vaccine Design in Api m3 Allergen of Apis mellifera: An Immunoinformatics Approach. JOURNAL OF MEDICAL SCIENCES 2017. [DOI: 10.3923/jms.2018.34.47] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
21
|
dNP2-ctCTLA-4 inhibits German cockroach extract-induced allergic airway inflammation and hyper-responsiveness via inhibition of Th2 responses. Exp Mol Med 2017; 49:e362. [PMID: 28775364 PMCID: PMC5579505 DOI: 10.1038/emm.2017.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 02/23/2017] [Accepted: 03/03/2017] [Indexed: 12/31/2022] Open
Abstract
German cockroaches are major household allergens that can trigger allergic airway inflammatory diseases with sensitive T-cell responses. Although the use of immune modulatory biologics, such as antibodies, to mediate allergic responses has recently been examined, only systemic administration is available because of the size limitations on intranasal administration. Here we utilized a cell-permeable peptide, dNP2, to deliver the cytoplasmic domain of cytotoxic T-lymphocyte antigen-4 (ctCTLA-4) through the airway epithelium to modulate Th2 responses in a German cockroach extract (GCE)-induced allergic airway inflammation model. The intranasal delivery efficiency of the dNP2-dTomato protein to the lungs was higher in GCE-induced asthmatic lung parenchymal cells compared to the sham cells. Intranasal administration of the dNP2-ctCTLA-4 protein inhibited airway hyper-responsiveness and reduced airway inflammation and remodeling, including goblet cell metaplasia and collagen deposition around the bronchi. The number of infiltrated cells, including eosinophils, and the levels of IL-4, IL-5, IL-13 and IFN-γ in the lungs were significantly reduced, presumably owing to inhibition of Th2 differentiation. However, intranasal administration of CTLA4-Ig did not inhibit airway inflammation. These results collectively suggest that dNP2-ctCTLA-4 is an efficient intranasally applicable candidate biologic for treating allergic asthma.
Collapse
|
22
|
Oseroff C, Christensen LH, Westernberg L, Pham J, Lane J, Paul S, Greenbaum J, Stranzl T, Lund G, Hoof I, Holm J, Würtzen PA, Meno KH, Frazier A, Schulten V, Andersen PS, Peters B, Sette A. Immunoproteomic analysis of house dust mite antigens reveals distinct classes of dominant T cell antigens according to function and serological reactivity. Clin Exp Allergy 2016; 47:577-592. [PMID: 27684489 DOI: 10.1111/cea.12829] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 08/11/2016] [Accepted: 08/30/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND House dust mite (HDM) allergens are a common cause of allergy and allergic asthma. A comprehensive analysis of proteins targeted by T cells, which are implicated in the development and regulation of allergic disease independent of their antibody reactivity, is still lacking. OBJECTIVE To comprehensively analyse the HDM-derived protein targets of T cell responses in HDM-allergic individuals, and investigate their correlation with IgE/IgG responses and protein function. METHODS Proteomic analysis (liquid chromatography-tandem mass spectrometry) of HDM extracts identified 90 distinct protein clusters, corresponding to 29 known allergens and 61 novel proteins. Peripheral blood mononuclear cells (PBMC) from 20 HDM-allergic individuals were stimulated with HDM extracts and assayed with a set of ~2500 peptides derived from these 90 protein clusters and predicted to bind the most common HLA class II types. 2D immunoblots were made in parallel to elucidate IgE and IgG reactivity, and putative function analyses were performed in silico according to Gene Ontology annotations. RESULTS Analysis of T cell reactivity revealed a large number of T cell epitopes. Overall response magnitude and frequency was comparable for known and novel proteins, with 15 antigens (nine of which were novel) dominating the total T cell response. Most of the known allergens that were dominant at the T cell level were also IgE reactive, as expected, while few novel dominant T cell antigens were IgE reactive. Among known allergens, hydrolase activity and detectable IgE/IgG reactivity are strongly correlated, while no protein function correlates with immunogenicity of novel proteins. A total of 106 epitopes accounted for half of the total T cell response, underlining the heterogeneity of T cell responses to HDM allergens. CONCLUSIONS AND CLINICAL RELEVANCE Herein, we define the T cell targets for both known allergens and novel proteins, which may inform future diagnostics and immunotherapeutics for allergy to HDM.
Collapse
Affiliation(s)
- Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Luise Westernberg
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - John Pham
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jerome Lane
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | - Gitte Lund
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Ilka Hoof
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - Jens Holm
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | | | - Kåre H Meno
- ALK-Abelló A/S, Global Research, Hørsholm, Denmark
| | - April Frazier
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | | | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| |
Collapse
|
23
|
Mazor R, Addissie S, Jang Y, Tai CH, Rose J, Hakim F, Pastan I. Role of HLA-DP in the Presentation of Epitopes from the Truncated Bacterial PE38 Immunotoxin. AAPS JOURNAL 2016; 19:117-129. [PMID: 27796910 DOI: 10.1208/s12248-016-9986-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/18/2016] [Indexed: 02/07/2023]
Abstract
Identification of helper T-cell epitopes is important in many fields of medicine. We previously used an experimental approach to identify T-cell epitopes in PE38, a truncated bacterial toxin used in immunotoxins. Here, we evaluated the ability of antibodies to DR, DP, or DQ to block T-cell responses to PE38 epitopes in 36 PBMC samples. We predicted the binding affinities of peptides to DR, DP, and DQ alleles using computational tools and analyzed their ability to predict the T-cell epitopes. We found that HLA-DR is responsible for 65% of the responses, DP 24%, and DQ 4%. One epitope that is presented in 20% of the samples (10/50) is entirely DP restricted and was not predicted to bind to DR or DP reference alleles using binding algorithms. We conclude that DP has an important role in helper T-cell response to PE38.
Collapse
Affiliation(s)
- Ronit Mazor
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Selamawit Addissie
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Youjin Jang
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Chin-Hsien Tai
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA
| | - Jeremy Rose
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Fran Hakim
- Experimental Transplantation and Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Ira Pastan
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Room 5106, Bethesda, Maryland, 20892-4264, USA.
| |
Collapse
|
24
|
Patel PS, King RG, Kearney JF. Pulmonary α-1,3-Glucan-Specific IgA-Secreting B Cells Suppress the Development of Cockroach Allergy. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2016; 197:3175-3187. [PMID: 27581173 PMCID: PMC5101147 DOI: 10.4049/jimmunol.1601039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/08/2016] [Indexed: 11/19/2022]
Abstract
There is a higher incidence of allergic conditions among children living in industrialized countries than those in developing regions. One explanation for this is reduced neonatal exposure to microbes and the consequent lack of immune stimulation. Sensitivity to cockroach allergen is highly correlated with the development of severe asthma. In this study, we determined that an Ab to microbial α-1,3-glucan binds an Enterobacter species and cockroach allergen. Neonatal, but not adult, mice immunized with this α-1,3-glucan-bearing Enterobacter (MK7) are protected against cockroach allergy. Following exposure to cockroach allergen, α-1,3-glucan-specific IgA-secreting cells are present in the lungs of mice immunized with MK7 as neonates but not in the lungs of those immunized as adults. Mice that are unable to generate anti-α-1,3-glucan IgA Abs were immunized with MK7 as neonates and were no longer protected against cockroach allergy. Thus, neonatal, but not adult, exposure to α-1,3-glucan results in suppressed development of cockroach allergy via pulmonary α-1,3-glucan-specific IgA-secreting cells.
Collapse
Affiliation(s)
- Preeyam S Patel
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - R Glenn King
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| | - John F Kearney
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294
| |
Collapse
|
25
|
Pham J, Oseroff C, Hinz D, Sidney J, Paul S, Greenbaum J, Vita R, Phillips E, Mallal S, Peters B, Sette A. Sequence conservation predicts T cell reactivity against ragweed allergens. Clin Exp Allergy 2016; 46:1194-205. [PMID: 27359111 DOI: 10.1111/cea.12772] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Revised: 06/01/2016] [Accepted: 06/01/2016] [Indexed: 01/03/2023]
Abstract
BACKGROUND Ragweed is a major cause of seasonal allergy, affecting millions of people worldwide. Several allergens have been defined based on IgE reactivity, but their relative immunogenicity in terms of T cell responses has not been studied. OBJECTIVE We comprehensively characterized T cell responses from atopic, ragweed-allergic subjects to Amb a 1, Amb a 3, Amb a 4, Amb a 5, Amb a 6, Amb a 8, Amb a 9, Amb a 10, Amb a 11, and Amb p 5 and examined their correlation with serological reactivity and sequence conservation in other allergens. METHODS Peripheral blood mononuclear cells (PBMCs) from donors positive for IgE towards ragweed extracts after in vitro expansion for secretion of IL-5 (a representative Th2 cytokine) and IFN-γ (Th1) in response to a panel of overlapping peptides spanning the above-listed allergens were assessed. RESULTS Three previously identified dominant T cell epitopes (Amb a 1 176-191, 200-215, and 344-359) were confirmed, and three novel dominant epitopes (Amb a 1 280-295, 304-319, and 320-335) were identified. Amb a 1, the dominant IgE allergen, was also the dominant T cell allergen, but dominance patterns for T cell and IgE responses for the other ragweed allergens did not correlate. Dominance for T cell responses correlated with conservation of ragweed epitopes with sequences of other well-known allergens. CONCLUSIONS AND CLINICAL RELEVANCE These results provide the first assessment of the hierarchy of T cell reactivity in ragweed allergens, which is distinct from that observed for IgE reactivity and influenced by T cell epitope sequence conservation. The results suggest that ragweed allergens associated with lesser IgE reactivity and significant T cell reactivity may be targeted for T cell immunotherapy, and further support the development of immunotherapies against epitopes conserved across species to generate broad reactivity against many common allergens.
Collapse
Affiliation(s)
- J Pham
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - C Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - D Hinz
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - S Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Greenbaum
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - R Vita
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - E Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - S Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - B Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| |
Collapse
|
26
|
Lindestam Arlehamn CS, McKinney DM, Carpenter C, Paul S, Rozot V, Makgotlho E, Gregg Y, van Rooyen M, Ernst JD, Hatherill M, Hanekom WA, Peters B, Scriba TJ, Sette A. A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans. PLoS Pathog 2016; 12:e1005760. [PMID: 27409590 PMCID: PMC4943605 DOI: 10.1371/journal.ppat.1005760] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/18/2016] [Indexed: 12/13/2022] Open
Abstract
We performed a quantitative analysis of the HLA restriction, antigen and epitope specificity of human pathogen specific responses in healthy individuals infected with M. tuberculosis (Mtb), in a South African cohort as a test case. The results estimate the breadth of T cell responses for the first time in the context of an infection and human population setting. We determined the epitope repertoire of eleven representative Mtb antigens and a large panel of previously defined Mtb epitopes. We estimated that our analytic methods detected 50-75% of the total response in a cohort of 63 individuals. As expected, responses were highly heterogeneous, with responses to a total of 125 epitopes detected. The 66 top epitopes provided 80% coverage of the responses identified in our study. Using a panel of 48 HLA class II-transfected antigen-presenting cells, we determined HLA class II restrictions for 278 epitope/donor recognition events (36% of the total). The majority of epitopes were restricted by multiple HLA alleles, and 380 different epitope/HLA combinations comprised less than 30% of the estimated Mtb-specific response. Our results underline the complexity of human T cell responses at a population level. Efforts to capture and characterize this broad and highly HLA promiscuous Mtb-specific T cell epitope repertoire will require significant peptide multiplexing efforts. We show that a comprehensive "megapool" of Mtb peptides captured a large fraction of the Mtb-specific T cells and can be used to characterize this response.
Collapse
Affiliation(s)
- Cecilia S. Lindestam Arlehamn
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Denise M. McKinney
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Chelsea Carpenter
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Virginie Rozot
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Edward Makgotlho
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Yolande Gregg
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Michele van Rooyen
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Joel D. Ernst
- Department of Medicine, Division of Infectious Diseases, New York University School of Medicine, New York, New York, United States of America
| | - Mark Hatherill
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Willem A. Hanekom
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| | - Thomas J. Scriba
- South African Tuberculosis Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, and Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, Department of Vaccine Discovery, La Jolla, California, United States of America
| |
Collapse
|
27
|
Hinz D, Oseroff C, Pham J, Sidney J, Peters B, Sette A. Definition of a pool of epitopes that recapitulates the T cell reactivity against major house dust mite allergens. Clin Exp Allergy 2016; 45:1601-12. [PMID: 25652035 DOI: 10.1111/cea.12507] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
BACKGROUND Allergens from house dust mites (HDM) are a common cause of asthma. Der p and Der f from Dermatophagoides sp. are strong immunogens in humans. Allergen extracts are used to study T helper (Th2) cell responses to HDM, which are implicated in the development and regulation of allergic disease. OBJECTIVE To define an epitope mixture that recapitulates, and might substitute for, HDM extract in terms of detecting and characterizing Th2 cell responses. METHODS Peripheral blood mononuclear cells (PBMC) from 52 HDM allergic and 10 non-allergic individuals were stimulated with HDM extracts and assayed with a set of 178 peptides spanning mite allergens group Der p 1, 2, 23 and Der f group 1 and 2 allergens. A pool of the most dominant T cell epitopes identified in the present study and from published literature was assembled and tested for ex vivo T cell responses. Correlation with HDM-specific IgE titres was examined. RESULTS Patterns of T cell reactivity to Der p and Der f - derived peptides revealed a large number of epitopes. Clear patterns of immunodominance were apparent, with HDM allergen group 1 and 2 dominant over group 23. Furthermore, within a given antigen, 6-11 epitopes accounted for the vast majority of responses. Based on these results and published data, a comprehensive dust mite pool (DMP) of epitopes was designed and found to allow detection of ex vivo T cell responses. DMP ex vivo reactivity correlated with HDM-specific IgE titres and was similar to that detected with commonly used HDM extracts. Ex vivo DMP stimulation was associated with a predominant Th2 response in allergic donors, and minor reactivity of T cells producing IFNγ, IL17 and IL10. CONCLUSIONS & CLINICAL RELEVANCE A detailed map of Der p and Der f antigens defined a pool of epitopes that can be used to detect ex vivo HDM responses.
Collapse
Affiliation(s)
- D Hinz
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - C Oseroff
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - J Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - B Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| |
Collapse
|
28
|
Gruchalla RS, Sampson HA, Liu AH, Shreffler W, Wallace PK, Togias A, David G, Calatroni A, LeBeau P. Effects of omalizumab on T lymphocyte function in inner-city children with asthma. Pediatr Allergy Immunol 2016; 27:328-31. [PMID: 26573086 PMCID: PMC4888877 DOI: 10.1111/pai.12508] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
While omalizumab treatment of inner city children and adolescents with asthma results in improvement in clinical parameters, no change in peripheral blood T cell responses could be demonstrated. Thus, omalizumab appears not to affect T cell function.
Collapse
Affiliation(s)
- R S Gruchalla
- University of Texas Southwestern Medical Center, Dallas, TX, USA.
| | - H A Sampson
- Mount Sinai School of Medicine, New York, NY, USA
| | - A H Liu
- National Jewish Health, University of Colorado Denver School of Medicine, Denver, CO, USA
| | | | - P K Wallace
- Roswell Park Cancer Institute, Buffalo, NY, USA
| | - A Togias
- Division of Allergy, Immunology and Transplantation, NIH, Bethesda, MD, USA
| | - G David
- Rho Federal Systems Division Inc., Chapel Hill, NC, USA
| | - A Calatroni
- Rho Federal Systems Division Inc., Chapel Hill, NC, USA
| | - P LeBeau
- Rho Federal Systems Division Inc., Chapel Hill, NC, USA
| | | |
Collapse
|
29
|
Bresciani A, Paul S, Schommer N, Dillon MB, Bancroft T, Greenbaum J, Sette A, Nielsen M, Peters B. T-cell recognition is shaped by epitope sequence conservation in the host proteome and microbiome. Immunology 2016; 148:34-9. [PMID: 26789414 DOI: 10.1111/imm.12585] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/09/2016] [Accepted: 01/14/2016] [Indexed: 01/15/2023] Open
Abstract
Several mechanisms exist to avoid or suppress inflammatory T-cell immune responses that could prove harmful to the host due to targeting self-antigens or commensal microbes. We hypothesized that these mechanisms could become evident when comparing the immunogenicity of a peptide from a pathogen or allergen with the conservation of its sequence in the human proteome or the healthy human microbiome. Indeed, performing such comparisons on large sets of validated T-cell epitopes, we found that epitopes that are similar with self-antigens above a certain threshold showed lower immunogenicity, presumably as a result of negative selection of T cells capable of recognizing such peptides. Moreover, we also found a reduced level of immune recognition for epitopes conserved in the commensal microbiome, presumably as a result of peripheral tolerance. These findings indicate that the existence (and potentially the polarization) of T-cell responses to a given epitope is influenced and to some extent predictable based on its similarity to self-antigens and commensal antigens.
Collapse
Affiliation(s)
- Anne Bresciani
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,Department of Systems Biology, Centre for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Nina Schommer
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Myles B Dillon
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Tara Bancroft
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Jason Greenbaum
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Morten Nielsen
- Department of Systems Biology, Centre for Biological Sequence Analysis, The Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Buenos Aires, Argentina
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| |
Collapse
|
30
|
Woodfolk JA, Glesner J, Wright PW, Kepley CL, Li M, Himly M, Muehling LM, Gustchina A, Wlodawer A, Chapman MD, Pomés A. Antigenic Determinants of the Bilobal Cockroach Allergen Bla g 2. J Biol Chem 2015; 291:2288-301. [PMID: 26644466 DOI: 10.1074/jbc.m115.702324] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Indexed: 01/01/2023] Open
Abstract
Bla g 2 is a major indoor cockroach allergen associated with the development of asthma. Antigenic determinants on Bla g 2 were analyzed by mutagenesis based on the structure of the allergen alone and in complex with monoclonal antibodies that interfere with IgE antibody binding. The structural analysis revealed mechanisms of allergen-antibody recognition through cation-π interactions. Single and multiple Bla g 2 mutants were expressed in Pichia pastoris and purified. The triple mutant K132A/K251A/F162Y showed an ∼100-fold reduced capacity to bind IgE, while preserving the native molecular fold, as proven by x-ray crystallography. This mutant was still able to induce mast cell release. T-cell responses were assessed by analyzing Th1/Th2 cytokine production and the CD4(+) T-cell phenotype in peripheral blood mononuclear cell cultures. Although T-cell activating capacity was similar for the KKF mutant and Bla g 2 based on CD25 expression, the KKF mutant was a weaker inducer of the Th2 cytokine IL-13. Furthermore, this mutant induced IL-10 from a non-T-cell source at higher levels that those induced by Bla g 2. Our findings demonstrate that a rational design of site-directed mutagenesis was effective in producing a mutant with only 3 amino acid substitutions that maintained the same fold as wild type Bla g 2. These residues, which were involved in IgE antibody binding, endowed Bla g 2 with a T-cell modulatory capacity. The antigenic analysis of Bla g 2 will be useful for the subsequent development of recombinant allergen vaccines.
Collapse
Affiliation(s)
- Judith A Woodfolk
- From the Allergy Division, Department of Medicine, University of Virginia, Charlottesville, Virginia 22903
| | - Jill Glesner
- INDOOR Biotechnologies, Inc., Charlottesville, Virginia 22908
| | - Paul W Wright
- From the Allergy Division, Department of Medicine, University of Virginia, Charlottesville, Virginia 22903
| | - Christopher L Kepley
- the Joint School of Nanoscience and Nanoengineering, University of North Carolina, Greensboro, North Carolina 27401
| | - Mi Li
- the Macromolecular Crystallography Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702, Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory, Frederick, Maryland 21702, and
| | - Martin Himly
- the Department of Molecular Biology, University of Salzburg, 5020 Salzburg, Austria
| | - Lyndsey M Muehling
- From the Allergy Division, Department of Medicine, University of Virginia, Charlottesville, Virginia 22903
| | - Alla Gustchina
- the Macromolecular Crystallography Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | - Alexander Wlodawer
- the Macromolecular Crystallography Laboratory, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702
| | | | - Anna Pomés
- INDOOR Biotechnologies, Inc., Charlottesville, Virginia 22908,
| |
Collapse
|
31
|
Dillon MBC, Schulten V, Oseroff C, Paul S, Dullanty LM, Frazier A, Belles X, Piulachs MD, Visness C, Bacharier L, Bloomberg GR, Busse P, Sidney J, Peters B, Sette A. Different Bla-g T cell antigens dominate responses in asthma versus rhinitis subjects. Clin Exp Allergy 2015; 45:1856-67. [PMID: 26414909 PMCID: PMC4654660 DOI: 10.1111/cea.12643] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 07/29/2015] [Accepted: 08/19/2015] [Indexed: 02/05/2023]
Abstract
BACKGROUND AND OBJECTIVE The allergenicity of several German cockroach (Bla-g) antigens at the level of IgE responses is well established. However, less is known about the specificity of CD4+ TH responses, and whether differences exist in associated magnitude or cytokine profiles as a function of disease severity. METHODS Proteomic and transcriptomic techniques were used to identify novel antigens recognized by allergen-specific T cells. To characterize different TH functionalities of allergen-specific T cells, ELISPOT assays with sets of overlapping peptides covering the sequences of known allergens and novel antigens were employed to measure release of IL-5, IFNγ, IL-10, IL-17 and IL-21. RESULTS Using these techniques, we characterized TH responses in a cohort of adult Bla-g-sensitized subjects, either with (n = 55) or without (n = 17) asthma, and nonsensitized controls (n = 20). T cell responses were detected for ten known Bla-g allergens and an additional ten novel Bla-g antigens, representing in total a 5-fold increase in the number of antigens demonstrated to be targeted by allergen-specific T cells. Responses of sensitized individuals regardless of asthma status were predominantly TH 2, but higher in patients with diagnosed asthma. In asthmatic subjects, Bla-g 5, 9 and 11 were immunodominant, while, in contrast, nonasthmatic-sensitized subjects responded mostly to Bla-g 5 and 4 and the novel antigen NBGA5. CONCLUSIONS Asthmatic and nonasthmatic cockroach-sensitized individuals exhibit similar TH 2-polarized responses. Compared with nonasthmatics, however, asthmatic individuals have responses of higher magnitude and different allergen specificity.
Collapse
Affiliation(s)
- M B C Dillon
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - V Schulten
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - C Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - S Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - L M Dullanty
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Frazier
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - X Belles
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - M D Piulachs
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - C Visness
- Federal Systems Division, Rho Inc., Chapel Hill, NC, USA
| | - L Bacharier
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - G R Bloomberg
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - P Busse
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai School of Medicine, New York, NY, USA
| | - J Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - B Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - A Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| |
Collapse
|
32
|
Cockroach allergy and allergen-specific immunotherapy in asthma: potential and pitfalls. Curr Opin Allergy Clin Immunol 2015; 14:535-41. [PMID: 25144264 DOI: 10.1097/aci.0000000000000106] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
PURPOSE OF REVIEW To provide a summary and discussion of cockroach allergy and clinical trials of cockroach allergen immunotherapy. RECENT FINDINGS Cockroach allergen exposure among sensitized children is increasingly recognized as a key factor contributing to asthma morbidity. Recent trials suggest that cockroach immunotherapy holds promise as a treatment strategy with studies demonstrating immunomodulatory and clinical effects. However, a few obstacles need to be overcome to realize the full potential of this treatment modality as cockroach-allergic patients often exhibit complex sensitization patterns to multiple cockroach-associated proteins, and an immunodominant allergen has not been identified. These factors have made it difficult to produce standardized cockroach allergen extracts that are potent and provide the broad allergen profiles needed for optimal treatment. There have been important advances in the identification and cloning of cockroach allergens, and several strategies are being developed to provide therapeutic cockroach allergen products with enhanced clinical efficacy. SUMMARY Allergen immunotherapy has the capability of modulating the immune response to cockroach allergen and has potential as a valuable treatment modality. Further studies of the clinical efficacy, along with the development of improved therapeutic products, are needed to advance our knowledge and realize the full potential of this promising therapy.
Collapse
|
33
|
Paul S, Dillon MBC, Arlehamn CSL, Huang H, Davis MM, McKinney DM, Scriba TJ, Sidney J, Peters B, Sette A. A population response analysis approach to assign class II HLA-epitope restrictions. THE JOURNAL OF IMMUNOLOGY 2015; 194:6164-6176. [PMID: 25948811 DOI: 10.4049/jimmunol.1403074] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 04/04/2015] [Indexed: 11/19/2022]
Abstract
Identification of the specific HLA locus and allele presenting an epitope for recognition by specific TCRs (HLA restriction) is necessary to fully characterize the immune response to Ags. Experimental determination of HLA restriction is complex and technically challenging. As an alternative, the restricting HLA locus and allele can be inferred by genetic association, using response data in an HLA-typed population. However, simple odds ratio (OR) calculations can be problematic when dealing with large numbers of subjects and Ags, and because the same epitope can be presented by multiple alleles (epitope promiscuity). In this study, we develop a tool, denominated Restrictor Analysis Tool for Epitopes, to extract inferred restriction from HLA class II-typed epitope responses. This automated method infers HLA class II restriction from large datasets of T cell responses in HLA class II-typed subjects by calculating ORs and relative frequencies from simple data tables. The program is validated by: 1) analyzing data of previously determined HLA restrictions; 2) experimentally determining in selected individuals new HLA restrictions using HLA-transfected cell lines; and 3) predicting HLA restriction of particular peptides and showing that corresponding HLA class II tetramers efficiently bind to epitope-specific T cells. We further design a specific iterative algorithm to account for promiscuous recognition by calculation of OR values for combinations of different HLA molecules while incorporating predicted HLA binding affinity. The Restrictor Analysis Tool for Epitopes program streamlines the prediction of HLA class II restriction across multiple T cell epitopes and HLA types.
Collapse
Affiliation(s)
- Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Myles B C Dillon
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | | | - Huang Huang
- The Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | - Mark M Davis
- The Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305
| | | | - Thomas Jens Scriba
- Vaccine Initiative, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037
| |
Collapse
|
34
|
Mueller GA, Pedersen LC, Glesner J, Edwards LL, Zakzuk J, London RE, Arruda LK, Chapman MD, Caraballo L, Pomés A. Analysis of glutathione S-transferase allergen cross-reactivity in a North American population: Relevance for molecular diagnosis. J Allergy Clin Immunol 2015; 136:1369-1377. [PMID: 25930195 DOI: 10.1016/j.jaci.2015.03.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/06/2015] [Accepted: 03/13/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND It is not clear whether cross-reactivity or cosensitization to glutathione S-transferases (GSTs) occurs in tropical and subtropical environments. In the United States, Bla g 5 is the most important GST allergen and lack of coexposure to GSTs from certain species allows a better assessment of cross-reactivity. OBJECTIVES To examine the molecular structure of GST allergens from cockroach (Bla g 5), dust mites (Der p 8 and Blo t 8), and helminth (Asc s 13) for potential cross-reactive sites, and to assess the IgE cross-reactivity of sensitized patients from a temperate climate for these allergens for molecular diagnostic purposes. METHODS Four crystal structures were determined. Sera from patients allergic to cockroach and mite were tested for IgE reactivity to these GSTs. A panel of 6 murine anti-Bla g 5 mAb was assessed for cross-reactivity with the other 3 GSTs using antibody binding assays. RESULTS Comparisons of the allergen structures, formed by 2-domain monomers that dimerize, revealed few contiguous regions of similar exposed residues, rendering cross-reactivity unlikely. Accordingly, anti-Bla g 5 or anti-Der p 8 IgE from North American patients did not recognize Der p 8 or Bla g 5, respectively, and neither showed binding to Blo t 8 or Asc s 13. A weaker binding of anti-Bla g 5 IgE to Der p 8 versus Bla g 5 (∼ 100-fold) was observed by inhibition assays, similar to a weak recognition of Der p 8 by anti-Bla g 5 mAb. Patients from tropical Colombia had IgE to all 4 GSTs. CONCLUSIONS The lack of significant IgE cross-reactivity among the 4 GSTs is in agreement with the low shared amino acid identity at the molecular surface. Each GST is needed for accurate molecular diagnosis in different geographic areas.
Collapse
Affiliation(s)
- Geoffrey A Mueller
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC
| | - Jill Glesner
- INDOOR Biotechnologies, Inc. Charlottesville, VA
| | - Lori L Edwards
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC
| | - Josefina Zakzuk
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia.,Foundation for the Development of Medical and Biological Sciences, Cartagena, Colombia
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park , NC
| | | | | | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia.,Foundation for the Development of Medical and Biological Sciences, Cartagena, Colombia
| | - Anna Pomés
- INDOOR Biotechnologies, Inc. Charlottesville, VA
| |
Collapse
|
35
|
Paul S, Lindestam Arlehamn CS, Scriba TJ, Dillon MBC, Oseroff C, Hinz D, McKinney DM, Carrasco Pro S, Sidney J, Peters B, Sette A. Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. J Immunol Methods 2015; 422:28-34. [PMID: 25862607 DOI: 10.1016/j.jim.2015.03.022] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/31/2015] [Indexed: 01/01/2023]
Abstract
Computational prediction of HLA class II restricted T cell epitopes has great significance in many immunological studies including vaccine discovery. In recent years, prediction of HLA class II binding has improved significantly but a strategy to globally predict the most dominant epitopes has not been rigorously defined. Using human immunogenicity data associated with sets of 15-mer peptides overlapping by 10 residues spanning over 30 different allergens and bacterial antigens, and HLA class II binding prediction tools from the Immune Epitope Database and Analysis Resource (IEDB), we optimized a strategy to predict the top epitopes recognized by human populations. The most effective strategy was to select peptides based on predicted median binding percentiles for a set of seven DRB1 and DRB3/4/5 alleles. These results were validated with predictions on a blind set of 15 new allergens and bacterial antigens. We found that the top 21% predicted peptides (based on the predicted binding to seven DRB1 and DRB3/4/5 alleles) were required to capture 50% of the immune response. This corresponded to an IEDB consensus percentile rank of 20.0, which could be used as a universal prediction threshold. Utilizing actual binding data (as opposed to predicted binding data) did not appreciably change the efficacy of global predictions, suggesting that the imperfect predictive capacity is not due to poor algorithm performance, but intrinsic limitations of HLA class II epitope prediction schema based on HLA binding in genetically diverse human populations.
Collapse
Affiliation(s)
- Sinu Paul
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA.
| | | | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative (SATVI), School of Child and Adolescent Health, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Myles B C Dillon
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Carla Oseroff
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Denise Hinz
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Denise M McKinney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Sebastian Carrasco Pro
- Laboratorio de Bioinformática y Biología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, CA 92037, USA
| |
Collapse
|
36
|
Rönkä AL, Kinnunen TT, Goudet A, Rytkönen-Nissinen MA, Sairanen J, Kailaanmäki AHT, Randell JT, Maillère B, Virtanen TI. Characterization of human memory CD4(+) T-cell responses to the dog allergen Can f 4. J Allergy Clin Immunol 2015; 136:1047-54.e10. [PMID: 25843313 DOI: 10.1016/j.jaci.2015.02.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 12/23/2014] [Accepted: 02/02/2015] [Indexed: 01/08/2023]
Abstract
BACKGROUND The recently identified dog lipocalin allergen Can f 4 is an important respiratory allergen. OBJECTIVE We sought to comprehensively characterize the memory CD4(+) T-cell responses of allergic and nonallergic subjects to Can f 4. METHODS Can f 4-specific CD4(+)CD45RO(+) T-cell lines (TCLs) from allergic and healthy subjects were established and characterized by their functional and phenotypic properties. The epitope specificity of the TCLs was tested with 48 overlapping 16-mer peptides spanning the sequence of Can f 4. HLA restriction of the specific TCLs and the binding capacity of the epitope-containing peptides to common HLA class II molecules were studied. RESULTS Can f 4-specific memory CD4(+) TCLs were obtained at an 8-fold higher frequency from allergic than from nonallergic subjects. Functionally, the TCLs of allergic subjects exhibited a higher T-cell receptor avidity and expression of CD25 and predominantly produced IL-4 and IL-5. The TCLs of nonallergic subjects mostly secreted IFN-γ and IL-10, with high CXCR3 expression. Several distinct T-cell epitope regions along the allergen were identified. Importantly, the peptides from the region between amino acids 43 and 67 showed promiscuous HLA-binding capacity and induced memory CD4(+) T-cell responses in 90% of the allergic donors. CONCLUSION Productive TH2-deviated memory T-cell responses to Can f 4 are observed in allergic but not nonallergic subjects. A 19-mer peptide sequence covering the core of the immunodominant region of the allergen is a potential target for the development of peptide-based allergen immunotherapy.
Collapse
Affiliation(s)
- Aino L Rönkä
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland.
| | - Tuure T Kinnunen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Amélie Goudet
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies, Service d'Ingénierie Moléculaire des Protéines, Gif-Sur-Yvette, France
| | - Marja A Rytkönen-Nissinen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland; Institute of Dentistry, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Joni Sairanen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Anssi H T Kailaanmäki
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Jukka T Randell
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | - Bernard Maillère
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies, Service d'Ingénierie Moléculaire des Protéines, Gif-Sur-Yvette, France
| | - Tuomas I Virtanen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
37
|
Jug r 2-reactive CD4(+) T cells have a dominant immune role in walnut allergy. J Allergy Clin Immunol 2015; 136:983-92.e7. [PMID: 25772597 PMCID: PMC4568181 DOI: 10.1016/j.jaci.2015.01.029] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 01/20/2015] [Accepted: 01/22/2015] [Indexed: 12/24/2022]
Abstract
Background Allergic reactions to walnut can be life threatening. While IgE epitopes of walnut have been studied, CD4+ T-cell specific epitopes for walnut remain uncharacterized. Particularly, the relationship of both phenotype and frequency of walnut specific T-cells to the disease have not been examined. Objectives We sought to provide a thorough phenotypic analysis for walnut reactive T-cells in allergic and non-allergic subjects. Particularly, the relationship of phenotypes and frequencies of walnut specific T-cells with the disease. Methods CD154 up-regulation assay was used to examine CD4+ T-cell reactivity towards walnut allergens.Jug r 1, Jug r 2 and Jug r 3. Tetramer-Guided epitope mapping approach was utilized to identify HLA-restricted CD4+ T-cells epitopes in Jug r 2. Direct ex vivo staining with peptide-major histocompatibility complex class II (pMHC-II) tetramers enabled the comparison of frequency and phenotype of Jug r 2-specific CD4+ T-cells between allergic and non-allergic subjects. Jug r 2-specific T-cell-clones were also generated and mRNA transcription factor levels were assessed by RT qPCR. Intracellular cytokine staining (ICS) assays were performed for further phenotypical analyses. Results Jug r 2 was identified as the major allergen that elicited CD4+ T-cell responses. Multiple Jug r 2 T-cell epitopes were identified. The majority of these T-cells in allergic subjects have a CCR4+ TCM (central memory) phenotype. A subset of these T-cells express CCR4+CCR6+ irrespectively of the asthmatic status of the allergic subjects. ICS confirmed these TH2, TH2/TH17 and TH17-like heterogenic profiles. Jug r 2-specific T-cell-clones from allergic subjects mainly expressed GATA3; nonetheless, a portion of T-cell clones expressed either GATA3 and RORC, or RORC, confirming the presence of TH2, TH2/TH17 and TH17 cells. Conclusions Jug r 2 specific responses dominate walnut T-cell responses in subjects with walnut allergy. Jug r 2 central memory CD4+ cells and terminal effector T-cells were detected in peripheral blood with the central memory phenotype as the most prevalent phenotype. In addition to conventional TH2-cells, TH2/TH17 and TH17 cells were also detected in non-asthmatic and asthmatic subjects with walnut allergy. Understanding this T-cell heterogeneity may render better understanding of the disease manifestation.
Collapse
|
38
|
Frazier A, Schulten V, Hinz D, Oseroff C, Sidney J, Peters B, Sette A. Allergy-associated T cell epitope repertoires are surprisingly diverse and include non-IgE reactive antigens. World Allergy Organ J 2014; 7:26. [PMID: 25352946 PMCID: PMC4210551 DOI: 10.1186/1939-4551-7-26] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/12/2014] [Indexed: 12/16/2022] Open
Abstract
We recently identified T cell epitopes associated with human allergic responses. In a majority of cases, responses focused on a few immunodominant epitopes which can be predicted on the basis of MHC binding characteristics. Several observations from our studies challenged the assumption that T cell epitopes are derived from the same allergen proteins that bind IgE. Transcriptomic and proteomics analysis identified pollen proteins, not bound by IgE. These novel Timothy Grass proteins elicited vigorous Th2 responses, suggesting that unlinked T cell help is operational in pollen-specific responses. Thus, the repertoire of antigens recognized by T cells is much broader than IgE-binding allergens. Additionally, we evaluated the use of epitopes from these novel antigens to assess immunological changes associated with Specific Immunotherapy (SIT). We found that a marked decrease in IL5 production is associated with clinically efficacious SIT, suggesting that these novel antigens are potential immunomarkers for SIT efficacy.
Collapse
Affiliation(s)
- April Frazier
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - Veronique Schulten
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - Denise Hinz
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - Carla Oseroff
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - John Sidney
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - Bjoern Peters
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| | - Alessandro Sette
- La Jolla Institute for Allergy & Immunology, 9420 Athena Circle, La Jolla, CA 92037 USA
| |
Collapse
|
39
|
Liukko ALK, Kinnunen TT, Rytkönen-Nissinen MA, Kailaanmäki AHT, Randell JT, Maillère B, Virtanen TI. Human CD4+ T cell responses to the dog major allergen Can f 1 and its human homologue tear lipocalin resemble each other. PLoS One 2014; 9:e98461. [PMID: 24875388 PMCID: PMC4038554 DOI: 10.1371/journal.pone.0098461] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/03/2014] [Indexed: 01/21/2023] Open
Abstract
Lipocalin allergens form a notable group of proteins, as they contain most of the significant respiratory allergens from mammals. The basis for the allergenic capacity of allergens in the lipocalin family, that is, the development of T-helper type 2 immunity against them, is still unresolved. As immunogenicity has been proposed to be a decisive feature of allergens, the purpose of this work was to examine human CD4+ T cell responses to the major dog allergen Can f 1 and to compare them with those to its human homologue, tear lipocalin (TL). For this, specific T cell lines were induced in vitro from the peripheral blood mononuclear cells of Can f 1-allergic and healthy dog dust-exposed subjects with peptides containing the immunodominant T cell epitopes of Can f 1 and the corresponding TL peptides. We found that the frequency of Can f 1 and TL-specific T cells in both subject groups was low and close to each other, the difference being about two-fold. Importantly, we found that the proliferative responses of both Can f 1 and TL-specific T cell lines from allergic subjects were stronger than those from healthy subjects, but that the strength of the responses within the subject groups did not differ between these two antigens. Moreover, the phenotype of the Can f 1 and TL-specific T cell lines, determined by cytokine production and expression of cell surface markers, resembled each other. The HLA system appeared to have a minimal role in explaining the allergenicity of Can f 1, as the allergic and healthy subjects' HLA background did not differ, and HLA binding was very similar between Can f 1 and TL peptides. Along with existing data on lipocalin allergens, we conclude that strong antigenicity is not decisive for the allergenicity of Can f 1.
Collapse
Affiliation(s)
- Aino L. K. Liukko
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Tuure T. Kinnunen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Marja A. Rytkönen-Nissinen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
- Institute of Dentistry, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Anssi H. T. Kailaanmäki
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| | - Jukka T. Randell
- Department of Pulmonary Diseases, Kuopio University Hospital, Kuopio, Finland
| | - Bernard Maillère
- Commissariat à l'Energie Atomique, Institut de Biologie et de Technologies, Service d'Ingénierie Moléculaire des Protéines, Gif Sur Yvette, France
| | - Tuomas I. Virtanen
- Department of Clinical Microbiology, Institute of Clinical Medicine and Biocenter Kuopio, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
40
|
Lindestam Arlehamn CS, Lewinsohn D, Sette A, Lewinsohn D. Antigens for CD4 and CD8 T cells in tuberculosis. Cold Spring Harb Perspect Med 2014; 4:a018465. [PMID: 24852051 DOI: 10.1101/cshperspect.a018465] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tuberculosis (TB), caused by infection with Mycobacterium tuberculosis (MTB), represents an important cause of morbidity and mortality worldwide for which an improved vaccine and immunodiagnostics are urgently needed. CD4(+) and CD8(+) T cells play an important role in host defense to TB. Definition of the antigens recognized by these T cells is critical for improved understanding of the immunobiology of TB and for development of vaccines and diagnostics. Herein, the antigens and epitopes recognized by classically HLA class I- and II-restricted CD4(+) and CD8(+) T cells in humans infected with MTB are reviewed. Immunodominant antigens and epitopes have been defined using approaches targeting particular TB proteins or classes of proteins and by genome-wide discovery approaches. Antigens and epitopes recognized by classically restricted CD4(+) and CD8(+) T cells show extensive breadth and diversity in MTB-infected humans.
Collapse
Affiliation(s)
| | - David Lewinsohn
- Oregon Health and Science University, Portland, Oregon 97239 Portland VA Medical Center, Portland, Oregon 97239
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, California 92037
| | | |
Collapse
|
41
|
Abstract
As investigations into the innate immune responses that lead to allergic sensitization become better defined, there is a need to determine how allergens could interact with pattern recognition receptors that bind non-proteinaceous moieties. Many important allergens are not covalently bound to lipid or carbohydrate, but have structures belonging to lipid, glycan and glycolipid-binding families. These include ML-domain proteins, lipopolysaccharide-binding/cell permeability-increasing proteins, von Ebner gland lipocalins, salivary lipocalins/major urinary proteins, plant pathogenesis-related proteins PR-5 and -10, uteroglobins, non-specific lipid transfer proteins, large lipid transfer proteins and proteins with chitin and other carbohydrate-binding modules. The binding expected is overviewed with regard to importance of the allergens and their ability to elicit responses proposed from experimental models. The evidence compiled showing that allergens from the same source sensitize for different types of adaptive immune responses supports the concept that individual allergens within these sources have their own distinctive interactions with innate immunity.
Collapse
|
42
|
Lindestam Arlehamn CS, Sette A. Definition of CD4 Immunosignatures Associated with MTB. Front Immunol 2014; 5:124. [PMID: 24715893 PMCID: PMC3970006 DOI: 10.3389/fimmu.2014.00124] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Accepted: 03/11/2014] [Indexed: 01/05/2023] Open
Abstract
We have recently described the first true genome-wide screen for CD4(+) T-cell reactivity directed against Mycobacterium tuberculosis (MTB) in latent TB-infected individuals. The approach relied on predictions of HLA-binding capacity for a panel of DR, DP, and DQ alleles representative of those most commonly expressed in the general population, coupled with high throughput ELISPOT assays. The results identified hundreds of novel epitopes and antigens, and documented the novel observation that T cells in latent MTB infection are confined to the CXCR3(+)CCR6(+) phenotype and largely directed against three antigenic "islands" within the MTB genome. In parallel, we have made generally available to the scientific community the technical approaches and reagents developed in the process, such as motifs, algorithms, and binding assays for several common HLA class II alleles, and a panel of single allele HLA class II transfected cell lines representative of the most frequent specificities in the general population. Recent efforts have been focused on characterization of epitopes and antigens recognized by patients with active TB and individuals vaccinated with BCG, with the aim of providing the first systematic evaluation of the overlap between latent, active, and BCG cohorts. The definition of a broad range of epitopes restricted by common HLA molecules, will facilitate development of diagnostic reagents, allow a rigorous evaluation of T-cell responses associated with TB infection in humans, and enable the evaluation of the immunogenicity of different vaccine candidates. Furthermore, it might suggest new candidates for vaccine and diagnostic development.
Collapse
Affiliation(s)
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology , La Jolla, CA , USA
| |
Collapse
|
43
|
Characterization of an anti-Bla g 1 scFv: epitope mapping and cross-reactivity. Mol Immunol 2014; 59:200-7. [PMID: 24667070 DOI: 10.1016/j.molimm.2014.02.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 02/06/2014] [Indexed: 11/21/2022]
Abstract
Bla g 1 is a major allergen from Blatella germanica and one of the primary allergens used to assess cockroach allergen exposure. The epitope of an anti-Bla g 1 scFv was mapped in order to better understand cross reactivity with other group 1 cockroach allergens and patient IgE epitopes. X-ray crystallography was used to determine the structure of the scFv. The scFv epitope on Bla g 1 was located by alanine scanning site-directed mutagenesis and ELISA. Twenty-six rBla g 1-GST alanine mutants were evaluated for variations in binding to the scFv compared to the wild type allergen. Six mutants showed a significant difference in scFv binding affinity. These mutations clustered to form a discontinuous epitope mainly comprising two helices of Bla g 1. The allergen-scFv complex was modeled based on the results, and the epitope region was found to have low sequence similarity with Per a 1, especially among the residues identified as functionally important for the scFv binding to Bla g 1. Indeed, the scFv failed to bind Per a 1 in American cockroach extract. The scFv was unable to inhibit the binding of IgE antibodies from a highly cockroach allergic patient to Bla g 1. Based on the surface area of Bla g 1 occluded by the scFv, putative regions of patient IgE-Bla g 1 interactions can be inferred. This scFv could be best utilized as a capture antibody in an IgE detection ELISA, or to differentiate Bla g 1 from Per a 1 in environmental exposure assays.
Collapse
|
44
|
Reubsaet LL, Meerding J, Scholman R, Arets B, Prakken BJ, van Wijk F, Knol EF. Allergen-specific Th2 responses in young children precede sensitization later in life. Allergy 2014; 69:406-10. [PMID: 24467266 DOI: 10.1111/all.12366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/25/2013] [Indexed: 12/28/2022]
Abstract
Allergic sensitization is initiated by allergen-specific Th2-cell responses. Data on early allergen-specific T-cell responses in allergic children are scarce. We hypothesized that allergen-specific Th2-cell responses can be detected preceding sensitization. Therefore, peripheral blood mononuclear cells (PBMC) of nonsensitized, 'not-yet' sensitized or sensitized children were cultured with highly purified allergens. Cytokine levels in supernatant were determined using multiplex assay and GATA3 expression by flow cytometry. PBMC of sensitized children aged 3 and 5 years showed higher production of IL4, IL5 and IL13 and higher expression of GATA3 in response to purified allergens compared to nonsensitized children. PBMC of children that were 'not-yet' sensitized already showed higher levels of IL5 and IL13 and higher GATA3 expression at age 3 years. This shows that allergen-specific in vitro Th2 responses precede the detection of allergen-specific IgE, which can provide a window of opportunity for novel therapeutic interventions.
Collapse
Affiliation(s)
- L. L. Reubsaet
- Laboratory for Translational Immunology; Department of Pediatric Immunology; University Medical Centre Utrecht; Wilhelmina Children's Hospital; Utrecht the Netherlands
| | - J. Meerding
- Laboratory for Translational Immunology; Department of Pediatric Immunology; University Medical Centre Utrecht; Wilhelmina Children's Hospital; Utrecht the Netherlands
| | - R. Scholman
- Laboratory for Translational Immunology; Department of Pediatric Immunology; University Medical Centre Utrecht; Wilhelmina Children's Hospital; Utrecht the Netherlands
| | - B. Arets
- Department of Pediatric Respiratory Medicine; Wilhelmina Children's Hospital; University Medical Centre Utrecht; Utrecht the Netherlands
| | - B. J. Prakken
- Laboratory for Translational Immunology; Department of Pediatric Immunology; University Medical Centre Utrecht; Wilhelmina Children's Hospital; Utrecht the Netherlands
| | - F. van Wijk
- Laboratory for Translational Immunology; Department of Pediatric Immunology; University Medical Centre Utrecht; Wilhelmina Children's Hospital; Utrecht the Netherlands
| | - E. F. Knol
- Laboratory for Translational Immunology; Department of Immunology; University Medical Centre Utrecht; Utrecht the Netherlands
- Department of Dermatology/Allergology; University Medical Centre Utrecht; Utrecht the Netherlands
| |
Collapse
|
45
|
Evaluating the immunogenicity of protein drugs by applying in vitro MHC binding data and the immune epitope database and analysis resource. Clin Dev Immunol 2013; 2013:467852. [PMID: 24222776 PMCID: PMC3816028 DOI: 10.1155/2013/467852] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Accepted: 09/03/2013] [Indexed: 12/20/2022]
Abstract
The immune system has evolved to become highly specialized in recognizing and responding to pathogens and foreign molecules. Specifically, the function of HLA class II is to ensure that a sufficient sample of peptides derived from foreign molecules is presented to T cells. This leads to an important concern in human drug development as the possible immunogenicity of biopharmaceuticals, especially those intended for chronic administration, can lead to reduced efficacy and an undesired safety profile for biological therapeutics. As part of this review, we will highlight the molecular basis of antigen presentation as a key step in the induction of T cell responses, emphasizing the events associated with peptide binding to polymorphic and polygenic HLA class II molecules. We will further review methodologies that predict HLA class II binding peptides and candidate epitopes. We will focus on tools provided by the Immune Epitope Database and Analysis Resource, discussing the basic features of different prediction methods, the objective evaluation of prediction quality, and general guidelines for practical use of these tools. Finally the use, advantages, and limitations of the methodology will be demonstrated in a review of two previous studies investigating the immunogenicity of erythropoietin and timothy grass pollen.
Collapse
|
46
|
Pomés A, Arruda LK. Investigating cockroach allergens: aiming to improve diagnosis and treatment of cockroach allergic patients. Methods 2013; 66:75-85. [PMID: 23916425 DOI: 10.1016/j.ymeth.2013.07.036] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 07/24/2013] [Accepted: 07/26/2013] [Indexed: 12/16/2022] Open
Abstract
Cockroach allergy is an important health problem associated with the development of asthma, as a consequence of chronic exposure to low levels of allergens in susceptible individuals. In the last 20 years, progress in understanding the disease has been possible, thanks to the identification and molecular cloning of cockroach allergens and their expression as recombinant proteins. Assays for assessment of environmental allergen exposure have been developed and used to measure Bla g 1 and Bla g 2, as markers of cockroach exposure. IgE antibodies to cockroach extracts and to specific purified allergens have been measured to assess sensitization and analyze association with exposure and disease. With the development of the field of structural biology and the expression of recombinant cockroach allergens, insights into allergen structure, function, epitope mapping and allergen-antibody interactions have provided further understanding of mechanisms of cockroach allergic disease at the molecular level. This information will contribute to develop new approaches to allergen avoidance and to improve diagnosis and therapy of cockroach allergy.
Collapse
Affiliation(s)
- Anna Pomés
- Indoor Biotechnologies, Inc., Charlottesville, VA, USA.
| | | |
Collapse
|
47
|
Mueller GA, Pedersen LC, Lih FB, Glesner J, Moon AF, Chapman MD, Tomer KB, London RE, Pomés A. The novel structure of the cockroach allergen Bla g 1 has implications for allergenicity and exposure assessment. J Allergy Clin Immunol 2013; 132:1420-6. [PMID: 23915714 DOI: 10.1016/j.jaci.2013.06.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/28/2013] [Accepted: 06/19/2013] [Indexed: 10/26/2022]
Abstract
BACKGROUND Sensitization to cockroach allergens is a major risk factor for asthma. The cockroach allergen Bla g 1 has multiple repeats of approximately 100 amino acids, but the fold of the protein and its biological function are unknown. OBJECTIVE We sought to determine the structure of Bla g 1, investigate the implications for allergic disease, and standardize cockroach exposure assays. METHODS nBla g 1 and recombinant constructs were compared by using ELISA with specific murine IgG and human IgE. The structure of Bla g 1 was determined by x-ray crystallography. Mass spectrometry and nuclear magnetic resonance spectroscopy were used to examine the ligand-binding properties of the allergen. RESULTS The structure of an rBla g 1 construct with comparable IgE and IgG reactivity to the natural allergen was solved by x-ray crystallography. The Bla g 1 repeat forms a novel fold with 6 helices. Two repeats encapsulate a large and nearly spherical hydrophobic cavity, defining the basic structural unit. Lipids in the cavity varied depending on the allergen origin. Palmitic, oleic, and stearic acids were associated with nBla g 1 from cockroach frass. One unit of Bla g 1 was equivalent to 104 ng of allergen. CONCLUSIONS Bla g 1 has a novel fold with a capacity to bind various lipids, which suggests a digestive function associated with nonspecific transport of lipid molecules in cockroaches. Defining the basic structural unit of Bla g 1 facilitates the standardization of assays in absolute units for the assessment of environmental allergen exposure.
Collapse
Affiliation(s)
- Geoffrey A Mueller
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC.
| | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Previously undescribed grass pollen antigens are the major inducers of T helper 2 cytokine-producing T cells in allergic individuals. Proc Natl Acad Sci U S A 2013; 110:3459-64. [PMID: 23401558 DOI: 10.1073/pnas.1300512110] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
T cells play an important role in the pathogenesis of allergic diseases. However, the proteins considered as potential immunogens of allergenic T-cell responses have traditionally been limited to those that induce IgE responses. Timothy grass (TG) pollen is a well-studied inhaled allergen for which major IgE-reactive allergens have also been shown to trigger T helper 2 (Th2) responses. Here we examined whether other TG pollen proteins are recognized by Th2 responses independently of IgE reactivity. A TG pollen extract was analyzed by 2D gel electrophoresis and IgE/IgG immunoblots using pooled sera from allergic donors. Mass spectrometry of selected protein spots in combination with de novo sequencing of the whole TG pollen transcriptome identified 93 previously undescribed proteins for further study, 64 of which were not targeted by IgE. Predicted MHC binding peptides from the previoulsy undescribed TG proteins were screened for T-cell reactivity in peripheral blood mononuclear cells from allergic donors. Strong IL-5 production was detected in response to peptides from several of the previously undescribed proteins, most of which were not targeted by IgE. Responses against the dominant undescribed epitopes were associated with the memory T-cell subset and could even be detected directly ex vivo after Th2 cell enrichment. These findings demonstrate that a combined unbiased transcriptomic, proteomic, and immunomic approach identifies a greatly broadened repertoire of protein antigens targeted by T cells involved in allergy pathogenesis. The discovery of proteins that induce Th2 cells but are not IgE reactive may allow the development of safer immunotherapeutic strategies.
Collapse
|
49
|
A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. Immunogenetics 2013; 65:357-70. [PMID: 23392739 DOI: 10.1007/s00251-013-0684-y] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/19/2013] [Indexed: 01/04/2023]
Abstract
Classic ways to determine MHC restriction involve inhibition with locus-specific antibodies and antigen presentation assays with panels of cell lines matched or mismatched at the various loci of interest. However, these determinations are often complicated by T cell epitope degeneracy and promiscuity. We describe a selection of 46 HLA DR, DQ, and DP specificities that provide worldwide population (phenotypic) coverage of almost 90 % at each locus, and account for over 66 % of all genes at each locus. This panel afforded coverage of at least four HLA class II alleles in over 95 % of the individuals in four study populations of diverse ethnicity from the USA and South Africa. Next, a panel of single HLA class II-transfected cell lines, corresponding to these 46 allelic variants was assembled, consisting of lines previously developed and 15 novel lines generated for the present study. The novel lines were validated by assessing their HLA class II expression by FACS analysis, the in vitro peptide binding activity of HLA molecules purified from the cell lines, and their antigen presenting capacity to T cell lines of known restriction. We also show that these HLA class II-transfected cell lines can be used to rapidly and unambiguously determine HLA restriction of epitopes recognized by an individual donor in a single experiment. This panel of lines will enable high throughput determination of HLA restriction, enabling better characterization of HLA class II-restricted T cell responses and facilitating the development of HLA tetrameric staining reagents.
Collapse
|
50
|
Schulten V, Oseroff C, Alam R, Broide D, Vijayanand P, Peters B, Sette A. The identification of potentially pathogenic and therapeutic epitopes from common human allergens. Ann Allergy Asthma Immunol 2012; 110:7-10. [PMID: 23244651 DOI: 10.1016/j.anai.2012.10.015] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2012] [Revised: 10/01/2012] [Accepted: 10/23/2012] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To outline the processes involved in large-scale T-cell epitope identification from common allergens and illustrate their relevance to development of allergy specific immunotherapy. DATA SOURCES A set of studies recently published by our laboratory illustrating high-throughput identification of allergen specific T-cell epitopes. STUDY SELECTION T-cell responses contribute both directly and indirectly to allergy-related disease. However, the molecular targets (epitopes) recognized by allergen-specific T cells are largely undefined. We review several different studies in the last 2 years that identified novel T-cell epitopes from a panel of 32 different allergen sources. RESULTS Allergen-specific T-cell responses are highly heterogeneous. Epitopes prevalently recognized in allergic patients are often capable of binding to multiple HLA class II molecules. This feature can be used to predict these promiscuous epitopes by bioinformatic predictions. This approach was validated in the Timothy grass system and then applied to a panel of 31 other allergen sources. CONCLUSION T-cell epitopes for common allergens have been identified, and a general method to identify epitopes from additional allergens has been validated. Characterization of epitopes for common allergens might enable new diagnostics and immunotherapy regimens. These data will also allow the study of T-cell responses in different patient populations and throughout disease progression.
Collapse
|