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Panda S, Morgan J, Cheng C, Saito M, Gilman RH, Ciobanu N, Crudu V, Catanzaro DG, Catanzaro A, Rodwell T, Perera JSB, Chathuranga T, Gunasena B, DeSilva AD, Peters B, Sette A, Lindestam Arlehamn CS. Identification of differentially recognized T cell epitopes in the spectrum of tuberculosis infection. Nat Commun 2024; 15:765. [PMID: 38278794 PMCID: PMC10817963 DOI: 10.1038/s41467-024-45058-9] [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: 04/13/2023] [Accepted: 01/12/2024] [Indexed: 01/28/2024] Open
Abstract
There is still incomplete knowledge of which Mycobacterium tuberculosis (Mtb) antigens can trigger distinct T cell responses at different stages of infection. Here, a proteome-wide screen of 20,610 Mtb-derived peptides in 21 patients mid-treatment for active tuberculosis (ATB) reveals IFNγ-specific T cell responses against 137 unique epitopes. Of these, 16% are recognized by two or more participants and predominantly derived from cell wall and cell processes antigens. There is differential recognition of antigens, including TB vaccine candidate antigens, between ATB participants and interferon-gamma release assay (IGRA + /-) individuals. We developed an ATB-specific peptide pool (ATB116) consisting of epitopes exclusively recognized by ATB participants. This pool can distinguish patients with pulmonary ATB from IGRA + /- individuals from various geographical locations, with a sensitivity of over 60% and a specificity exceeding 80%. This proteome-wide screen of T cell reactivity identified infection stage-specific epitopes and antigens for potential use in diagnostics and measuring Mtb-specific immune responses.
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Affiliation(s)
- Sudhasini Panda
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeffrey Morgan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Catherine Cheng
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H Gilman
- Johns Hopkins School of Public Health, Baltimore, MD, USA
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Judy S B Perera
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Teshan Chathuranga
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | - Aruna D DeSilva
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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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.
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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
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3
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Lewis SA, Sutherland A, Soldevila F, Westernberg L, Aoki M, Frazier A, Maiche S, Erlewyn-Lajeunesse M, Arshad H, Leonard S, Laubach S, Dantzer JA, Wood RA, Sette A, Seumois G, Vijayanand P, Peters B. Identification of cow milk epitopes to characterize and quantify disease-specific T cells in allergic children. J Allergy Clin Immunol 2023; 152:1196-1209. [PMID: 37604312 PMCID: PMC10846667 DOI: 10.1016/j.jaci.2023.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/12/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023]
Abstract
BACKGROUND Cow milk (CM) allergy is the most prevalent food allergy in young children in the United States and Great Britain. Current diagnostic tests are either unreliable (IgE test and skin prick test) or resource-intensive with risks (food challenges). OBJECTIVE We sought to determine whether allergen-specific T cells in CM-allergic (CMA) patients have a distinct quality and/or quantity that could potentially be used as a diagnostic marker. METHODS Using PBMCs from 147 food-allergic pediatric subjects, we mapped T-cell responses to a set of reactive epitopes in CM that we compiled in a peptide pool. This pool induced cytokine responses in in vitro cultured cells distinguishing subjects with CMA from subjects without CMA. We further used the pool to isolate and characterize antigen-specific CD4 memory T cells using flow cytometry and single-cell RNA/TCR sequencing assays. RESULTS We detected significant changes in the transcriptional program and clonality of CM antigen-specific (CM+) T cells elicited by the pool in subjects with CMA versus subjects without CMA ex vivo. CM+ T cells from subjects with CMA had increased percentages of FOXP3+ cells over FOXP3- cells. FOXP3+ cells are often equated with regulatory T cells that have suppressive activity, but CM+ FOXP3+ cells from subjects with CMA showed significant expression of interferon-responsive genes and dysregulated chemokine receptor expression compared with subjects without CMA, suggesting that these are not conventional regulatory T cells. The CM+ FOXP3+ cells were also more clonally expanded than the FOXP3- population. We were further able to use surface markers (CD25, CD127, and CCR7) in combination with our peptide pool stimulation to quantify these CM+ FOXP3+ cells by a simple flow-cytometry assay. We show increased percentages of CM+ CD127-CD25+ cells from subjects with CMA in an independent cohort, which could be used for diagnostic purposes. Looking specifically for TH2 cells normally associated with allergic diseases, we found a small population of clonally expanded CM+ cells that were significantly increased in subjects with CMA and that had high expression of TH2 cytokines and pathogenic TH2/T follicular helper markers. CONCLUSIONS Overall, these findings suggest that there are several differences in the phenotypes of CM+ T cells with CM allergy and that the increase in CM+ FOXP3+ cells is a potential diagnostic marker of an allergic state. Such markers have promising applications in monitoring natural disease outgrowth and/or the efficacy of immunotherapy that will need to be validated in future studies.
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Affiliation(s)
| | | | | | | | - Minori Aoki
- La Jolla Institute for Immunology, San Diego, Calif
| | | | | | - Mich Erlewyn-Lajeunesse
- University Hospital Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Hasan Arshad
- University Hospital Southampton, Southampton, United Kingdom; Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Stephanie Leonard
- Division of Allergy and Immunology, Department of Pediatrics, University of California San Diego, Rady Children's Hospital, San Diego, Calif
| | - Susan Laubach
- Division of Allergy and Immunology, Department of Pediatrics, University of California San Diego, Rady Children's Hospital, San Diego, Calif
| | - Jennifer A Dantzer
- Division of Allergy and Immunology, Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Md
| | - Robert A Wood
- Division of Allergy and Immunology, Department of Pediatrics, The Johns Hopkins University School of Medicine, Baltimore, Md
| | - Alessandro Sette
- La Jolla Institute for Immunology, San Diego, Calif; Department of Medicine, University of California San Diego, San Diego, Calif
| | | | - Pandurangan Vijayanand
- La Jolla Institute for Immunology, San Diego, Calif; Department of Medicine, University of California San Diego, San Diego, Calif
| | - Bjoern Peters
- La Jolla Institute for Immunology, San Diego, Calif; Department of Medicine, University of California San Diego, San Diego, Calif.
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Sethi GS, Gracias DT, Gupta RK, Carr D, Miki H, Da Silva Antunes R, Croft M. Anti-CD3 inhibits circulatory and tissue-resident memory CD4 T cells that drive asthma exacerbations in mice. Allergy 2023; 78:2168-2180. [PMID: 36951658 DOI: 10.1111/all.15722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 03/24/2023]
Abstract
BACKGROUND Exacerbations of asthma are thought to be strongly dependent on reactivation of allergen-induced lung tissue-resident and circulatory memory CD4 T cells. Strategies that broadly inhibit multiple T cell populations might then be useful to limit asthma. Accordingly, we tested whether targeting CD3 during exposure to inhaled allergen could prevent the accumulation of lung-localized effector memory CD4 T cells and block exacerbations of asthmatic inflammation. METHODS House dust mite-sensitized and repetitively challenged BL/6 mice were transiently treated therapeutically with F(ab')2 anti-CD3ε and memory T cell responses and lung inflammation were assessed. PBMCs from HDM-allergic donors were examined for the effect of anti-CD3 on expansion of allergen-reactive T cells. RESULTS Allergen-sensitized mice undergoing exacerbations of asthma were protected from lung inflammation by transient therapeutic treatment with F(ab')2 anti-CD3. Regardless of whether sensitized mice underwent a secondary or tertiary recall response to inhaled allergen, anti-CD3 inhibited all phenotypes of effector memory CD4 T cells in the lung tissue and lung vasculature by 80%-90%, including those derived from tissue-resident and circulatory memory T cells. This did not depend on Treg cells suggesting it was primarily a blocking effect on memory T cell signaling. Correspondingly, anti-CD3 also strongly inhibited proliferation of human allergen-reactive memory CD4 T cells from allergic individuals. In contrast, the number of surviving tissue-resident memory CD4 T cells that were maintained in the lungs at later times was not robustly reduced by anti-CD3. CONCLUSION Anti-CD3 F(ab')2 administration at the time of allergen exposure represents a viable strategy for limiting the immediate activity of allergen-responding memory T cells and asthma exacerbations.
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Affiliation(s)
- Gurupreet S Sethi
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Donald T Gracias
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Rinkesh K Gupta
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Daniel Carr
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Haruka Miki
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Ricardo Da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Michael Croft
- Center for Autoimmunity and Inflammation, La Jolla Institute for Immunology, La Jolla, California, USA
- Department of Medicine, University of California San Diego, La Jolla, California, USA
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5
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Panda S, Morgan J, Cheng C, Saito M, Gilman RH, Ciobanu N, Crudu V, Catanzaro DG, Catanzaro A, Rodwell T, Perera JS, Chathuranga T, Gunasena B, DeSilva AD, Peters B, Sette A, Lindestam Arlehamn CS. Identification of differentially recognized T cell epitopes in the spectrum of Mtb infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536550. [PMID: 37090558 PMCID: PMC10120689 DOI: 10.1101/2023.04.12.536550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Tuberculosis caused by Mycobacterium tuberculosis is one of the leading causes of death from a single infectious agent. Identifying dominant epitopes and comparing their reactivity in different tuberculosis (TB) infection states can help design diagnostics and vaccines. We performed a proteome-wide screen of 20,610 Mtb derived peptides in 21 Active TB (ATB) patients 3-4 months post-diagnosis of pulmonary TB (mid-treatment) using an IFNγ and IL-17 Fluorospot assay. Responses were mediated exclusively by IFNγ and identified a total of 137 unique epitopes, with each patient recognizing, on average, 8 individual epitopes and 22 epitopes (16%) recognized by 2 or more participants. Responses were predominantly directed against antigens part of the cell wall and cell processes category. Testing 517 peptides spanning TB vaccine candidates and ESAT-6 and CFP10 antigens also revealed differential recognition between ATB participants mid-treatment and healthy IGRA+ participants of several vaccine antigens. An ATB-specific peptide pool consisting of epitopes exclusively recognized by participants mid-treatment, allowed distinguishing participants with active pulmonary TB from healthy interferon-gamma release assay (IGRA)+/- participants from diverse geographical locations. Analysis of longitudinal samples indicated decreased reactivity during treatment for pulmonary TB. Together, these results show that a proteome-wide screen of T cell reactivity identifies epitopes and antigens that are differentially recognized depending on the Mtb infection stage. These have potential use in developing diagnostics and vaccine candidates and measuring correlates of protection.
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Affiliation(s)
- Sudhasini Panda
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jeffrey Morgan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Catherine Cheng
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Johns Hopkins School of Public Health, Baltimore, MD, USA
- Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Timothy Rodwell
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Judy S.B. Perera
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Teshan Chathuranga
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bandu Gunasena
- National Hospital for Respiratory Diseases, Welisara, Sri Lanka
| | - Aruna D. DeSilva
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Faculty of Medicine, General Sir John Kotelawala Defense University, Ratmalana, Sri Lanka
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alessandro Sette
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
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Fernandes AMS, da Silva ES, Silveira EF, Belitardo EMMDA, Santiago LF, Silva RC, Dos Santos Alves V, Carneiro DM, Ferreira F, Jacquet A, Pacheco LGC, Alcantara-Neves NM, Pinheiro CS. Recombinant T-cell epitope conjugation: A new approach for Dermatophagoides hypoallergen design. Clin Exp Allergy 2023; 53:198-209. [PMID: 36176209 DOI: 10.1111/cea.14238] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/15/2022] [Accepted: 09/25/2022] [Indexed: 12/01/2022]
Abstract
BACKGROUND Allergen-specific immunotherapy (AIT) is the only clinical approach that can potentially cure some allergic diseases by inducing immunological tolerance. Dermatophagoides pteronyssinus is considered as the most important source of mite allergens worldwide, with high sensitization rates for the major allergens Der p 1, Der p 2 and Der p 23. The aim of this work is to generate a hypoallergenic hybrid molecule containing T-cell epitopes from these three major allergens. METHODS The hybrid protein termed Der p 2231 containing T-cell epitopes was purified by affinity chromatography. The human IgE reactivity was verified by comparing those with the parental allergens. The hybrid was also characterized immunologically through an in vivo mice model. RESULTS The hybrid rDer p 2231 stimulated in peripheral blood mononuclear cells (PBMCs) isolated from allergic patients with higher levels of IL- 2, IL-10, IL-15 and IFN-γ, as well as lower levels of IL-4, IL-5, IL-13, TNF-α and GM-CSF. The use of hybrid molecules as a therapeutic model in D. pteronyssinus allergic mice led to the reduction of IgE production and lower eosinophilic peroxidase activity in the airways. We found increased levels of IgG antibodies that blocked the IgE binding to the parental allergens in the serum of allergic patients. Furthermore, the stimulation of splenocytes from mice treated with rDer p 2231 induced higher levels of IL-10 and IFN-γ and decreased the secretion of IL-4 and IL-5, when compared with parental allergens and D. pteronyssinus extract. CONCLUSIONS rDer p 2231 has the potential to be used in AIT in patients co-sensitized with D. pteronyssinus major allergens, once it was able to reduce IgE production, inducing allergen-specific blocking antibodies, restoring and balancing Th1/Th2 immune responses, and inducing regulatory T-cells.
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Affiliation(s)
- Antônio Márcio Santana Fernandes
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programas de Pós-Graduação em Biotecnologia da Universidade Federal da Bahia, Salvador, Brazil
| | - Eduardo Santos da Silva
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Elisânia Fontes Silveira
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | | | - Leonardo Freire Santiago
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Raphael Chagas Silva
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Vitor Dos Santos Alves
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Deise Malta Carneiro
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil
| | - Fatima Ferreira
- Department of Biosciences and Medical Biology, University of Salzburg, Salzburg, Austria
| | - Alain Jacquet
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Luis Gustavo Carvalho Pacheco
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programas de Pós-Graduação em Biotecnologia da Universidade Federal da Bahia, Salvador, Brazil
| | - Neuza Maria Alcantara-Neves
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programas de Pós-Graduação em Biotecnologia da Universidade Federal da Bahia, Salvador, Brazil
| | - Carina Silva Pinheiro
- Laboratório de Alergia e Acarologia, Departamento de Ciências da Biointeração, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador, Brazil.,Programas de Pós-Graduação em Biotecnologia da Universidade Federal da Bahia, Salvador, Brazil
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7
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Sakakibara M, Maeda Y, Nakamura K. Fetal loss due to Th1-skewed Th1/Th2 balance with increase (not decrease) of regulatory T cells in abortion-prone mouse model. J Toxicol Sci 2022; 47:327-336. [PMID: 35908933 DOI: 10.2131/jts.47.327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We used an abortion-prone mouse model, generated by mating female CBA/J mice with male DBA/2JJcl mice, to examine the effects of changes in the Th1/Th2 cell ratio and the percentage of regulatory T (Treg) cells on the maintenance of pregnancy. We subcutaneously injected female CBA/J mice once each with 50 μg/mouse of Dermatophagoides farinae (Df) extract and the squalene-based adjuvant (SquA); 10 days later, these mice were mated with male DBA/2JJcl mice. Compared with injection of vehicle or adjuvant, the Df treatment decreased the Th1/Th2 cell ratio and concomitantly increased the percentage of Treg cells in the spleen. In addition, fetal death rates were decreased. We then explored a substance which shifted the Th1/Th2 balance toward Th1 side. We found that 50 μg/mouse of keyhole limpet hemocyanin (KLH) increased the splenic Th1/Th2 cell ratio of nonpregnant female CBA/J mice. We subcutaneously injected female CBA/J mice with KLH and SquA; 10 days later, these mice were mated with male DBA/2JJcl mice. Compared with injection of vehicle or adjuvant, treatment with KLH enhanced the Th1 bias during pregnancy and increased the fetal death rate. The percentage of Treg cells, however, was increased in these KLH-injected pregnant mice contrary to our presumption. All collected data showed strong positive correlation between the Th1/Th2 cell ratio and fetal death rate. The increase in Treg cells independent of effects on the fetal death rate suggests that Treg cells do not necessarily induce maternal tolerance to the fetus but may prevent excessive Th1/Th2 imbalance during pregnancy.
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Affiliation(s)
| | - Yosuke Maeda
- School of Veterinary Medicine, Kitasato University
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8
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Seumois G, Ramírez-Suástegui C, Schmiedel BJ, Liang S, Peters B, Sette A, Vijayanand P. Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma. Sci Immunol 2021; 5:5/48/eaba6087. [PMID: 32532832 DOI: 10.1126/sciimmunol.aba6087] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 05/22/2020] [Indexed: 12/19/2022]
Abstract
CD4+ T helper (TH) cells and regulatory T (Treg) cells that respond to common allergens play an important role in driving and dampening airway inflammation in patients with asthma. Until recently, direct, unbiased molecular analysis of allergen-reactive TH and Treg cells has not been possible. To better understand the diversity of these T cell subsets in allergy and asthma, we analyzed the single-cell transcriptome of ~50,000 house dust mite (HDM) allergen-reactive TH cells and Treg cells from asthmatics with HDM allergy and from three control groups: asthmatics without HDM allergy and nonasthmatics with and without HDM allergy. Our analyses show that HDM allergen-reactive TH and Treg cells are highly heterogeneous and certain subsets are quantitatively and qualitatively different in individuals with HDM-reactive asthma. The number of interleukin-9 (IL-9)-expressing HDM-reactive TH cells is greater in asthmatics with HDM allergy compared with nonasthmatics with HDM allergy, and this IL-9-expressing TH subset displays enhanced pathogenic properties. More HDM-reactive TH and Treg cells expressing the interferon response signature (THIFNR and TregIFNR) are present in asthmatics without HDM allergy compared with those with HDM allergy. In cells from these subsets (THIFNR and TregIFNR), expression of TNFSF10 was enriched; its product, tumor necrosis factor-related apoptosis-inducing ligand, dampens activation of TH cells. These findings suggest that the THIFNR and TregIFNR subsets may dampen allergic responses, which may help explain why only some people develop TH2 responses to nearly ubiquitous allergens.
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Affiliation(s)
- Grégory Seumois
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
| | | | | | - Shu Liang
- 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.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA
| | - Pandurangan Vijayanand
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA. .,Department of Medicine, University of California San Diego, La Jolla, CA 92037, USA.,Clinical and Experimental Sciences, National Institute for Health Research Southampton Respiratory Biomedical Research Unit, Faculty of Medicine, University of Southampton, Southampton SO166YD, UK
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9
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Coquet JM. A singular role for interleukin-9 in the development of asthma. Sci Immunol 2021; 5:5/48/eabc4021. [PMID: 32532833 DOI: 10.1126/sciimmunol.abc4021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 05/21/2020] [Indexed: 12/16/2022]
Abstract
Interleukin-9 expression by T helper cells marks allergic individuals who develop asthma (see the related Research Article by Seumois et al.).
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Affiliation(s)
- Jonathan M Coquet
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden.
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10
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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.
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11
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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.
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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.
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12
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Mateus J, Grifoni A, Tarke A, Sidney J, Ramirez SI, Dan JM, Burger ZC, Rawlings SA, Smith DM, Phillips E, Mallal S, Lammers M, Rubiro P, Quiambao L, Sutherland A, Yu ED, da Silva Antunes R, Greenbaum J, Frazier A, Markmann AJ, Premkumar L, de Silva A, Peters B, Crotty S, Sette A, Weiskopf D. Selective and cross-reactive SARS-CoV-2 T cell epitopes in unexposed humans. Science 2020; 370:89-94. [PMID: 32753554 PMCID: PMC7574914 DOI: 10.1126/science.abd3871] [Citation(s) in RCA: 794] [Impact Index Per Article: 198.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 07/30/2020] [Indexed: 12/11/2022]
Abstract
Many unknowns exist about human immune responses to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. SARS-CoV-2-reactive CD4+ T cells have been reported in unexposed individuals, suggesting preexisting cross-reactive T cell memory in 20 to 50% of people. However, the source of those T cells has been speculative. Using human blood samples derived before the SARS-CoV-2 virus was discovered in 2019, we mapped 142 T cell epitopes across the SARS-CoV-2 genome to facilitate precise interrogation of the SARS-CoV-2-specific CD4+ T cell repertoire. We demonstrate a range of preexisting memory CD4+ T cells that are cross-reactive with comparable affinity to SARS-CoV-2 and the common cold coronaviruses human coronavirus (HCoV)-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Thus, variegated T cell memory to coronaviruses that cause the common cold may underlie at least some of the extensive heterogeneity observed in coronavirus disease 2019 (COVID-19) disease.
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Affiliation(s)
- Jose Mateus
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alba Grifoni
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alison Tarke
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - John Sidney
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Sydney I Ramirez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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
| | - Jennifer M Dan
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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
| | - Zoe C Burger
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Stephen A Rawlings
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Davey M Smith
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, La Jolla, CA 92037, USA
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA 6150, Australia
| | - Marshall Lammers
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Paul Rubiro
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Lorenzo Quiambao
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Aaron Sutherland
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Esther Dawen Yu
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Ricardo da Silva Antunes
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Jason Greenbaum
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - April Frazier
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Alena J Markmann
- Department of Medicine, Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Aravinda de Silva
- Department of Microbiology and Immunology, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Bjoern Peters
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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
| | - Shane Crotty
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, 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, 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
| | - Daniela Weiskopf
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA.
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13
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Würtzen PA, Hoof I, Christensen LH, Váczy Z, Henmar H, Salamanca G, Lundegaard C, Lund L, Kráľova T, Brooks EG, Andersen PS. Diverse and highly cross-reactive T-cell responses in ragweed allergic patients independent of geographical region. Allergy 2020; 75:137-147. [PMID: 31325327 DOI: 10.1111/all.13992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 01/05/2023]
Abstract
BACKGROUND Ragweed frequently causes seasonal allergies in North America and Europe. In the United States, several related ragweed species with diverse geographical distribution cause allergic symptoms. Cross-reactivity towards related ragweed species of IgE and treatment-induced IgG4 has been demonstrated previously. However, less is known about the underlying T-cell cross-reactivity. METHODS The allergen content of ragweed extracts was determined by mass spectrometry and related to T-cell epitopes of Amb a allergens (group 1, 3, 4, 5, 8 and 11) in 20 American ragweed allergic patients determined by FluoroSpot and proliferation assays. T-cell responses to 50 frequently recognized Amb a-derived T-cell epitopes and homologous peptides from western ragweed (Amb p), giant ragweed (Amb t) and mugwort (Art v) were investigated in an additional 11 American and 14 Slovakian ragweed allergic donors. RESULTS Ragweed extracts contained all known allergens and isoallergens thereof. Donor T-cell responses were diverse and directed against all Amb a 1 isoallergens and to most minor allergens investigated. Similar response patterns were seen in American and Slovakia donors. Several epitopes were cross-reactive between isoallergens and ragweed species, some even including mugwort. T-cell cross-reactivity generally correlated with allergen sequence homology. CONCLUSION T-cell epitopes of multiple allergens/isoallergens are involved in the diverse T-cell responses in ragweed allergic individuals. T-cell lines were highly cross-reactive to epitopes of related ragweed species without any apparent geographical response bias. These data support that different ragweed species can be considered an allergen homology group with Amb a as the representative species regarding diagnosis as well as allergy immunotherapy.
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Affiliation(s)
| | - Ilka Hoof
- Global Research ALK Hørsholm Denmark
| | | | - Zuzana Váczy
- Louis Pasteur University Hospital Košice Slovak Republic
| | | | | | | | - Lise Lund
- Global Research ALK Hørsholm Denmark
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14
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Huang H, Curin M, Banerjee S, Chen K, Garmatiuk T, Resch‐Marat Y, Carvalho‐Queiroz C, Blatt K, Gafvelin G, Grönlund H, Valent P, Campana R, Focke‐Tejkl M, Valenta R, Vrtala S. A hypoallergenic peptide mix containing T cell epitopes of the clinically relevant house dust mite allergens. Allergy 2019; 74:2461-2478. [PMID: 31228873 PMCID: PMC7078969 DOI: 10.1111/all.13956] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 04/29/2019] [Accepted: 05/01/2019] [Indexed: 12/31/2022]
Abstract
Background In the house dust mite (HDM) Dermatophagoides pteronyssinus, Der p 1, 2, 5, 7, 21, and 23 have been identified as the most important allergens. The aim of this study was to define hypoallergenic peptides derived from the sequences of the six allergens and to use the peptides and the complete allergens to study antibody, T cell, and cytokine responses in sensitized and nonsensitized subjects. Methods IgE reactivity of HDM‐allergic and non‐HDM‐sensitized individuals to 15 HDM allergens was established using ImmunoCAP ISAC technology. Thirty‐three peptides covering the sequences of the six HDM allergens were synthesized. Allergens and peptides were tested for IgE and IgG reactivity by ELISA and ImmunoCAP, respectively. Allergenic activity was determined by basophil activation. CD4+ T cell and cytokine responses were determined in PBMC cultures by CFSE dilution and Luminex technology, respectively. Results House dust mite allergics showed IgE reactivity only to complete allergens, whereas 31 of the 33 peptides lacked relevant IgE reactivity and allergenic activity. IgG antibodies of HDM‐allergic and nonsensitized subjects were directed against peptide epitopes and higher allergen‐specific IgG levels were found in HDM allergics. PBMC from HDM‐allergics produced higher levels of IL‐5 whereas non‐HDM‐sensitized individuals mounted higher levels of IFN‐gamma, IL‐17, pro‐inflammatory cytokines, and IL‐10. Conclusion IgG antibodies in HDM‐allergic patients recognize peptide epitopes which are different from the epitopes recognized by IgE. This may explain why naturally occurring allergen‐specific IgG antibodies do not protect against IgE‐mediated allergic inflammation. A mix of hypoallergenic peptides containing T cell epitopes of the most important HDM allergens was identified.
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Affiliation(s)
- Huey‐Jy Huang
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Mirela Curin
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Srinita Banerjee
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Kuan‐Wei Chen
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Tetiana Garmatiuk
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Yvonne Resch‐Marat
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Claudia Carvalho‐Queiroz
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit Karolinska Institutet Stockholm Sweden
| | - Katharina Blatt
- Division of Hematology&Hemostaseology, Department of Internal Medicine I Medical University of Vienna Vienna Austria
| | - Guro Gafvelin
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit Karolinska Institutet Stockholm Sweden
| | - Hans Grönlund
- Department of Clinical Neuroscience, Therapeutic Immune Design Unit Karolinska Institutet Stockholm Sweden
| | - Peter Valent
- Division of Hematology&Hemostaseology, Department of Internal Medicine I Medical University of Vienna Vienna Austria
| | - Raffaela Campana
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Margarete Focke‐Tejkl
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
| | - Rudolf Valenta
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
- NRC Institute of Immunology FMBA of Russia Moscow Russia
- Department of Clinical Immunology and Allergy, Laboratory for Immunopathology Sechenov First Moscow State Medical University Moscow Russia
| | - Susanne Vrtala
- Division of Immunopathology, Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology Medical University of Vienna Vienna Austria
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15
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Singh G, Pritam M, Banerjee M, Singh AK, Singh SP. Genome based screening of epitope ensemble vaccine candidates against dreadful visceral leishmaniasis using immunoinformatics approach. Microb Pathog 2019; 136:103704. [PMID: 31479726 DOI: 10.1016/j.micpath.2019.103704] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/12/2019] [Accepted: 08/31/2019] [Indexed: 01/09/2023]
Abstract
Visceral leishmaniasis (VL) is a dreadful protozoan disease caused by Leishmania donovani that severely affects huge populations in tropical and sub-tropical regions. The present study reports an unbiased genome based screening of 4 potent vaccine antigens against 8023 L. donovani proteins by following the criteria of presence of signal peptides, GPI-anchors and ≤1 transmembrane helix using advanced bioinformatics tools viz. SignalP4.0, PredGPI and TMHMM2.0, respectively. They are designated as genome based predicted signal peptide antigens (GBPSPA). The antigenicity/immunogenicity of chosen vaccine antigens (GBPSPA) with 4 randomly selected known leishmanial antigens (RSKLA) was compared by simulation study employing C-ImmSim software for human immune responses. This revealed better immunological responses. These antigens were further evaluated for the presence of B- and T-cell epitopes using immune epitope database (IEDB) based recommended consensus method of MHC class I and II tools. It was found to forecast CD4+ and CD8+ T-cell responses in genetically diverse human population worldwide as well as different endemic regions through IEDB based predicted population coverage (PPC) analysis tool. The worldwide percent PPC value of combined (HLA class I and II) epitope ensemble forecast was found to be 99.98, 99.96 and 50.04, respectively for GBPSPA, RSKLA and experimentally known epitopes (EKE) of L. donovani. Therefore, these potential antigens/epitope ensembles could favor the design of prospective and novel vaccine constructs like self-assembled epitopes as nano vaccine formulations against VL. Overall, the present study will serve as a model framework that might improve the effectiveness of designed vaccine against L. donovani and other related pathogens.
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Affiliation(s)
- Garima Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Manisha Pritam
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Monisha Banerjee
- Molecular and Human Genetics Laboratory, Department of Zoology, University of Lucknow, Lucknow- 226007, India.
| | - Akhilesh Kumar Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India.
| | - Satarudra Prakash Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow-226028, India; Department of Biotech and Genome, School of Life Sciences, Mahatma Gandhi Central University, Motihari-845401, India.
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16
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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.
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17
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Dhanda SK, Vaughan K, Schulten V, Grifoni A, Weiskopf D, Sidney J, Peters B, Sette A. Development of a novel clustering tool for linear peptide sequences. Immunology 2018; 155:331-345. [PMID: 30014462 PMCID: PMC6187223 DOI: 10.1111/imm.12984] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 06/28/2018] [Accepted: 07/11/2018] [Indexed: 02/06/2023] Open
Abstract
Epitopes identified in large-scale screens of overlapping peptides often share significant levels of sequence identity, complicating the analysis of epitope-related data. Clustering algorithms are often used to facilitate these analyses, but available methods are generally insufficient in their capacity to define biologically meaningful epitope clusters in the context of the immune response. To fulfil this need we developed an algorithm that generates epitope clusters based on representative or consensus sequences. This tool allows the user to cluster peptide sequences on the basis of a specified level of identity by selecting among three different method options. These include the 'clique method', in which all members of the cluster must share the same minimal level of identity with each other, and the 'connected graph method', in which all members of a cluster must share a defined level of identity with at least one other member of the cluster. In cases where it is not possible to define a clear consensus sequence with the connected graph method, a third option provides a novel 'cluster-breaking algorithm' for consensus sequence driven sub-clustering. Herein we demonstrate the tool's clustering performance and applicability using (i) a selection of dengue virus epitopes for the 'clique method', (ii) sets of allergen-derived peptides from related species for the 'connected graph method' and (iii) large data sets of eluted ligand, major histocompatibility complex binding and T-cell recognition data captured within the Immune Epitope Database (IEDB) with the newly developed 'cluster-breaking algorithm'. This novel clustering tool is accessible at http://tools.iedb.org/cluster2/.
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Affiliation(s)
- Sandeep K. Dhanda
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Kerrie Vaughan
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Veronique Schulten
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Alba Grifoni
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Daniela Weiskopf
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - John Sidney
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
| | - Bjoern Peters
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
- Department of MedicineUniversity of CaliforniaSan DiegoCAUSA
| | - Alessandro Sette
- Division of Vaccine DiscoveryLa Jolla Institute for Allergy and ImmunologyLa JollaCAUSA
- Department of MedicineUniversity of CaliforniaSan DiegoCAUSA
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18
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Paul S, Karosiene E, Dhanda SK, Jurtz V, Edwards L, Nielsen M, Sette A, Peters B. Determination of a Predictive Cleavage Motif for Eluted Major Histocompatibility Complex Class II Ligands. Front Immunol 2018; 9:1795. [PMID: 30127785 PMCID: PMC6087742 DOI: 10.3389/fimmu.2018.01795] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 07/20/2018] [Indexed: 01/13/2023] Open
Abstract
CD4+ T cells have a major role in regulating immune responses. They are activated by recognition of peptides mostly generated from exogenous antigens through the major histocompatibility complex (MHC) class II pathway. Identification of epitopes is important and computational prediction of epitopes is used widely to save time and resources. Although there are algorithms to predict binding affinity of peptides to MHC II molecules, no accurate methods exist to predict which ligands are generated as a result of natural antigen processing. We utilized a dataset of around 14,000 naturally processed ligands identified by mass spectrometry of peptides eluted from MHC class II expressing cells to investigate the existence of sequence signatures potentially related to the cleavage mechanisms that liberate the presented peptides from their source antigens. This analysis revealed preferred amino acids surrounding both N- and C-terminuses of ligands, indicating sequence-specific cleavage preferences. We used these cleavage motifs to develop a method for predicting naturally processed MHC II ligands, and validated that it had predictive power to identify ligands from independent studies. We further confirmed that prediction of ligands based on cleavage motifs could be combined with predictions of MHC binding, and that the combined prediction had superior performance. However, when attempting to predict CD4+ T cell epitopes, either alone or in combination with MHC binding predictions, predictions based on the cleavage motifs did not show predictive power. Given that peptides identified as epitopes based on CD4+ T cell reactivity typically do not have well-defined termini, it is possible that motifs are present but outside of the mapped epitope. Our attempts to take that into account computationally did not show any sign of an increased presence of cleavage motifs around well-characterized CD4+ T cell epitopes. While it is possible that our attempts to translate the cleavage motifs in MHC II ligand elution data into T cell epitope predictions were suboptimal, other possible explanations are that the cleavage signal is too diluted to be detected, or that elution data are enriched for ligands generated through an antigen processing and presentation pathway that is less frequently utilized for T cell epitopes.
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Affiliation(s)
- Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Edita Karosiene
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Vanessa Jurtz
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark
| | - Lindy Edwards
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Department of Bio and Health Informatics, Technical University of Denmark, Lyngby, Denmark.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, San Martín, Argentina
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
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19
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IgE and T-cell responses to house dust mite allergen components. Mol Immunol 2018; 100:120-125. [DOI: 10.1016/j.molimm.2018.03.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 03/19/2018] [Indexed: 01/10/2023]
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20
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Dhanda SK, Karosiene E, Edwards L, Grifoni A, Paul S, Andreatta M, Weiskopf D, Sidney J, Nielsen M, Peters B, Sette A. Predicting HLA CD4 Immunogenicity in Human Populations. Front Immunol 2018; 9:1369. [PMID: 29963059 PMCID: PMC6010533 DOI: 10.3389/fimmu.2018.01369] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 06/01/2018] [Indexed: 12/12/2022] Open
Abstract
Background Prediction of T cell immunogenicity is a topic of considerable interest, both in terms of basic understanding of the mechanisms of T cells responses and in terms of practical applications. HLA binding affinity is often used to predict T cell epitopes, since HLA binding affinity is a key requisite for human T cell immunogenicity. However, immunogenicity at the population it is complicated by the high level of variability of HLA molecules, potential other factors beyond HLA as well as the frequent lack of HLA typing data. To overcome those issues, we explored an alternative approach to identify the common characteristics able to distinguish immunogenic peptides from non-recognized peptides. Methods Sets of dominant epitopes derived from peer-reviewed published papers were used in conjunction with negative peptides from the same experiments/donors to train neural networks and generate an “immunogenicity score.” We also compared the performance of the immunogenicity score with previously described method for immunogenicity prediction based on HLA class II binding at the population level. Results The immunogenicity score was validated on a series of independent datasets derived from the published literature, representing 57 independent studies where immunogenicity in human populations was assessed by testing overlapping peptides spanning different antigens. Overall, these testing datasets corresponded to over 2,000 peptides and tested in over 1,600 different human donors. The 7-allele method prediction and the immunogenicity score were associated with similar performance [average area under the ROC curve (AUC) values of 0.703 and 0.702, respectively] while the combined methods reached an average AUC of 0.725. This increase in average AUC value is significant compared with the immunogenicity score (p = 0.0135) and a strong trend toward significance is observed when compared to the 7-allele method (p = 0.0938). The new immunogenicity score method is now freely available using CD4 T cell immunogenicity prediction tool on the Immune Epitope Database website (http://tools.iedb.org/CD4episcore). Conclusion The new immunogenicity score predicts CD4 T cell immunogenicity at the population level starting from protein sequences and with no need for HLA typing. Its efficacy has been validated in the context of different antigen sources, ethnicities, and disparate techniques for epitope identification.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Edita Karosiene
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Lindy Edwards
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sinu Paul
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Massimo Andreatta
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina
| | - Daniela Weiskopf
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Morten Nielsen
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, Buenos Aires, Argentina.,Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Bjoern Peters
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego, La Jolla, CA, United States
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21
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Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes. PLoS One 2018; 13:e0196551. [PMID: 29734356 PMCID: PMC5937769 DOI: 10.1371/journal.pone.0196551] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 04/16/2018] [Indexed: 12/22/2022] Open
Abstract
The microbiome influences adaptive immunity and molecular mimicry influences T cell reactivity. Here, we evaluated whether the sequence similarity of various antigens to the microbiota dampens or increases immunogenicity of T cell epitopes. Sets of epitopes and control sequences derived from 38 antigenic categories (infectious pathogens, allergens, autoantigens) were retrieved from the Immune Epitope Database (IEDB). Their similarity to microbiome sequences was calculated using the BLOSUM62 matrix. We found that sequence similarity was associated with either dampened (tolerogenic; e.g. most allergens) or increased (inflammatory; e.g. Dengue and West Nile viruses) likelihood of a peptide being immunogenic as a function of epitope source category. Ten-fold cross-validation and validation using sets of manually curated epitopes and non-epitopes derived from allergens were used to confirm these initial observations. Furthermore, the genus from which the microbiome homologous sequences were derived influenced whether a tolerogenic versus inflammatory modulatory effect was observed, with Fusobacterium most associated with inflammatory influences and Bacteroides most associated with tolerogenic influences. We validated these effects using PBMCs stimulated with various sets of microbiome peptides. "Tolerogenic" microbiome peptides elicited IL-10 production, "inflammatory" peptides elicited mixed IL-10/IFNγ production, while microbiome epitopes homologous to self were completely unreactive for both cytokines. We also tested the sequence similarity of cockroach epitopes to specific microbiome sequences derived from households of cockroach allergic individuals and non-allergic controls. Microbiomes from cockroach allergic households were less likely to contain sequences homologous to previously defined cockroach allergens. These results are compatible with the hypothesis that microbiome sequences may contribute to the tolerization of T cells for allergen epitopes, and lack of these sequences might conversely be associated with increased likelihood of T cell reactivity against the cockroach epitopes. Taken together this study suggests that microbiome sequence similarity influences immune reactivity to homologous epitopes encoded by pathogens, allergens and auto-antigens.
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22
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da Silva Antunes R, Pham J, McMurtrey C, Hildebrand WH, Phillips E, Mallal S, Sidney J, Busse P, Peters B, Schulten V, Sette A. Urinary Peptides As a Novel Source of T Cell Allergen Epitopes. Front Immunol 2018; 9:886. [PMID: 29755469 PMCID: PMC5932195 DOI: 10.3389/fimmu.2018.00886] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 04/10/2018] [Indexed: 12/13/2022] Open
Abstract
Mouse allergy in both laboratory workers and in inner-city children is associated with allergic rhinitis and asthma, posing a serious public health concern. Urine is a major source of mouse allergens, as mice spray urine onto their surroundings, where the proteins dry up and become airborne on dust particles. Here, we tested whether oligopeptides that are abundant in mouse urine may contribute to mouse allergic T cell response. Over 1,300 distinct oligopeptides were detected by mass spectrometry analysis of the low molecular weight filtrate fraction of mouse urine (LoMo). Posttranslationally modified peptides were common, accounting for almost half of total peptides. A pool consisting of 225 unique oligopeptides of 13 residues or more in size identified within was tested for its capacity to elicit T cell reactivity in mouse allergic donors. Following 14-day in vitro stimulation of PBMCs, we detected responses in about 95% of donors tested, directed against 116 distinct peptides, predominantly associated with Th2 cytokines (IL-5). Peptides from non-urine related proteins such as epidermal growth factor, collagen, and Beta-globin accounted for the highest response (15.9, 9.1, and 8.1% of the total response, respectively). Peptides derived from major urinary proteins (MUPs), kidney androgen-regulated protein (KAP), and uromodulin were the main T cell targets from kidney or urine related sources. Further ex vivo analysis of enrichment of 4-1BB expressing cells demonstrated that LoMo pool-specific T cell reactivity can be detected directly ex vivo in mouse allergic but not in non-allergic donors. Further cytometric analysis of responding cells revealed a bone fide memory T cell phenotype and confirmed their Th2 polarization. Overall, these data suggest that mouse urine-derived oligopeptides are a novel target for mouse allergy-associated T cell responses, which may contribute to immunopathological mechanisms in mouse allergy.
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Affiliation(s)
| | - John Pham
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Curtis McMurtrey
- Department of Microbiology and Immunology, University of Oklahoma, Oklahoma City, OK, United States
| | - William H Hildebrand
- Department of Microbiology and Immunology, University of Oklahoma, Oklahoma City, OK, United States
| | - Elizabeth Phillips
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - Simon Mallal
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, Australia.,Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, United States
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Paula Busse
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego School of Medicine, La Jolla, CA, United States
| | - Véronique Schulten
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,University of California San Diego School of Medicine, La Jolla, CA, United States
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23
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Schulten V, Westernberg L, Birrueta G, Sidney J, Paul S, Busse P, Peters B, Sette A. Allergen and Epitope Targets of Mouse-Specific T Cell Responses in Allergy and Asthma. Front Immunol 2018; 9:235. [PMID: 29487600 PMCID: PMC5816932 DOI: 10.3389/fimmu.2018.00235] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 01/26/2018] [Indexed: 11/13/2022] Open
Abstract
Mouse allergy has become increasingly common, mainly affecting laboratory workers and inner-city households. To date, only one major allergen, namely Mus m 1, has been described. We sought to identify T cell targets in mouse allergic patients. PBMC from allergic donors were expanded with either murine urine or epithelial extract and subsequently screened for cytokine production (IL-5 and IFNγ) in response to overlapping peptides spanning the entire Mus m 1 sequence, peptides from various Mus m 1 isoforms [major urinary proteins (MUPs)], peptides from mouse orthologs of known allergens from other mammalian species and peptides from proteins identified by immunoproteomic analysis of IgE/IgG immunoblots of mouse urine and epithelial extracts. This approach let to the identification of 106 non-redundant T cell epitopes derived from 35 antigens. Three major T cell-activating regions were defined in Mus m 1 alone. Moreover, our data show that immunodominant epitopes were largely shared between Mus m 1 and other MUPs even from different species, suggesting that sequence conservation in different allergens is a determinant for immunodominance. We further identified several novel mouse T cell antigens based on their homology to known mammalian allergens. Analysis of cohort-specific T cell responses revealed that rhinitis and asthmatic patients recognized different epitope repertoires. Epitopes defined herein can be formulated into an epitope "megapool" used to diagnose mouse allergy and study mouse-specific T cell responses directly ex vivo. This analysis of T cell epitopes provides a good basis for future studies to increase our understanding of the immunopathology associated with MO-allergy and asthma.
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Affiliation(s)
- Véronique Schulten
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Luise Westernberg
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Giovanni Birrueta
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Sinu Paul
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States
| | - Paula Busse
- Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bjoern Peters
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Alessandro Sette
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, United States.,Department of Medicine, University of California San Diego, La Jolla, CA, United States
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24
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Roberts G, Boyle R, Bryce PJ, Crane J, Hogan SP, Saglani S, Wickman M, Woodfolk JA. Developments in the field of allergy mechanisms in 2015 through the eyes of Clinical & Experimental Allergy. Clin Exp Allergy 2017; 46:1248-57. [PMID: 27682977 DOI: 10.1111/cea.12823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In the first of two papers we described the development in the field of allergy mechanisms as described by Clinical and Experimental Allergy in 2015. Experimental models of allergic disease, basic mechanisms, clinical mechanisms and allergens are all covered. A second paper will cover clinical aspects.
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Affiliation(s)
- G Roberts
- Clinical and Experimental Sciences and Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK. .,NIHR Southampton Respiratory Biomedical Research Unit, University Hospital Southampton NHS Foundation Trust, Southampton, UK. .,The David Hide Asthma and Allergy Research Centre, St Mary's Hospital, Isle of Wight, UK.
| | - R Boyle
- Paediatric Research Unit, Imperial College London, London, UK
| | - P J Bryce
- Division of Allergy-Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - J Crane
- Department of Medicine, University of Otago Wellington, Wellington, New Zealand
| | - S P Hogan
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati School of Medicine, Cincinnati, OH, USA
| | - S Saglani
- National Heart & Lung Institute, Imperial College London, London, UK
| | - M Wickman
- Institute of Environmental Medicine, Karolinska Institute, Stockholm, Sweden
| | - J A Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, USA
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25
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Thomas WR. Broad perspectives of allergen specific immunotherapy. Hum Vaccin Immunother 2017; 13:2385-2389. [PMID: 28933669 PMCID: PMC5647984 DOI: 10.1080/21645515.2017.1374522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Wayne Robert Thomas
- Telethon Kids Institute, University of Western Australia , Subiaco, Western Australia, Australia
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26
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Dhanda SK, Grifoni A, Pham J, Vaughan K, Sidney J, Peters B, Sette A. Development of a strategy and computational application to select candidate protein analogues with reduced HLA binding and immunogenicity. Immunology 2017; 153:118-132. [PMID: 28833085 DOI: 10.1111/imm.12816] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/27/2017] [Accepted: 08/14/2017] [Indexed: 12/13/2022] Open
Abstract
Unwanted immune responses against protein therapeutics can reduce efficacy or lead to adverse reactions. T-cell responses are key in the development of such responses, and are directed against immunodominant regions within the protein sequence, often associated with binding to several allelic variants of HLA class II molecules (promiscuous binders). Herein, we report a novel computational strategy to predict 'de-immunized' peptides, based on previous studies of erythropoietin protein immunogenicity. This algorithm (or method) first predicts promiscuous binding regions within the target protein sequence and then identifies residue substitutions predicted to reduce HLA binding. Further, this method anticipates the effect of any given substitution on flanking peptides, thereby circumventing the creation of nascent HLA-binding regions. As a proof-of-principle, the algorithm was applied to Vatreptacog α, an engineered Factor VII molecule associated with unintended immunogenicity. The algorithm correctly predicted the two immunogenic peptides containing the engineered residues. As a further validation, we selected and evaluated the immunogenicity of seven substitutions predicted to simultaneously reduce HLA binding for both peptides, five control substitutions with no predicted reduction in HLA-binding capacity, and additional flanking region controls. In vitro immunogenicity was detected in 21·4% of the cultures of peptides predicted to have reduced HLA binding and 11·4% of the flanking regions, compared with 46% for the cultures of the peptides predicted to be immunogenic. This method has been implemented as an interactive application, freely available online at http://tools.iedb.org/deimmunization/.
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Affiliation(s)
- Sandeep Kumar Dhanda
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Alba Grifoni
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Pham
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Kerrie Vaughan
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - John Sidney
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Bjoern Peters
- 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
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27
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Thomas WR. House Dust Mite Allergens: New Discoveries and Relevance to the Allergic Patient. Curr Allergy Asthma Rep 2017; 16:69. [PMID: 27600386 DOI: 10.1007/s11882-016-0649-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Recent findings on house dust allergens and their contribution to knowledge that will significantly impact on current and future allergy treatments are appraised. RECENT FINDINGS Quantitation of IgE binding to a spectrum of allergen components in several independent studies in varying locations has largely affirmed the main components as the groups 1 and 2 and possibly 23 allergens with mid-tier contributions from the groups 4, 5, 7, and 21. Prevalent binding to Der p 23 has been recapitulated sometimes with low titers. The IgE of non-asthmatic atopic subjects binds at lower titer and to fewer components than that of asthmatics, and their IgG binding relative to IgE is higher especially for children hospitalized for exacerbation. The higher IgG ratios were associated with increased IL-10 a cytokine more readily induced from T cells of allergic subjects. Peptides representing the groups 1 and 2 allergens can be used to stimulate ex vivo T cells showing responses correlating with IgE binding and providing a valuable tool for ascertaining the contribution of IgE and T cells to disease. Also, the induction of Th2 and follicular helper T cells are shown to make different contributions in mice. Cross-reactivity of IgE binding assays with high-titer cross-reactive antibodies induced by scabies is a problem in the many areas of the world where scabies is highly prevalent and endemic and from recent increases in immigration. In the last few years, allergen research has produced results that warrant rapid translation into diagnostic tools and the formulation of allergen components for immunotherapy.
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Affiliation(s)
- Wayne R Thomas
- Telethon Kids Institute, University of Western Australia, 100 Roberts Road, Subiaco, Western Australia, 6008, Australia.
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28
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Muehling LM, Lawrence MG, Woodfolk JA. Pathogenic CD4 + T cells in patients with asthma. J Allergy Clin Immunol 2017; 140:1523-1540. [PMID: 28442213 DOI: 10.1016/j.jaci.2017.02.025] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Revised: 02/07/2017] [Accepted: 02/20/2017] [Indexed: 02/08/2023]
Abstract
Asthma encompasses a variety of clinical phenotypes that involve distinct T cell-driven inflammatory processes. Improved understanding of human T-cell biology and the influence of innate cytokines on T-cell responses at the epithelial barrier has led to new asthma paradigms. This review captures recent knowledge on pathogenic CD4+ T cells in asthmatic patients by drawing on observations in mouse models and human disease. In patients with allergic asthma, TH2 cells promote IgE-mediated sensitization, airway hyperreactivity, and eosinophilia. Here we discuss recent discoveries in the myriad molecular pathways that govern the induction of TH2 differentiation and the critical role of GATA-3 in this process. We elaborate on how cross-talk between epithelial cells, dendritic cells, and innate lymphoid cells translates to T-cell outcomes, with an emphasis on the actions of thymic stromal lymphopoietin, IL-25, and IL-33 at the epithelial barrier. New concepts on how T-cell skewing and epitope specificity are shaped by multiple environmental cues integrated by dendritic cell "hubs" are discussed. We also describe advances in understanding the origins of atypical TH2 cells in asthmatic patients, the role of TH1 cells and other non-TH2 types in asthmatic patients, and the features of T-cell pathogenicity at the single-cell level. Progress in technologies that enable highly multiplexed profiling of markers within a single cell promise to overcome barriers to T-cell discovery in human asthmatic patients that could transform our understanding of disease. These developments, along with novel T cell-based therapies, position us to expand the assortment of molecular targets that could facilitate personalized treatments.
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Affiliation(s)
- Lyndsey M Muehling
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Monica G Lawrence
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va
| | - Judith A Woodfolk
- Allergy Division, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Va.
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29
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Ahmad TA, Eweida AE, El-Sayed LH. T-cell epitope mapping for the design of powerful vaccines. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.vacrep.2016.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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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.
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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
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31
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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.
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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
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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.
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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
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Doshi A, Tripathi DM. Early House Dust Mite Sensitivity in Mumbai Children. Indian J Pediatr 2016; 83:386-90. [PMID: 26666904 DOI: 10.1007/s12098-015-1952-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 11/04/2015] [Indexed: 10/22/2022]
Abstract
OBJECTIVE To identify house dust mite (HDM) sensitivity by skin prick test in children with allergic rhinitis, allergic wheezing and eczema. METHODS In this prospective study, children with persistent or recurrent allergic symptoms of rhinitis, wheezing and eczema were enrolled to undergo skin prick testing. Sensitivity was checked for three mites: Dermatophagoide farinae, Dermatophagoide pteronyssinus, and Blomia tropicalis. RESULTS Total 92 children underwent skin prick test; 49 (53.2 %) showed significant positivity to one or more dust mite. In the HDM sensitized group, a positive family history of allergic disorders was present in 32 children (65.3 %). In the HDM sensitized group, 18 (36.7 %) children had allergic rhinitis. The youngest child in this group was 12-mo-old. Ten (55.55 %) children were less than 24 mo of age. Significant sensitization to mites was detected in 7 (14.28 %) children with eczema. All children were below 24 mo of age. In children with a tendency to wheeze frequently without any evidence of infections or other systemic disease, 24 (48.9 %) had sensitization to HDM. The youngest child was 15 mo of age. Ten (41.6 %) children were below 24 mo of age. Sensitivity to Blomia tropicalis was detected in 6 (12.24 %) children. Significantly more number of children were sensitive to D. pteronyssinus as compared to D. farinae (65.31 % vs. 46.94 %; p = 0.034). CONCLUSIONS Children in Mumbai show early sensitization to HDM. D. pteronyssinus is the commonest offending allergen in the index study.
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Affiliation(s)
- Arpit Doshi
- Department of Pediatrics, H. Bhagwati Municipal Hospital, Borivali West, Mumbai, Maharashtra, 400092, India.
| | - D M Tripathi
- Department of Allergy, Bombay Hospital, Institute of Postgraduate Medical Sciences, Mumbai, India
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34
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Hinz D, Seumois G, Gholami AM, Greenbaum JA, Lane J, White B, Broide DH, Schulten V, Sidney J, Bakhru P, Oseroff C, Wambre E, James EA, Kwok WW, Peters B, Vijayanand P, Sette A. Lack of allergy to timothy grass pollen is not a passive phenomenon but associated with the allergen-specific modulation of immune reactivity. Clin Exp Allergy 2016; 46:705-19. [PMID: 26662458 PMCID: PMC4846575 DOI: 10.1111/cea.12692] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 12/01/2015] [Accepted: 12/03/2015] [Indexed: 01/16/2023]
Abstract
BACKGROUND Timothy grass (TG) pollen is a common seasonal airborne allergen associated with symptoms ranging from mild rhinitis to severe asthma. OBJECTIVE The aim of this study was to characterize changes in TG-specific T cell responses as a function of seasonality. METHODS Peripheral blood mononuclear cells (PBMCs) obtained from allergic individuals and non-allergic controls, either during the pollen season or out of season, were stimulated with either TG extract or a pool of previously identified immunodominant antigenic regions. RESULTS PBMCs from allergic subjects exhibit higher IL-5 and IL-10 responses in season than when collected out of season. In the case of non-allergic subjects, as expected we observed lower IL-5 responses and robust production of IFN-γ compared to allergic individuals. Strikingly, non-allergic donors exhibited an opposing pattern, with decreased immune reactivity in season. The broad down-regulation in non-allergic donors indicates that healthy individuals are not oblivious to allergen exposure, but rather react with an active modulation of responses following the antigenic stimulus provided during the pollen season. Transcriptomic analysis of allergen-specific T cells defined genes modulated in concomitance with the allergen exposure and inhibition of responses in non-allergic donors. CONCLUSION AND CLINICAL RELEVANCE Magnitude and functionality of T helper cell responses differ substantially in season vs. out of season in allergic and non-allergic subjects. The results indicate the specific and opposing modulation of immune responses following the antigenic stimulation during the pollen season. This seasonal modulation reflects the enactment of specific molecular programmes associated with health and allergic disease.
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MESH Headings
- Allergens/immunology
- Case-Control Studies
- Cytokines/metabolism
- Female
- Gene Expression Profiling
- Gene Expression Regulation
- HLA Antigens/genetics
- HLA Antigens/immunology
- Humans
- Immunologic Memory
- Immunomodulation
- Leukocytes, Mononuclear/immunology
- Leukocytes, Mononuclear/metabolism
- Lymphocyte Activation
- Lymphocyte Count
- Male
- Phenotype
- Phleum/immunology
- Pollen/immunology
- RNA, Messenger/genetics
- Rhinitis, Allergic, Seasonal/diagnosis
- Rhinitis, Allergic, Seasonal/genetics
- Rhinitis, Allergic, Seasonal/immunology
- Rhinitis, Allergic, Seasonal/metabolism
- Seasons
- T-Cell Antigen Receptor Specificity
- T-Lymphocyte Subsets/immunology
- T-Lymphocyte Subsets/metabolism
- Transcriptome
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Affiliation(s)
- Denise Hinz
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Grégory Seumois
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Amin M. Gholami
- 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
| | - Brandie White
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | | | | | - John Sidney
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Pearl Bakhru
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Carla Oseroff
- La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA
| | - Erik Wambre
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - Eddie A. James
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, USA
| | - William W. Kwok
- Benaroya Research Institute at Virginia Mason, Seattle, WA 98101, 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
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35
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Batard T, Baron-Bodo V, Martelet A, Le Mignon M, Lemoine P, Jain K, Mariano S, Horiot S, Chabre H, Harwanegg C, Marquette CA, Corgier BP, Soh WT, Satitsuksanoa P, Jacquet A, Chew FT, Nony E, Moingeon P. Patterns of IgE sensitization in house dust mite-allergic patients: implications for allergen immunotherapy. Allergy 2016; 71:220-9. [PMID: 26485347 DOI: 10.1111/all.12796] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2015] [Indexed: 02/06/2023]
Abstract
BACKGROUND Understanding patterns of IgE sensitization in Dermatophagoides-allergic patients living in various geographical areas is necessary to design a product suitable for worldwide allergen immunotherapy (AIT). METHODS Using a HIFI Allergy customized microarray assay, IgEs specific for 12 purified allergens from Dermatophagoides pteronyssinus or D. farinae were assessed in sera from 1302 house dust mite (HDM)-allergic patients living in various areas. Comprehensive mass spectrometric (MS) analyses were conducted to characterize HDM extracts, as well as purified bodies and feces. RESULTS Patterns of IgE reactivity to HDM allergens are comparable in all cohorts of patients analyzed, encompassing adults and 5- to 17-year-old children, as well as American, Canadian, European, and Japanese patients. Overall, >70% and >80% of HDM-allergic patients are sensitized to group 1 and group 2 allergens, respectively, from D. pteronyssinus and/or D. farinae species. Furthermore, 20-47% of patients also have IgEs to allergens from groups 4, 5, 7, 13, 15, 21, and 23. All patients have IgEs to allergens present in mite bodies and feces. MS-based analyses confirmed the presence of mite allergens recorded by IUIS in D. pteronyssinus and D. farinae extracts, with groups 2, 8, 10, 11, 14, and 20 prominent in bodies and groups 1, 6, 18, and 23 well represented in feces. CONCLUSIONS Mite-specific AIT should rely upon a mixture of D. pteronyssinus and D. farinae extracts, manufactured from both feces and bodies. Such a combination is appropriate to treat children and adult Dermatophagoides-allergic patients from Asia, Europe, and North America.
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Affiliation(s)
- T. Batard
- Research and Development; Stallergenes; Antony France
| | - V. Baron-Bodo
- Research and Development; Stallergenes; Antony France
| | - A. Martelet
- Research and Development; Stallergenes; Antony France
| | - M. Le Mignon
- Research and Development; Stallergenes; Antony France
| | - P. Lemoine
- Research and Development; Stallergenes; Antony France
| | - K. Jain
- Research and Development; Stallergenes; Antony France
| | - S. Mariano
- Research and Development; Stallergenes; Antony France
| | - S. Horiot
- Research and Development; Stallergenes; Antony France
| | - H. Chabre
- Research and Development; Stallergenes; Antony France
| | - C. Harwanegg
- Thermo Fisher Scientific ImmunoDiagnostics/Phadia Austria GmbH; Vienna Austria
| | | | | | - W. T. Soh
- Chulalongkorn University; Bangkok Thailand
| | | | - A. Jacquet
- Chulalongkorn University; Bangkok Thailand
| | - F. T. Chew
- National University of Singapore; Singapore City Singapore
| | - E. Nony
- Research and Development; Stallergenes; Antony France
| | - P. Moingeon
- Research and Development; Stallergenes; Antony France
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36
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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.
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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
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