The overall scope of this program is to capitalize on the availability of well-characterized T cell allergen epitopes to test specific hypotheses that arose from analysis of the data generated by the previous Large Scale Allergen Epitope Identification contracts, awarded to LIAI and Benaroya Institutes. We previously noted that in response to Timothy Grass (TG) extract, as expected TH2 cytokines predominate. However, IFN? production was associated with allergic rhinitis and IL17 with allergic asthma. Project 1 (Sette PI) will test the hypothesis that different stages (in-season versus out-of-season), types (rhinitis versus asthma) and severities of allergic disease are associated with differential magnitude of T cell responses, and also distinctive interplay of different TH subsets. Here, longitudinal studies will determine the relative size of TH subsets specific for defined epitopes both ex vivo and after in vitro expansion and we will characterize their kinetics of appearance and interplay as a function of seasonality and disease severity. Project 2 (Peters PI) will test th hypothesis that SIT treatment and clinical efficacy is associated with modulating the T cell response. Specifically, we will test the hypothesis that SIT treatment affects T cell responses to a set of novel antigens that are being identified by our laboratory that are not recognized by IgE responses. Responses to both known and novel antigens will be measured longitudinally along with multiple phenotypic T cell markers. Specific hypotheses will examine the role of Tfh subsets in modulating antibody responses and the role of IL10 producing cells in suppressing TH2 responses. Project 3 (Rao PI) will identify epigenetic signatures that correlate with asthma development and severity, as well as SIT treatment, by comparing histone modifications and DNA methylation/ hydroxymethylation patterns in epitope specific T cells isolated from blood of asthmatic versus allergic rhinitis patients. Extensive preliminary data indicates that the interpla between transcription factors and epigenetic mechanisms not only initiates immune cell differentiation but also maintains the long-term differentiated state. Accordingly, we will test th hypothesis that asthma is characterized by long-range epigenetic changes at relevant disease-associated genomic loci. The outcome of the proposed research will be the generation of validated allergen epitope data, and its dissemination to the scientific community. This will fulfil the intent of the RFA "Allergen Epitope Research and Validation Centers", provide new insight into the targets and the nature of T cell responses in allergic disease, and provide potential avenues for diagnostic and therapeutic intervention.

Public Health Relevance

Despite the high incidence of allergic disease and the prominent T cell responses associated with allergic reaction, relatively little data exists characterizing allergen-derived epitope fragments and associated T cells. This application studies the nature of these responses and their evolution during seasons, treatment and as a function of different diseases (asthma versus rhinitis). These studies may reveal cellular and molecular pathways associated with allergic disease, and thus might suggest new therapeutic interventions.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
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Special Emphasis Panel (ZAI1-PA-I (J1))
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Minnicozzi, Michael
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La Jolla Institute
La Jolla
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Seumois, Grégory; Chavez, Lukas; Gerasimova, Anna et al. (2014) Epigenomic analysis of primary human T cells reveals enhancers associated with TH2 memory cell differentiation and asthma susceptibility. Nat Immunol 15:777-88
Schulten, Véronique; Peters, Bjoern; Sette, Alessandro (2014) New strategies for allergen T cell epitope identification: going beyond IgE. Int Arch Allergy Immunol 165:75-82
Arlehamn, Cecilia Lindestam; Seumois, Gregory; Gerasimova, Anna et al. (2014) Transcriptional profile of tuberculosis antigen-specific T cells reveals novel multifunctional features. J Immunol 193:2931-40
Huang, Yun; Chavez, Lukas; Chang, Xing et al. (2014) Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells. Proc Natl Acad Sci U S A 111:1361-6
Schulten, Véronique; Tripple, Victoria; Sidney, John et al. (2014) Association between specific timothy grass antigens and changes in TH1- and TH2-cell responses following specific immunotherapy. J Allergy Clin Immunol 134:1076-83
Gerasimova, Anna; Chavez, Lukas; Li, Bin et al. (2013) Predicting cell types and genetic variations contributing to disease by combining GWAS and epigenetic data. PLoS One 8:e54359
Vaughan, Kerrie; Peters, Bjoern; Larche, Mark et al. (2013) Strategies to query and display allergy-derived epitope data from the immune epitope database. Int Arch Allergy Immunol 160:334-45
McKinney, Denise M; Southwood, Scott; Hinz, Denise et al. (2013) A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. Immunogenetics 65:357-70
Schulten, Veronique; Oseroff, Carla; Alam, Rafeul et al. (2013) The identification of potentially pathogenic and therapeutic epitopes from common human allergens. Ann Allergy Asthma Immunol 110:7-10