In proposal we will investigate the role of epigenetic mechanisms in the pathogenesis of allergic asthma and rhinitis. Asthma affects 1 in 15 Americans - over 23 million people - thus making it one of the country's most common and also costly diseases. Current therapies do not cure asthma or control daily symptoms for patients with severe disease, prompting us to adopt "out-of-box" approaches to find novel therapies for asthma. Our goal is to directly address the unmet need for asthma sufferers by harnessing the seminal discoveries made in the field of epigenetics to benefit asthma research. Multiple lines of evidence suggest an important role for epigenetic mechanisms in asthma. Specifically, we have identified disease-specific epigenetic signatures in the T helper 2 (TH2) cytokine locus (encompassing the 1L4, IL5 and ILI 3 genes) in patients with moderate asthma compared to patients with mild asthma or controls. In addition, we recently discovered TET proteins that convert 5-methylcytosine (5mC) to 5-hydroxymethyl-cytosine (hmC)in DNA, thus creating a completely new epigenetic mark;and have shown that Tet proteins and 5hmC are expressed in T cells. These are exciting findings because hydroxylation of 5mC alters DNA methylation status in a hitherto unprecedented way, and because DNA methylation is relevant to several fields including mammalian development, cancer, aging, cell lineage specification, genome defense, stem cell function and immunology. We propose to extend these studies to identify epigenetic signatures that correlate with asthma development and severity, by comparing histone modifications and DNA methylation/ hydroxy-methylation patterns in enriched populations of pathogenic epitope-specific T cells isolated from blood of allergic rhinitis subjects and asthmatic patients, categorized based on clinical severity into mild and moderately severe asthmafics. Our study will be the first to define disease-related epigenetic changes in patients with wellcharacterized asthma, and to correlate these with disease severity to obtain specific markers for disfinguishable disease states.

Public Health Relevance

We will test the hypothesis that asthma - a chronic allergic disease - is characterized by perturbations in these epigenetic processes in epitope-specific T cells, that can be recognized and read out as long-range epigenetic changes at relevant disease-associated loci. In Aim 1, we will map histone modification patterns in T cells that initiate and maintain airway inflammafion in allergic asthma. In Aim 2, we will profile patterns of DNA methylation and hydroxymethylation in T cells in asthma. In Aim 3, we will identify epigenetic markers of disease by establishing and analyzing an integrated database of epigenefic, genetic, transcriptomic, funcfional and clinical data. These proposed studies are novel and innovative. They will have a broad impact on our understanding of asthma, and set an important precedent for invesfigafing the role of epigenetic mechanisms in other immune-mediated disorders.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Program--Cooperative Agreements (U19)
Project #
Application #
Study Section
Special Emphasis Panel (ZAI1-PA-I (J1))
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
La Jolla Institute
La Jolla
United States
Zip Code
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