In this multi-PI proposal we will investigate the role of epigenetic mechanisms in the development of asthma in children. Asthma affects 1 in 15 Americans -- over 23 million people -- thus making it one of the country's most common and also costly diseases. Among children, asthma is the third-ranking cause of all hospitalizations and the leading cause of school absenteeism. Current therapies do not cure asthma, prompting us to adopt ?out-of-box? approaches to find novel preventive therapies for asthma. Numerous genome-wide association studies (GWAS) have been instrumental in identifying common genetic variations that affect asthma susceptibility. By contrast, despite overwhelming evidence of the role of environmental exposures during fetal and early childhood in shaping disease outcomes, the systematic assessment of epigenetic variations has lagged behind. Here, we will conduct the first longitudinal epigenome-wide association study (EWAS) to identify epigenetic variations that are associated with asthma susceptibility in children. The proposal will capitalize on two unique recently established longitudinal birth cohorts in the United Kingdom. (i) The Immune Tolerance in Early Childhood (ITEC) is an observational cohort, which consists of 200 children at high risk of developing asthma. (ii) The Mite Allergen Prevention Study (MAPS, n=111) is a primary prevention randomized controlled trial in which house dust mite oral immunotherapy (OIT) was administered to 6-month-old infants at high risk of developing asthma. At 18 months, we found a significant reduction in allergic sensitization in the OIT group and a trend towards reduced onset of wheeze and eczema. We will test the hypothesis that asthma ? a chronic allergic disease -- is characterized by perturbations in these epigenetic processes in immune cells, that can be recognized and read out as long-range epigenetic changes at relevant disease-associated loci.
In Aim 1, we will identify `epigenetic variants' associated with the susceptibility to asthma in children (n=200, ITEC cohort). Then, we will validate our discovery set of `epigenetic variants' by performing a similar study in children from the MAPs cohorts (n=51, placebo arm); then, ask if asthma-risk `epigenetic variants', common to children in ITEC and MAPS cohort, are erased by preventive immunotherapy (n=53, treatment arm).
In Aim 2, we will define the target genes of asthma-risk associated `epigenetic variants' and verify if expression of target genes is affected by the presence or absence of `epigenetic variants'; These studies will allow us to predict sets of novel ?asthma-susceptibility genes? that are likely to have an important role in the development of CD4 T cell driving asthma pathogenesis. We will then test the function of these genes in primary human T cells using optimized micro-scaled immunological assays. Overall, our discovery-based EWAS and follow up functional studies will identify novel genes and pathways involved in the origins of asthma and could open ways to prevent or potentially cure asthma.

Public Health Relevance

Asthma can be a devastating illness for the 23 million Americans affected by this disease. The emerging field of epigenetics, which aims to define how genes are turned on and off in cells, has already shown great promise in finding new therapies for many human diseases, especially cancer. We have already identified epigenetic markers that are associated with pathogenic T cells and development of asthma in adults. In this proposal, we will extend our approach to investigate the origins of asthma by studying children from birth till they develop asthma later in life. Our findings should directly benefit human asthma research by identifying novel asthma- related genes that may be targets for new preventive or therapeutic drugs.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Research Project (R01)
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Special Emphasis Panel (ZRG1)
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Dong, Gang
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La Jolla Institute for Immunology
La Jolla
United States
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Youhanna Jankeel, Diana; Cayford, Justin; Schmiedel, Benjamin Joachim et al. (2018) An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies. Methods Mol Biol 1799:303-326