or ABSTRACT In this multi-PI proposal we will investigate the role of epigenetic mechanisms in the pathogenesis of allergic asthma. 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 IL4, IL5 and IL13 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 genome-wide to identify epigenomic signatures that correlate with asthma development and severity, by comparing histone modifications and DNA methylation/ hydroxy- methylation patterns in enriched populations of pathogenic T cells and innate immune cells freshly isolated from blood and airways of asthmatic patients versus control individuals. Our study will be the first to define disease-related epigenetic changes in patients with well-characterized asthma, and to correlate these with disease severity to obtain specific markers for distinguishable disease states. 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 map genome-wide transcriptional and histone modification patterns in immune cells that initiate and maintain airway inflammation in asthma.
In Aim 2, we will profile patterns of DNA methylation and hydroxymethylation in immune cells in asthma.
In Aim 3, we will identify epigenetic markers of disease by establishing and analyzing an integrated database of epigenomic, genetic, functional 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 investigating the role of epigenetic mechanisms in other immune-mediated disorders. )

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 changes in known asthma-related genes that correlate with moderate asthma but not mild asthma. In this proposal we will extend our findings to the entire epigenome of patients with asthma of varying severity. Our findings should directly benefit human asthma research by identifying novel asthma- related genes that may be targets for new therapeutic drugs. )

National Institute of Health (NIH)
National Heart, Lung, and Blood Institute (NHLBI)
Research Project (R01)
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Special Emphasis Panel (ZRG1-GGG-M (50))
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Gan, Weiniu
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La Jolla Institute
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
Patil, Veena S; Madrigal, Ariel; Schmiedel, Benjamin J et al. (2018) Precursors of human CD4+ cytotoxic T lymphocytes identified by single-cell transcriptome analysis. Sci Immunol 3:
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Schmiedel, Benjamin Joachim; Seumois, Grégory; Samaniego-Castruita, Daniela et al. (2016) 17q21 asthma-risk variants switch CTCF binding and regulate IL-2 production by T cells. Nat Commun 7:13426
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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
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