The Farm Effect and Asthma Risk: Determining the Multi-Omic Immune Cell Landscape in Amish and Hutterite Children

PROJECT SUMMARY/ABSTRACT While exposure to a traditional farm environment has been robustly demonstrated to reduce the risk of childhood asthma, and immune cells are key drivers of asthma pathogenesis, the mechanisms by which the farm environ- ment affects immune cells is not well characterized. This proposal focuses on children from two unique U.S. farming populations, the Amish, who have extensive early life exposure to barn animals and a low prevalence of asthma, and the Hutterites, who live on industrialized farms without early life exposure to barn animals and their microbes and have over 4-fold higher prevalence of asthma compared with the Amish. While prior studies have indicated that both innate and adaptive immune cells differ between Amish and Hutterite children, suggesting that farm exposures may perturb the immune system early in life, these were limited to focusing on specific subsets of immune cells. The current proposal seeks to leverage the natural environments of Amish and Hutterite children and to generate multi-omics datasets to characterize the immune cells in these two populations, thereby discovering novel immune cells and states in the Amish that are associated with protection from asthma. Aim 1a will define the transcriptional landscape of Amish and Hutterite peripheral immune cells using single cell RNA sequencing to annotate distinct cell populations and ask: i) What are the proportions of immune cell types thus identified? ii) Do these proportions differ in Amish and Hutterite children? iii) What genes differ between Amish and Hutterite within each annotated immune cell type? Aim 1b will complement and extend Aim 1a by measuring open chromatin using single nucleus assay for transposase-accessible chromatin sequencing in the same cells used in Aim 1a so as to delineate the regulatory chromatin underpinning gene expression and ask: i) What genomic regions demonstrate differential chromatin accessibility (DCA) in the major immune cell populations between high and low risk environments? ii) Are differentially expressed genes in Aim 1a in regions with DCA? iii) Which transcription factor binding motifs are enriched in DCA regions in high and low risk environments? Aim 2 will focus on genes at childhood-onset asthma-associated genomic loci and address: i) What cell types are enriched for expression of genes at childhood-onset asthma loci? ii) What regions of the genome and in which immune cells are there DCA regions between high and low risk environments that overlap with childhood-onset asthma loci? This contribution will determine the transcriptional and chromatin states of immune cells in two unique sets of children with different risk of asthma due to environmental exposures and will provide substantial clues about asthma risk. Insights from these studies will generate subsequent hypotheses that can then be empirically tested using functional studies of blood immune cells and will be the basis for subsequent R01 grant application(s), thereby paving a pathway from mentored to independent investigation. Achieving these goals will lead to the discovery of new mechanisms of immune regulation in asthma, ultimately leading to novel treatments for asthma.