I and my team made tremendous progress in understanding the underlying mechanisms by which the farm environment prevents allergic asthma, as observed in many human epidemiological studies. First, my team and I confirmed previous work by showing that intranasal administration of an extract prepared from dust collected in cow sheds (FD) prevents experimental allergic asthma in an ovalbumin (OVA)-induced murine model. Besides the known reduction in the cardinal features of allergic lung inflammation, i.e. airway hyperresponsiveness and airway eosinophilia, we observed that mice exposed to FD showed a strong increase in a specific type of immune cells in their lungs. We then applied single cell RNA sequencing (scRNA-seq) to 61,803 isolated lung cells. In contrast to allergic asthmatic mice these immune cells of FD-exposed mice displayed a significantly altered transcriptome, characterized by decreased expression of genes encoding for proteins which play a major role in the pathophysiology of asthmatic inflammation. Importantly, we confirmed these findings in human monocytes isolated from blood of healthy human donors. Treatment of these cells with FD also resulted in a downregulation of these genes even in the event of an additional inflammatory stimulus. Further mechanistic insights were obtained through multi-omic integration of RNA-seq and ATAC-seq data of FD treated murine immune cells in an ex vivo experiment. My team and I demonstrated that epigenetic silencing of these genes is facilitated by activation of an intracellular transcription factor that has previously been shown to bind bacterial metabolites.
To discover the active principle, we applied various extraction methods and fractionation steps to the farm dust. We analyzed the obtained fractions using NMR, proteomics and lipidomics, among other methods. Our knowledge of the involved receptor guided the next steps and allowed us to identify two relevant metabolites of presumably bacterial origin. We tested these in the same functional in vitro assays and in vivo models reported above and found that they fully replicated the asthma protective effects of the farm dust extracts. Therefore, I will now focus on further characterization of these metabolites.
