Epigenetic mechanisms regulate the expression of genes without affecting the underlying DNA sequence, thereby enabling the development of cell types with diverse functions from genetically identical progenitors. In addition to cell differentiation, epigenetic processes also mediate cellular responses to environmental stimuli and are often altered under exposures or diseases. A large proportion of epigenetic research has focused on DNA methylation – a relatively stable epigenetic mark that is covalently attached to the DNA. Changes in the DNA methylome were most frequently assessed in blood-derived samples, even when examining the impact of diseases or exposures that primarily affect the respiratory system, such as air pollution or respiratory infections. Although the cells of the upper respiratory tract represent the first contact point between inhaled substances and the human body, their epigenetic response to aerogenic hazards has been barely studied to date. The work included in this thesis aimed to characterize DNA methylome alterations in upper airway cells under exposure to ambient air pollution and SARS-CoV-2 infection. In contrary to the frequently used array platforms that are limited to a subset of preselected loci, whole-genome sequencing was used to determine DNA methylation patterns on a genome-wide scale. Analysis of the effects of air pollution showed that epigenetic changes are detectable at pollutant concentrations below current legal thresholds and affect genes involved in epithelial barrier function, oxidative stress response as well as genes of the HOXA cluster, all of which may be implicated in the development or air pollution-associated diseases. The assessment of the upper airway DNA methylome together with the single-cell transcriptome of COVID-19 patients gave new insights into the mechanisms of immune cell recruitment into the airways upon infection and provided initial evidence of a long-term impact on genes involved in ciliary function following SARS-CoV-2 infection. Lastly, the results of both studies were aligned to evaluate potential impacts of pollutant exposure on the susceptibility to SARS-CoV-2 infection. In summary, the data presented in this thesis demonstrate that immune and epithelial cells of the nasal mucosa can provide valuable insights into exposure-induced changes of gene regulatory mechanisms and may lead to a deeper understanding of the pathomechanisms underlying respiratory diseases or exposures.
