Glucocorticoids (GCs), which act by inducing the glucocorticoid receptor (GR) to regulate gene expression, are the primary therapy used to achieve long-term asthma control and are also used to treat asthma exacerbations, even among patients who exhibit relative baseline GC resistance. We hypothesized that analysis of the airway epithelial cistromes of GR, p65 (a component of the inflammatory nuclear factor [NF]-κB transcription factor complex), and RNA polymerase II (RNAP2) would provide new mechanistic insights into how GCs function in asthma. We performed chromatin immunoprecipitation and high-content sequencing (ChIP-seq) to determine genome-wide occupancy of GR, p65, and RNAP2 in BEAS-2B cells treated with vehicle, dexamethasone (dex, a potent GR agonist), tumor necrosis factor (TNF, which rapidly induces NF-κB activity), and a combination of dex and TNF. We identified thousands of genomic regions that are occupied by GR, p65 and RNAP2 in Beas-2B cells. GR and p65 co-occupancy resulted in surprisingly varied effects on RNAP2 occupancy at associated genes. GR was able to either antagonize or enhance the primary effects of TNF on RNAP2 occupancy and gene expression in a target-specific fashion. Through identifying genes in which RNAP2 occupancy was increased by both dex and TNF individually, with combinatorial treatment preserving or further enhancing RNAP2 levels, we defined novel, induced, antiinflammatory effectors of GCs in the airway, including TNFAIP3 and TNIP1. Taken together, our data strongly refute the long-standing model in which antagonism of NF-κB by GCs in the airway has been primarily attributed to GR tethering with NF-κB and reducing its activity. Instead, coinduction of shared antiinflammatory targets of GR and NF-κB is now also implicated in mediating beneficial effects of GCs in asthma. These data have important implications for current models of steroid-resistant airway disease.
Footnotes
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