Nasal gene expression changes with inhaled corticosteroid treatment in asthma

To the Editor, Inhaled corticosteroids (ICS) improve asthma control in most, but not all patients.1,2 Currently, biomarkers that help clinicians to pre‐ dict individual ICS responsiveness or monitor effects of therapy are limited. Gene expression profiling in bronchial tissue has revealed a signature related to ICS response,3 but access to this tissue is diffi‐ cult. We recently showed that nasal gene expression can serve as a proxy to study effects of smoking in the lower airways,4 thereby pro‐ viding a more accessible sampling alternative. In the current study, we aimed to investigate the effects of ICS treatment in nasal epithe‐ lium and confirmed results both in nasal brushes of patients after ICS withdrawal and in bronchial biopsies and air‐liquid‐interface (ALI) cultures after corticosteroid treatment. Data were collected from participants of two asthma studies on ICS treatment: OLiVIA (n = 39, 2‐week HFA‐beclomethasone 200 μg b.i.d.5 and NZRHS (n = 28, 12‐week budesonide 400 μg b.i.d6). Detailed information is available in the Appendix S1. In both studies, nasal brushes were obtained at baseline and after ICS treatment.7 A subpopulation of OLiVIA used ICS prior to the study and therefore had to withdraw their ICS 4‐6 weeks. In this subpopulation, an ad‐ ditional nasal brush was taken before ICS withdrawal (Figure S1). In NZRHS, all participants had not used ICS for at least 90 days prior to the study. RNA sequencing of the samples was performed in OLiVIA and microarray‐based profiling (Affymetrix HuGene 1.0) in NZRHS. We used R‐package limma (v3.30.13) to assess ICS‐induced gene expression changes in nasal epithelium in OLiVIA and NZRHS and performed a meta‐analysis to identify which genes are universally changed by ICS in both studies. P‐values were adjusted for multi‐ ple testing using Benjamini‐Hochberg procedure.8 Next, we com‐ pared results with nasal gene expression changes after withdrawal of ICS in OLiVIA using Gene Set Enrichment Analysis (GSEA, v3.09). Additionally, we compared ICS‐induced changes in gene expression from nasal samples with two independent asthma datasets of bron‐ chial biopsies using GSEA (dataset 1: n = 12, 8‐week budesonide 180μg b.i.d.; dataset 2: n = 20, 1‐week fluticasone 500μg b.i.d.). Finally, we compared our findings with results of corticosteroid‐in‐ duced changes in gene expression in ALI cultures of primary human bronchial epithelial cells (Table S1). In OLiVIA, mean age was 44 years (±standard deviation [SD] 13), 20 (51%) subjects were current‐smokers, 19 (49%) ex‐smokers; mean FEV1 was 84 (±SD 14) %predicted. In NZRHS, mean age was 45 years (±SD 12), 2 (7%) subjects were current‐smokers, 10 (36%) ex‐smokers, and 16 (57%) never‐smokers; mean FEV1 was 88 (±SD 14) %predicted (Table S2). We identified 135 genes that signifi‐ cantly changed in expression with ICS treatment in our meta‐anal‐ ysis, 79 being up‐ and 56 downregulated (FDR meta‐analysis 0.05, nominal P < 0.05 in both studies; Figure 1; Table S3). Unsupervised clustering of subjects was performed and showed clustering of NZRHS and OLiVIA‐subjects, but no clear clustering based on atopy‐status, gender, or clinical improvement after ICS treatment (responder/nonresponder) (Figure S2). Genes downregulated after ICS treatment (n = 56) were significantly enriched among genes up‐ regulated after ICS withdrawal (Figure 2A). Genes upregulated after ICS treatment (n = 79) were not significantly enriched among genes downregulated after ICS withdrawal (Figure 2B). When comparing our findings in nasal epithelium to those of the two independent studies using bronchial biopsies, GSEA showed that genes upreg‐ ulated with ICS treatment in nasal epithelium were significantly enriched among genes upregulated with ICS treatment in bron‐ chial biopsies (Figure 2C,E). Furthermore, genes downregulated after ICS treatment in nasal epithelium were significantly enriched among genes downregulated after ICS treatment in bronchial bi‐ opsies in both datasets (Figure 2D,F). Next, we compared results with corticosteroid‐induced gene expression changes in ALI cul‐ tures (Table S4). GSEA analysis showed that genes upregulated with ICS treatment in nasal epithelium significantly overlap with upregulated genes in ALI cultures (Figure 2G). For downregulated genes, there was no significant overlap between downregulated genes in nasal epithelium and downregulated genes in ALI cultures