Airway barriers during inflammatory diseases : discovery of genome-based alterations by using next-generation sequencing

Inflammatory upper airway diseases are prevalent worldwide and can lead to functional impairment in patients. However, their effects on upper airway gene expression remain poorly understood. This dissertation aims to assess the clinical airway characteristics of chronic rhinosinusitis (CRS) patients and to gain insights into the transcriptome as well as the microbiome of subjects sensitized to aero- or food-allergens, from the nasal epithelium and tonsillar tissues. In pub I, we comprehensively studied variables regarding demographics, off-seasonal symptoms, and clinical findings from CRS patients (n = 74) and controls (n = 80). For pub II, nasal epithelial samples for RNA-sequencing (RNA-seq) were taken from five healthy subjects and 6 Allergic rhinitis (AR) patients with and without allergen immunotherapy (AIT) in 2 springs and winters. Tonsillar samples for RNA-seq were taken from atopic (n = 24) and non-atopic (n = 29) subjects. The data was analysed using standard bioinformatics tools in R software. In pub I, we identified clusters of CRS patients based on the distinct phenotypes, severe or moderate symptoms, and the presence of other comorbidities. Clusters indicated the presence of sinonasal symptoms and a high prevalence of facial pain. The findings of the pub II revealed that during allergen seasons, both AR-AIT and AR-noAIT subjects showed variation in the levels of pathways such as asthma, toll-like receptor (TLR), and chemokine signaling. Furthermore, the microbiome results highlighted the most common genera including Bacillus (42.23 %), Methanocaldococcus (35.72 %), and Alpharetrovirus (4.32%). We observed the reduction of microbial diversity in the AR-AIT group compared to the AR-noAIT and control group. In pub III, a low microbial diversity and abundance was observed in the atopic subjects. We identified significant positive correlations between pathogenic bacteria as well as lower abundance of two specific taxa, Clostridium Botulinum and Moraxella Osloensis, in atopic subjects. In pub IV, we found key genes such as encoding the chemokine (C-X-C motif) ligand (CXCL) 2, 8, 10, 11; interleukin 20 receptor subunit alpha (IL-20RA) and Mucin (MUC1 and MUC20), associated with allergic sensitization. Pathway analysis revealed enrichment of the IL-17 and TLR signaling in aeroallergen-sensitized subjects. In conclusion, this thesis demonstrates that CRS with nasal polyps (CRSwNP), CRS without nasal polyps (CRSsNP), and asymptomatic control phenotypes might be distinguishable based on off-seasonal symptoms and clinical information (pub I). Findings of pub II imply that AIT may restore epithelial gene expression and microbiome to normal. Furthermore, we identified that tonsils contain rich bacterial species and contain significant differences in microbial balance between atopic and non-atopic subjects (pub III). In addition, the findings highlight the active involvement of innate immunity in allergic sensitization, providing a deeper understanding of the components of the IL-17, TLR, and chemokines in allergic-sensitized subjects (pub IV).