Abstract:
Chronic rhinosinusitis (CRS) is a spectrum of inflammatory conditions of the sinonasal mucosa. Complex patterns of inflammatory and microbial heterogeneity underlie CRS. Further resolving this heterogeneity is vital to inform research approaches and guide clinical management decisions. The overall scope of this thesis was to investigate the inflammatory and microbial heterogeneity of CRS, with the intent to differentiate potential subtypes of CRS, and to examine mechanisms of disease. CRS-associated tissue processes and microbiota were investigated via gene-targeted amplicon sequencing, quantitative PCR, immunohistochemistry, cluster analysis, whole transcriptome sequencing (RNAseq), and proteomics (SWATH LC-MS/MS). Through the course of this thesis, the optimal method for characterising the human mycobiota was determined, bacterial and fungal associations with CRS phenotypes and endotypes were comprehensively described, inflammatory heterogeneity in phenotypes of CRS were investigated, putative inflammatory endotypes of CRS were identified, tissue and microbial temporal changes and local response to treatment were described, associations between microbiota patterns and mechanisms of disease were investigated, and finally, methods for the identification of CRS biomarkers in the routine clinical setting were validated. Inflammatory patterns were inconsistent within CRS phenotypes. Alternatively, eight putative CRS endotypes were identified based on inflammatory markers and clinical parameters, including IL-2, IL-5, IL-6, IL-8, IL-10, IFN-γ, TNF, asthma, and polyposis. Bacterial community dysbiosis was more apparent than specific associations with putative pathogenic taxa. Dysbiotic bacterial communities were characterised by altered community membership and structure, reduced diversity, increased bacterial load, increased inter-and intra-patient variability, and were associated with elevated inflammatory markers and clinical severity. Patterns of inflammatory and microbial natural temporal variability were identified, including for several previous biomarker candidates in CRS, such as MUC5B, MUC5AC, S100 calcium binding proteins, CST1, EPX, CLC, POSTN, and CXCL8 (IL-8). Finally, sampling methods that can be introduced to diagnose CRS endotypes in the clinic setting were validated for several, but not all, biomarkers of interest in CRS. This thesis contributes to ongoing efforts to tease apart inter-patient, intra-patient, and temporal inflammatory and microbial heterogeneity in CRS, define distinct inflammatory endotypes of CRS, and also offers compelling evidence of a link between bacterial community dysbiosis and inflammation in CRS.