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Graduate Student Supervision
Doctoral Student Supervision (Jan 2008 - Nov 2020)
Cystic fibrosis (CF) is characterized by a progressive decline in lung function due to airway obstruction, infection, and inflammation. CF patients are particularly susceptible to respiratory infection by a variety of pathogens, and the inflammatory response in CF is dysregulated and prolonged. This thesis identifies and characterizes BPI fold containing family A, member 1 (BPIFA1) and BPIFB1 as putative anti-inflammatory molecules in CF, and explores the CF inflammatory response to rhinovirus infection. BPIFA1 and BPIFB1 are proposed innate immune molecules expressed in the upper airways. We interrogated BPIFA1/BPIFB1 single-nucleotide polymorphisms in data from the North American genome-wide association study (GWAS) for lung disease severity in CF and discovered that the G allele of rs1078761 was associated with reduced lung function in CF patients. Microarray and qPCR gene expression analysis implicated rs1078761 G as being associated with reduced BPIFA1 and BPIFB1 gene expression, suggesting that decreased levels of these genes are detrimental in CF.Functional assays to characterize the role of BPIFA1 and BPIFB1 in CF indicated that these molecules do not have an anti-bacterial role against P. aeruginosa, but do have an immunomodulatory function in CF airway epithelial cells. To further investigate the mechanism of action of BPIFA1 and BPIFB1 during bacterial infection, gene expression was profiled using RNA-Seq in airway epithelial cells stimulated with P. aeruginosa and treated with recombinant BPIFA1 and BPIFB1.Viral infections are now recognized to play an important role in the short and long term health of CF patients. Rhinovirus is emerging as a lead viral pathogen although little is known about the inflammatory response triggered by rhinovirus in the CF lung. To investigate whether CF patients have a dysregulated response to rhinovirus infection, primary airway epithelial cells from CF and healthy control children were infected with rhinovirus and gene expression profiles were assessed by RNA-Seq. Although rhinovirus stimulation resulted significantly altered gene expression, the response to infection was not different in CF patients compared to healthy controls. However, CF cells had significantly higher rhinovirus levels than controls, indicating that CF patients may have a deficient antiviral response allowing for increased rhinovirus replication.
Thymic stromal lymphopoietin (TSLP) and Interleukin 1 receptor-like 1 (IL1RL1) are important for the initiation and maintenance of a Th2 inflammatory environment in the asthmatic lung. TSLP and IL-33, the exclusive IL1RL1 ligand, are secreted by epithelial cells and other immune cells and play essential roles in Th2 polarization, activation and proliferation of immune cells and participate in many asthma cardinal features such as chronic inflammation, airway remodeling and mucus production. TSLP and IL1RL1 are two of the most consistently associated genes in genome-wide association studies of asthma. rs1837253 in TSLP was identified as a putative causal SNP based on consistent association data both from candidate gene and genome-wide association studies; as well as the absence of significant linkage disequilibrium with other single nucleotide polymorphisms (SNPs) in the region. In contrast, there are several asthma-associated IL1RL1 variants and due to the extensive linkage disequilibrium in the region encompassing IL1RL1 and many other genes, potential causal SNP(s) are unknown.In this thesis, I describe the functional analysis of the TSLP SNP rs1837253, the study of SNPs in the IL1RL1 region to identify potentially functional variants by in silico analysis using a lung expression Quantitative Trait Locus dataset and published association data, the functional analysis of the IL1RL1 SNPs: rs1420101 and rs3771180 and finally an analysis of gene expression of TSLP short and long isoforms as well as IL1RL1 receptor and soluble isoforms in relation to clinical phenotypes.