Understanding the Transcriptomic and Epigenetic Drivers of Cigarette Smoke Susceptibility in Chronic Obstructive Pulmonary Disease (COPD)
- Publication Type:
- Thesis
- Issue Date:
- 2023
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| Filename | Description | Size | |||
|---|---|---|---|---|---|
| thesis.pdf | thesis | 14.95 MB |
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COPD is a main non-communicable disease around the globe. One of the leading risk-factors for this disease progression is noxious particles and gases, mainly cigarette-smoke. Most in-vitro and in-vivo studies that have been done so far focused on understanding transcriptomic, genetic, and epigenetic drivers of COPD progression separately.
This thesis investigated the functional consequences of smoking and smoking-cessation on human airway epithelium at transcriptomic, genetic, and epigenetic levels. It further investigates the interaction between transcriptomics and epigenetics levels upon smoking and smoking-cessation. Initially, we investigated how Parametric-Response-Mapping (PRM) measured emphysema signature can be correlated to gene-expression. Then, the smoking-induced shifts in bronchial-epithelial-cell-composition and transcriptome of current vs never smokers and ex vs current COPD-smokers and how specific Single-Nucleotide-Polymorphism(SNP)s can alter sRAGE-COPD biomarker expression. Furthermore, we investigated impact of genetic and epigenetic drivers, mainly DNA-methylation, on transcriptome of COPD and asymptomatic-smokers (AS) and how that impacts downstream gene-expression changes associated with smoking-cessation.
Bronchial biopsies collected from never-smokers, ex and current smokers with and without COPD were used to investigate transcriptomic, DNA-methylation and cell-composition-shifts with and without smoking. The single-cell-RNA-seq-based cellular-deconvolution(CD) method investigated the relative cell population shifts with smoking. The expression Quantitative Trait Methylation(eQTM) sites associated with 1-year of smoking-cessation were then studied further in-vitro by creating CRISPR-based gene-knockout cell lines and functional consequences of smoking in context to cell survival, IL6, CXCL8-like cytokine production and transcriptome shifts were observed.
The PRM-derived emphysema signature has successfully been replicated in independent study cohorts, suggesting the robustness of the signature. The differential-expression and bulk-RNA-sequencing-based CD between current vs never-smokers, ex vs current COPD-smokers, reveals that smoking increases relative abundance of goblet cells in airways and is partially reversible after 1-year of smoking-cessation in COPD and AS. Furthermore, the validation of CD method with IHC confirms the use of this method to predict cellular compositions in bulk-RNA-seq. The sRAGE-associated study shows that rs2070600-SNP affects sputum sRAGE levels for the first time. Finally, impact of one-year-smoking-cessation on bronchial transcriptome and eQTM analysis reveals most of the downregulated genes and eQTMs after smoking-cessation belong to xenobiotic-metabolism and detoxification, which clarifies cellular regulation of high-energy conserving pathways in the absence of stress-stimuli. Moreover, the observed changes in gene-expression and DNA-methylation with 1-year of smoking-cessation are moving towards never smokers' direction. Overall, this thesis has shown the impact of smoking on the airways of COPD patients and how the interaction between transcriptomics and epigenetics can influence COPD-disease progression.
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