Aberrant DNA methylation and its regulation of gene expression in airway smooth muscle cells of individuals with asthma

Clifford, Rachel Louise (2023) Aberrant DNA methylation and its regulation of gene expression in airway smooth muscle cells of individuals with asthma. MRes thesis, University of Nottingham.

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Asthma is a chronic airways disease affecting 262 million people worldwide, over 8 million people in the UK. Symptoms include wheezing, breathlessness, chest tightness and coughing, and are truly debilitating. Asthma exacerbations cause more severe versions of these symptom and 1200 people a year die from asthma. There is no cure for asthma. Current treatments aim to alleviate symptoms and prevent exacerbations, but do not prevent, reduce, or reverse the pathological changes in the asthmatic airway. A better understanding of the molecular mechanisms driving asthma pathology will identify new therapeutic targets and drive benefit for patients in the long term.

Asthma is caused by a complex interaction between genetic and environmental exposures. Epigenetic mechanisms sit at the nexus of environmental exposures and genetics – they respond to environmental exposures to regulate gene expression and cell function without altering the underlying genetic code, contributing to disease risk. Our lungs are the organ most vulnerable to environmental exposures highlighting epigenetics as an important process to understand in the disease.

Airway smooth muscle (ASM) cells contribute to all aspects of asthma pathology; airway hyperresponsiveness, inflammation and remodelling, but their molecular dysfunction remains poorly explored. Here we profiled DNA methylation and gene expression in ASM cells isolated from individuals with and without asthma to understand the contribution of DNA methylation to aberrant ASM cell function.

We identified 356 significantly differentially methylated CpG sites (BH p<0.05) between ASM cells from individuals with asthma versus healthy controls. Genome wide no gene expression probes were identified as significantly differentially expressed in association with asthma status. However, of 263 genes annotated to the 356 differentially methylated CpGs sites, 231 genes were present within in the gene expression data, and 22 genes displayed a nominally significant differential gene expression in ASM cells in association with asthma (p<0.05). Expression quantitative trait methylation (eQTM) analysis of the 356 differentially methylated CpGs against all gene expression probes showed that the methylation levels of 24 of the 356 differentially methylated CpGs correlated with the expression values of 145 genes, 120 of which were differentially expressed between ASM cells from individuals with and without asthma.

17 differentially methylated CpGs and six differentially expressed genes were differentially methylated/expressed in a publicly available ASM cell dataset, with 3 CpGs and 3 genes displaying the same direction of effect change in asthma.

Future work will focus on identifying larger samples sizes to improve validity and replication, assessing protein expression in addition to gene expression, modulating DNA methylation level in vitro to provide direct evidence of gene/protein expression regulation, and distinguishing between DNA base modifications.

Item Type: Thesis (University of Nottingham only) (MRes)
Supervisors: Archer, Nathan
Stoger, Reinhard
Keywords: airway smooth muscle, DNA methylation, gene expression, asthma
Subjects: R Medicine > RB Pathology
R Medicine > RC Internal medicine
Faculties/Schools: UK Campuses > Faculty of Medicine and Health Sciences > School of Veterinary Medicine and Science
Item ID: 76545
Depositing User: Clifford, Rachel
Date Deposited: 29 Feb 2024 14:42
Last Modified: 29 Feb 2024 14:42
URI: https://eprints.nottingham.ac.uk/id/eprint/76545

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