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Title: Epigenetic modifications in primary human T cells and the role of DNA methylation in asthma
Author: Hendy, Ellie
ISNI:       0000 0004 9357 6745
Awarding Body: King's College London
Current Institution: King's College London (University of London)
Date of Award: 2020
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Asthma is a heterogeneous disease with varying ages of onset, immunopathology and severity. The mainstay treatment for asthma is corticosteroids, however, a subset of asthmatics are not responsive to this treatment. Both the transcriptome of T cells and the effect of corticosteroids on gene expression have been well studied. However, the epigenetic mechanisms causing the differences in gene expression in these cells has yet to be fully studied. This thesis uses the Illumina MethylationEPIC arrays to study the DNA methylation of naïve CD4⁺ T (Th0) cells and T helper 2 (Th2) cells. With the aim to study the difference in DNA methylation between Th0 cells and Th2 cells, the effect of dexamethasone on Th2 cell DNA methylation and the difference in DNA methylation of Th0 cells between asthmatics on STEP2 and STEP5 of the BTS/SIGN guidelines. To reduce the complexity of DNA methylation data this thesis focused on single cell types rather than whole blood analysis in orderto offer a better insight into changes in DNA methylation. Data from this thesis suggests that there are a plethora of genes that have differential DNA methylation between Th0 cells and Th2 cells. As well as changes in DNA methylation at key T helper cell cytokine genes, this study reveals potential novel genes and mechanisms that are involved in T cell differentiation such as the methylation of TRPS1 in Th2 cells. Data from this thesis suggests that the treatment of Th2 cells with a single dose of 10-7M dexamethasone for 48 hours does not have a marked effect on DNA methylation. However, single-cell transcriptomics data from this thesis does identify potential mechanisms of glucocorticoid action including alternative exon usage and alternative polyadenylation sites. The study into the difference in DNA methylation between steroid-sensitive and steroid-resistant asthmatics revealed that, unlike in rheumatoid arthritis and systemic lupus erythematosus, there was no apparent difference in the DNA methylation at key immune genes. However, data from this thesis does suggest that there are sex-specific differences in DNA methylation on both autosomal and sex chromosomes. The pattern of asthma presentation and endotypes differ in males and females. However, asthma is a very heterogeneous disease with differences in disease incidence not limited to gender but to many other factors including ethnicity, biological age, disease duration and treatment. To decipher the mechanisms of asthma, again, this thesis focused on a single cell type, however, data suggests that to begin to attempt to reduce the complexity of DNA methylation data in asthma we need to reduce the variability from other factors. The number of CpGs assayed in this project was limited by the array format and future work will benefit by utilising new technologies that can assay CpGs genome-wide at the single-cell level.
Supervisor: Lavender, Paul ; Corrigan, Christopher John Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available