| Summary: | <p>This thesis aimed to determine the functional genomic changes specific to Ankylosing Spondylitis (AS) for different disease relevant immune cell types and relate this to disease associated genetic variants. AS is a highly heritable inflammatory disease mainly affecting the spine. Functional genomic approaches at the transcriptomic and epigenetic level in the context of disease are accelerating the understanding of the functional consequences of genetic variation, and how this may impact disease susceptibility and aetiology. Diseaseassociated genetic variants may be active only in certain cell types; therefore understanding the underlying functional mechanisms requires investigation in relevant tissues and cells, and in the disease state. TNF-α inhibition as a current biologic therapy has proved very effective in the majority but not all AS patients. To understand this response further, cell type specific changes in treatment responders were also investigated.</p> <p>The transcriptomic profile in 15 AS patients with active disease is reported here for six immune blood cell types (CD4<sup>+</sup> and CD8<sup>+</sup> T cells, CD14<sup>+</sup> monocytes, CD16<sup>+</sup> neutrophils, NK cells and CD19<sup>+</sup> B cells) using RNA-seq, in purified cell types for messenger RNAs, long non-coding RNAs and microRNAs. Enrichment for NF-κB signalling and HDAC Class I signalling was found across cell types, most significantly in CD14<sup>+</sup> monocytes and CD16<sup>+</sup> neutrophils. The gene expression profile 3 months after commencing anti-TNF therapy is reported for three cell types, providing insights into the molecular basis of treatment response. NEAT1, a long non-coding RNA was found to be correlated with disease activity following anti-TNF therapy (P=0.031) in CD14<sup>+</sup> monocytes.</p> <p>Changes in chromatin accessibility are informative for putative regulatory DNA elements and may inform hypotheses for molecular mechanisms modulated by genetic variation. Here, the chromatin accessibility landscapes in 5 AS patients are established for three cell types using an Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq). In CD14<sup>+</sup> monocytes, 437 genes were found differentially expressed in AS patients in both RNA-seq and ATAC-seq (observed enrichment P=2.2x10<sup>-16</sup>). Following TNF-α inhibition therapy, differentially expressed genes in both datasets were found in CD8+ T cells (P= 0.02). PTGER4, a GWAS reported gene was found down-regulated in CD8<sup>+</sup> T cells from treated AS patients (FDR=0.0002). Integration of ATAC-seq data with fine-mapped SNPs also revealed a differentially closed chromatin peak in one patient at rs4672505 (locus 2p15), specifically in CD8<sup>+</sup> T cells. This SNP may explain the association signal found at this locus, with evidence of regulating B3GNT2. Future work aims to validate these findings in a larger cohort and collect AS specific epigenetic marks using ChIP-seq, along with functional validation of rs4672505 using Capture-C and CRISPR.</p>
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