| Summary: | <p>Psoriasis and psoriatic arthritis (PsA) are chronic inflammatory diseases mainly affecting
the skin and joints that result from the interaction of genetic and environmental
factors. Despite the success of genome-wide association studies (GWAS) in uncovering
genetic risk loci, the functional mechanisms underlying these associations remain largely
unresolved. This thesis aims to establish genome-wide epigenetic and gene expression
profiles for immune cells isolated from blood and disease-relevant tissues to inform the
understanding of pathogenesis and GWAS in psoriasis and PsA.</p>
<p>The first results chapter establishes methodological and analytical pipelines for novel
chromatin profiling techniques in challenging clinical samples. Importantly, OmniATAC, a variant of Assay for Transposase-Accessible Chromatin using sequencing (ATACseq), demonstrated the best performance for skin biopsies. Moreover, the use of
cryopreservation and fixation in blood-isolated immune cells showed cell-type specific
impact on the chromatin accessibility landscape that should be taken into consideration
when planning the experimental design.</p>
<p>The second results chapter compares chromatin accessibility, histone acetylation and
gene expression between psoriasis patients (n=8) and controls (n=10) for blood
monocytes, B cells, CD4<sup>+</sup> and CD8<sup>+</sup> T cells. Only CD8+ T cells showed a substantial
number of differentially accessible regions (DARs) (n=55, FDR< 0.05), and intersection
with differential H3K27ac was only seen at an intron of DTD1. Monocytes and
CD8<sup>+</sup> T cells showed highest numbers of differentially expressed genes (n=671 and
651 respectively, FDR<0.05) with enrichment of MAPK and IL-12 signalling (both
cell types) and NF-κB, TNF and chemokine signalling (CD8<sup>+</sup> T cells). Overall
1,227 genes (FDR<0.05) were differentially expressed between uninvolved and lesional
psoriasis epidermis (n=3) with enrichment of metabolic and immune-related pathways.
Integration of GWAS fine-mapping data with epigenetic and gene expression profiles
implicated a potentially functional variant in the 2p15 GWAS locus modulating B3GNT2.</p>
<p>The third results chapter analyses differences in chromatin accessibility, gene and protein
expression of immune cells between synovial fluid and peripheral blood of PsA patients
(n=3). The highest number of DARs were found in monocytes (5,285 FDR<0.01) for both
tissues with synovial fluid monocytes specifically enriched for interleukin and NF-κB
signalling pathways. Single-cell RNA-seq identified two functionally relevant synovial
fluid monocyte subpopulations characterised by up-regulation of IFN signalling and
IL7R genes, respectively. Mass-cytometry analysis (n=10) confirmed increased CCL2 and
CXCL10 protein levels in monocytes from synovial fluid. Furthermore, statistical finemapping of PsA GWAS loci and integration with ATAC data suggested rs11249213 as a
possible regulator of RUNX3 in CD8<sup>+</sup>
cells in the inflamed synovium.</p>
<p>Overall this thesis highlights the context-specificity of the epigenomic landscape in
psoriasis and PsA, and the potential of a multi-omics approach to provide new insights
into pathophysiology and interpretation of GWAS.</p>
|
|---|