Cell and tissue specific functional genomics of psoriasis and psoriatic arthritis

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.
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.
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+ and CD8+ 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+ 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+ 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.
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+ cells in the inflamed synovium.
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.

Keywords: immunology
epigenetics
psoriasis
chromatin accessibility
Advisor: Knight, JC
Berlanga-Taylor, AJ