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Most candidate drugs currently fail later-stage clinical trials, largely due to poor prediction of efficacy on early target selection 1 . Drug targets with genetic support are more likely to be therapeutically valid 2 , 3 , but the translational use of genome-scale data such as from genome-wide association studies for drug target discovery in complex diseases remains challenging 4 – 6 . Here, we show that integration of functional genomic and immune-related annotations, together with knowledge of network connectivity, maximizes the informativeness of genetics for target validation, defining the target prioritization landscape for 30 immune traits at the gene and pathway level. We demonstrate how our genetics-led drug target prioritization approach (the priority index) successfully identifies current therapeutics, predicts activity in high-throughput cellular screens (including L1000, CRISPR, mutagenesis and patient-derived cell assays), enables prioritization of under-explored targets and allows for determination of target-level trait relationships. The priority index is an open-access, scalable system accelerating early-stage drug target selection for immune-mediated disease. A genetics-led translational approach integrating functional genomic predictors, knowledge of network connectivity and immune ontologies defines the drug target prioritization landscape for 30 immune traits at the gene and pathway level.

ObjectivesA number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine production ex vivo in unstimulated lymphoid and myeloid cells.MethodsFresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 hours. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations, single-cell RNA-seq, ELISA and LEGENDplex analysis of PsA SF were also performed.ResultsWe observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of any in vitro stimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be among those most highly upregulated by PsA monocytes/macrophages in SF; and both proteins were elevated in PsA SF.ConclusionsUsing multiomic analyses, we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance.

Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. Here we use complementary single-cell approaches to study leukocytes from PsA joints. Mass cytometry demonstrates a 3-fold expansion of memory CD8 T cells in the joints of PsA patients compared to peripheral blood. Meanwhile, droplet-based and plate-based single-cell RNA sequencing of paired T cell receptor alpha and beta chain sequences show pronounced CD8 T cell clonal expansions within the joints. Transcriptome analyses find these expanded synovial CD8 T cells to express cycling, activation, tissue-homing and tissue residency markers. T cell receptor sequence comparison between patients identifies clonal convergence. Finally, chemokine receptor CXCR3 is upregulated in the expanded synovial CD8 T cells, while two CXCR3 ligands, CXCL9 and CXCL10, are elevated in PsA synovial fluid. Our data thus provide a quantitative molecular insight into the cellular immune landscape of psoriatic arthritis. Psoriatic arthritis (PsA) commonly affects patients with skin psoriasis, but its pathogenesis is still unclear. Here the authors use two types of single-cells data, mass cytometry and RNA sequencing, to describe the expansion and diversity of synovial, but not peripheral blood, CD8 T cells from PsA patients to provide a molecular immune landscape for PsA.

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.

Abstract Objectives A number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine production ex vivo in unstimulated lymphoid and myeloid cells. Methods Fresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 h. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations and single-cell RNA-seq, and ELISA and LEGENDplex analysis of PsA SF were also performed. Results We observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of any in vitro stimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be amongst those most highly upregulated by PsA monocytes/macrophages; and both proteins were elevated in PsA SF. Conclusions Using multiomic analyses we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance. Competing Interest Statement The authors have declared no competing interest.

Psoriatic arthritis (PsA) is a debilitating immune-mediated inflammatory arthritis of unknown pathogenesis commonly affecting patients with skin psoriasis. We used three complementary single cell approaches to study leukocytes from PsA joints. Mass cytometry (CyTOF) demonstrated marked (>3 fold) expansion of memory CD8 T cells in the joints compared to matched blood. Further exploration of the memory CD8 compartment using both droplet and plate based single cell RNA sequencing of paired alpha and beta chain T cell receptor sequences identified pronounced CD8 T cell clonal expansions within the joints, strongly suggesting antigen driven expansion. These clonotypes exhibited distinct gene expression profiles including cycling, activation, tissue homing and tissue residency markers. Pseudotime analysis of these clonal CD8 populations identified trajectories in which tissue residency can represent an intermediate developmental state giving rise to activated, cycling and exhausted CD8 populations. Comparing T-cell clonality across patients further revealed specificity convergence of clones against a putative common antigen. We identify chemokine receptor CXCR3 as upregulated in expanded synovial clones, and elevation of two CXCR3 ligands, CXCL9 and CXCL10, in PsA synovial fluid.