Stephen Eyre

FcγRIIa, encoded by FCGR2A, is a widely expressed Fc receptor implicated in autoimmunity and infectious disease susceptibility. To fine-map the rheumatoid arthritis (RA) association at the complex FCGR locus, we combined gene-specific resequencing, genetic association studies in UK and Spanish European cohorts, functional genomics, structural biology, biophysical analyses, and cellular assays. We identified a common European FCGR2A haplotype (2A.3), defined by Q27W, H131H, and the RA-associated SNP rs12746613, which showed the strongest association with RA. Multi-omics analyses demonstrated that 2A.3 is associated with reduced expression of the soluble FCGR2A splice variant and lower circulating soluble FcγRIIa levels. Functional studies revealed altered IgG interactions and delayed FcγRIIa signal transduction associated with Q27W, while structural analyses found no evidence for stable ectodomain dimerisation. Together, these findings identify 2A.3 as an important functional contributor to RA susceptibility and provide mechanistic insight into how FCGR2A variation may influence immune regulation and disease risk in Europeans.

Objectives: Research of refractory disease in juvenile idiopathic arthritis (JIA) is limited, and a potential genetic contribution has yet to be investigated. This study aimed to explore the presence of rare monogenic disease gene coding variants in a refractory JIA population. Methods: Cases were included with a record of inefficacy for methotrexate and ≥1 biologic drug or exposure to methotrexate and ≥2 biologic drugs for any reason. Whole exome sequencing data were analysed using VarSeq. rarity and pathogenicity filters were applied. Variants within an OMIM curated paediatric monogenic gene list, arthritis OMIM gene list, primary immunodeficiency gene panel (PanelApp) or gene reported for JIA drug response or toxicity (ClinPGX) were retained. ACMG classification excluded benign or likely benign variants. Results: In total, 83 individuals were included. Twelve variants were previously reported in other paediatric onset diseases with similar phenotypes to JIA. Seventeen variants were detected in twelve genes with an arthritis OMIM phenotype. Seventeen variants were detected within fourteen genes that were reported on the primary immunodeficiency panel (PanelApp) and were previously reported in a publication. A total of 39 variants were detected in genes from a JIA drug response or toxicity gene list (ClinPGX). Conclusions: This study evidences that 66 individuals with refractory JIA carry rare variants associated with paediatric diseases, JIA susceptibility loci or drug response and toxicity. These variants could contribute to refractory disease, mimics of JIA/complicated phenotypes or effect treatment response. Longitudinal data are needed to confirm these findings.

Precision application of targeted therapies is urgently needed to improve long-term clinical outcomes for children affected by inflammatory arthritis, known as juvenile idiopathic arthritis (JIA). Progress has been hampered by our limited understanding of the cellular basis of inflammation in the target tissue of the disease, the synovial membrane. Here, we analyzed biopsies from the inflamed joints of treatment-naïve children with JIA, early in the course of their disease, using single-cell RNA sequencing, multiplexed immunofluorescence, and spatial transcriptomics to establish a cellular atlas of the JIA synovium. We identified distinct spatial tissue niches, composed of specific stromal and immune cell populations. In addition, we localized genes linked to arthritis severity and disease risk to effector cell populations, including tissue resident SPP1 ⁺ macrophages and fibrin-associated myeloid cells. Combined analyses of synovial fluid and peripheral blood from matched individuals revealed differences in cellular composition, signaling pathways, and transcriptional programs across these distinct anatomical compartments. Furthermore, our analysis revealed several pathogenic cell populations that are shared with adult-onset inflammatory arthritis, as well as age-associated differences in tissue vascularity, prominence of innate immunity, and enrichment of TGF-β–responsive stromal subsets that up-regulate expression of disease risk–associated genes. Overall, our findings demonstrate the need for age-specific analyses of synovial tissue pathology to guide targeted treatment strategies in JIA.

Psoriasis (Ps) is a debilitating immune-mediated chronic skin condition. It affects about 1–3% of the world population, with an 8–11% prevalence in Northern European populations. Tyrosine kinase 2 (TYK2) is a newly identified target for Ps. An independent non-coding genetic association with Ps has been identified ~400 kb upstream of TYK2. The variants making up the credible Ps Single-Nucleotide Polymorphism (SNP) set were identified in their genomic context with the potential to influence TYK2 expression by interacting with regulatory elements involved in gene regulation. Previous evidence from our laboratory has suggested that credible SNP sets in intronic regions can be distal regulators of the genes of interest through long-range chromatin interactions. We hypothesise that SNPs at ILF3 are distal regulators of TYK2 expression via long-range chromatin interactions and Ps risk. The dysregulation of the TYK2 pathway in Ps may be mediated by a combination of GWAS risk SNPs at ILF3 and TYK2 and downstream genes. We investigated this by employing functional genomics and molecular biology methods. We developed a CD4 T cell model system with Jurkat-dCAS9-VP64 and Jurkat-dCAS9-KRAB cells using CRISPR activation and CRISPR inhibition of the risk variants rs892086 and rs7248205, selected from the latest Ps GWAS SNP set for their long-range interaction and light Linkage Disequilibrium (R² > 0.8), respectively. Using CRISPR activation, we demonstrate here that these risk SNPs, although distal to TYK2, do indeed regulate the TYK2 gene. Investigations into annotating the TYK2 pathway using RNA-seq analysis revealed differentially regulated genes, including VEGFA, C1R, ADORA1, GLUD2, NDUFB8, and FCGR2C, which are thought to be implicated in Ps. These genes were observed to be associated with conditions such as psoriatic arthritis, atopic dermatitis, and systemic sclerosis when compared using published databases, which confirms their relevance and importance in inflammatory conditions. With the developed cell model systems using CRISPR technology and differential gene regulation, we demonstrate here that these genes have the potential to define the TYK2/Ps pathway and our understanding of the disease biology.

Psoriasis is an autoimmune cutaneous condition that significantly impacts quality of life and represents a burden on society due to its prevalence. Genome-wide association studies (GWASs) have pinpointed several psoriasis-related risk loci, underlining the disease’s complexity. Functional genomics is paramount to unveiling the role of such loci in psoriasis and disentangling its complex nature. In this review, we aim to elucidate the main findings in this field and integrate our discussion with gold-standard techniques in molecular biology—i.e., Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)—and high-throughput technologies. These tools are vital to understanding how disease risk loci affect gene expression in psoriasis, which is crucial in identifying new targets for personalized treatments in advanced precision medicine.

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1–3% of the world’s population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with Genome-Wide Association (GWAS) studies showing that many psoriasis risk genes lie along the IL-23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. This review is focused on the IL-23/Th17 axis, providing an insight into key cell types, cytokines, and intracellular signaling pathways involved. This includes examination of currently available biological treatments, time to relapse post drug withdrawal, and rates of primary/secondary drug failure, showing the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely to reduce the burden of disease for the longest period possible.

Psoriasis is a lifelong, systemic, immune mediated inflammatory skin condition, affecting 1-3% of the world’s population, with an impact on quality of life similar to diseases like cancer or diabetes. Genetics are the single largest risk factor in psoriasis, with GWAS studies showing that many psoriasis risk genes lie along the IL23/Th17 axis. Potential psoriasis risk genes determined through GWAS can be annotated and characterised using functional genomics, allowing the identification of novel drug targets and the repurposing of existing drugs. The pathogenesis of psoriasis is complex and focusing on the IL23/Th17 axis can provide insight into key cell types, cytokines and intracellular signaling pathways involved. Examination of currently available biological treatments, time to relapse post drug withdrawal and rates of drug primary/secondary drug failure show the need for greater understanding of the underlying genetic mechanisms of psoriasis and how they can impact treatment. This could allow for patient stratification towards the treatment most likely reduce dis-ease burden for the longest period possible.

Background: Psoriasis and its associated inflammatory arthritis Psoriatic Arthritis (PsA) are potentially life-ruining conditions associated with numerous comorbidities. A previously-identified genetic risk association for psoriasis and PsA lies in a non-coding region at chromosome 1p36.23, and as such functional validation is required to determine the genetic mechanism contributing to psoriatic disease risk. Results: rs11121131 – a variant in tight linkage with rs11121129, the lead GWAS variant for the 1p36.23 association – lies in a putative enhancer active in keratinocytes but not in immune cells. Promoter-capture Hi-C and H3K27Ac HiChIP showed keratinocyte-specific interactions between 1p36.23 and the TNFRSF9/PARK7/ERRFI1 gene locus ∼200Kb upstream of the risk locus. Deletion of the enhancer in HaCat keratinocytes led to a reduction in transcript levels of the gene ERRFI1 , a negative regulator of Epidermal Growth Factor Receptor (EGFR) signalling. CRISPR activation of the enhancer also affected ERRFI1 levels, but paradoxically showed that steady-state activation led to repression of ERRFI1 , accompanied by significant deposition of H3K27Me3 histone marks at both the enhancer and the ERRFI1 gene locus. ERRFI1 levels were shown to be increased in inflamed skin from a mouse model of psoriasis, further suggesting its involvement in disease. Conclusions: These data indicate rs11121131 lies in an enhancer which modulates ERRFI1 expression in keratinocytes, providing a likely risk mechanism for the 1p36.23 risk association. ERRFI1 represents a novel gene in the pathogenesis of psoriasis and PsA – improving our understanding of these diseases – and the ERRFI1/EGFR signalling axis may therefore be a target for new treatment modalities for psoriatic disease.