Gene regulation in T-cells from PsA patients differs between peripheral blood and the inflamed joints: implications for the interpretation of GWAS signals

BackgroundGenome-wide association studies (GWAS) have identified variants that are associated with complex diseases such as Psoriatic Arthritis (PsA). The majority of these variants do not affect the coding sequence of proteins but rather regulatory elements which are highly cell type and state specific, and can affect distally located genes via chromatin interaction mechanisms.We and others have previously analysed GWAS loci for multiple conditions (including PsA and Rheumatoid Arthrtitis) in cell lines using functional genomics techniques, providing putative mechanisms to many loci with previously unknown function [1].However, multiple studies have identified large differences in gene regulatory mechanisms between cell lines and primary cells, which could significantly alter the proposed mechanisms. Differences between between samples from healthy volunteers and patients, in particular from the affected tissue, have although not been exhaustively investigated.ObjectivesTo assess the impact of using primary cells derived from PsA patients compared to healthy volunteers in functional genomics studies.MethodsCD4+ and CD8+ T cells were isolated from peripherial blood from 10 healthy controls and 48 PsA patients and from 6 PsA synovial fluid samples.We performed RNA-seq and ATAC-seq on these two cell types to analyse the global patterns of gene expression and chromatin activity.ResultsWe find subtle differences between PsA patients and healthy controls in cells isolated from blood. RNA-seq analysis identified only a handful of differentially expressed genes whilst ATAC-seq analysis identified only 28 differential loci.On the other hand, T cells isolated from synovial fluid showed significant differences compared to T cells isolated from patient’s blood. Interestingly, we find that CD4+ T cells show substantially more differentially expressed genes compared to CD8+ T cells (1168 vs 346 Log2FoldChange > 1, FDR < 0.01). Genes overexpressed in synovial CD4+ T cells are more strongly enriched for immune pathways such as cytokine signaling and T cell proliferation compared to synovial CD8+ T cellsWe also find that synovial CD4+ T cells highly overexpress MHC class II genes (Figure 1).Figure 1.Normalized counts of the alpha chains of MHC class 2 genes in CD4+ and CD8+ T cells purified from blood from healthy subjects and patients and synovial fluid.ConclusionThis preliminary analysis suggests that T cells isolated from peripherial blood do not seem to differ significantly between PsA patients and healthy controls. In contrast, cells isolated from synovial fluid are highly specialized and activated. Moreover, these cells do not resemble canonically activated T cells which means that this state can not be easily emulated in vitro.This study indicates the importance of not only studying GWAS loci in relevant primary cells from patients, but also that attention needs to be given to cells isolated from the affected site.References[1]Shi C, Ray-Jones H, Ding J, et al (2021) Chromatin Looping Links Target Genes with Genetic Risk Loci for Dermatological Traits. J Invest Dermatol 141:1975–1984. https://doi.org/10.1016/J.JID.2021.01.015AcknowledgementsThis work was funded by the Wellcome Trust (award references 207491/Z/17/Z and 215207/Z/19/Z), the Versus Arthritis (award reference 21754), the NIHR Manchester Biomedical Research Centre, and the Medical Research Council (award reference MR/N00017X/1).Disclosure of InterestsNone declared