Identification of Mechanisms by Which Genetic Susceptibility Loci Influence Systemic Sclerosis Risk Using Functional Genomics in Primary T Cells and Monocytes

Abstract

Objective Systemic sclerosis (SSc) is a complex autoimmune disease with a strong genetic component. However, most of the genes associated with the disease are still unknown because associated variants affect mostly noncoding intergenic elements of the genome. We used functional genomics to translate the genetic findings into a better understanding of the disease. Methods Promoter capture Hi‐C and RNA‐sequencing experiments were performed in CD4+ T cells and CD14+ monocytes from 10 SSc patients and 5 healthy controls to link SSc‐associated variants with their target genes, followed by differential expression and differential interaction analyses between cell types. Results We linked SSc‐associated loci to 39 new potential target genes and confirmed 7 previously known SSc‐associated genes. We highlight novel causal genes, such as CXCR5, as the most probable candidate gene for the DDX6 locus. Some previously known SSc‐associated genes, such as IRF8, STAT4, and CD247, showed cell type–specific interactions. We also identified 15 potential drug targets already in use in other similar immune‐mediated diseases that could be repurposed for SSc treatment. Furthermore, we observed that interactions were directly correlated with the expression of important genes implicated in cell type–specific pathways and found evidence that chromatin conformation is associated with genotype. Conclusion Our study revealed potential causal genes for SSc‐associated loci, some of them acting in a cell type–specific manner, suggesting novel biologic mechanisms that might mediate SSc pathogenesis.

Unraveling a novel dual-function regulatory element showing epistatic interaction with a variant that escapes genome-wide association studies

“…Currently, the exact mechanism underlying these dual elements in the same cell type remains unknown. However, there is supporting evidence for a model of enhancer-silencer activity in which the ESpromoter would make direct 3D contact with the promoters of the regulated genes 27 , likely facilitated by TFs and cofactors acting as intermediaries. Cis-regulatory elements are DNA fragments that serve as active hubs to recruit TFs through short DNA motifs to regulate transcription.…”

“…Prediction of the interaction between Genehancer regulatory elements and neighboring genes suggested that the ATP2B4 Epromoter may have four target promoters, including ATP2B4 , LAX1 , ZC3H11A, and OPTC (Figure 1A). Promoter capture Hi-C data from CD4+ T cells 27 , revealed a significant T-cell specific interaction between ATP2B4 Epromoter and both LAX1 and ATP2B4 promoters (Figure 1B, Figure S1). However, no significant interaction was detected between the ATP2B4 Epromoter and the ZC3H11A and OPTC genes in CD4+ T cells 27 .…”

“…Promoter capture Hi-C data from CD4+ T cells 27 , revealed a significant T-cell specific interaction between ATP2B4 Epromoter and both LAX1 and ATP2B4 promoters (Figure 1B, Figure S1). However, no significant interaction was detected between the ATP2B4 Epromoter and the ZC3H11A and OPTC genes in CD4+ T cells 27 .…”

Using Polygenic Risk Scores to Aid Diagnosis of Patients With Early Inflammatory Arthritis: Results From the Norfolk Arthritis Register

“…37 Future genetic studies such as functional genomics studies, which discover new diseaseassociated variants and functionally annotate known genetic risk variants with target genes and regulatory elements, can be incorporated into further iterations of the G-PROB tool, which may further improve its cross-ancestry performance and utility. 38,39 A second limitation relates to power; despite including a sample size nearly four times larger than the original study, 25 we still had relatively low numbers of patients with diagnoses less commonly made in patients with suspected early inflammatory arthritis (including gout) (Figure 1). In the context of NOAR and UK clinical practice, this is likely because patients with gout are diagnosed by clinicians outside of the rheumatology outpatient setting (eg, in primary care or in hospital).…”

Chromosome conformation capture approaches to investigate 3D genome architecture in Ankylosing Spondylitis

“…On the same line, promoter capture Hi-C and RNA-sequencing approaches were recently used to link associated variants of systemic sclerosis (a connective tissue immune-mediated disease) with their target genes, especially in CD4+T cells and CD14 + monocytes obtained from 10 patients and five matched healthy controls. The authors identified new potential targets genes and 15 other potential drug targets for repurposing of drugs already in use in other immune-mediated diseases ( Gonzalez-Serna et al, 2022 ).…”