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IRF5 genetic risk variants drive myeloid-specific IRF5 hyperactivation and presymptomatic SLE
Dan Li, Bharati Matta, Su Song, Victoria Nelson, Kirsten Diggins, Kim R. Simpfendorfer, Peter K. Gregersen, Peter Linsley, Betsy J. Barnes
Dan Li, Bharati Matta, Su Song, Victoria Nelson, Kirsten Diggins, Kim R. Simpfendorfer, Peter K. Gregersen, Peter Linsley, Betsy J. Barnes
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Research Article Genetics Immunology

IRF5 genetic risk variants drive myeloid-specific IRF5 hyperactivation and presymptomatic SLE

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Abstract

Genetic variants within or near the interferon regulatory factor 5 (IRF5) locus associate with systemic lupus erythematosus (SLE) across ancestral groups. The major IRF5-SLE risk haplotype is common across populations, yet immune functions for the risk haplotype are undefined. We characterized the global immune phenotype of healthy donors homozygous for the major risk and nonrisk haplotypes and identified cell lineage–specific alterations that mimic presymptomatic SLE. Contrary to previous studies in B lymphoblastoid cell lines and SLE immune cells, IRF5 genetic variants had little effect on IRF5 protein levels in healthy donors. Instead, we detected basal IRF5 hyperactivation in the myeloid compartment of risk donors that drives the SLE immune phenotype. Risk donors were anti-nuclear antibody positive with anti-Ro and -MPO specificity, had increased circulating plasma cells and plasmacytoid dendritic cells, and had enhanced spontaneous NETosis. The IRF5-SLE immune phenotype was conserved over time and probed mechanistically by ex vivo coculture, indicating that risk neutrophils are drivers of the global immune phenotype. RNA-Seq of risk neutrophils revealed increased IRF5 transcript expression, IFN pathway enrichment, and decreased expression of ROS pathway genes. Altogether, the data support that individuals carrying the IRF5-SLE risk haplotype are more susceptible to environmental/stochastic influences that trigger chronic immune activation, predisposing to the development of clinical SLE.

Authors

Dan Li, Bharati Matta, Su Song, Victoria Nelson, Kirsten Diggins, Kim R. Simpfendorfer, Peter K. Gregersen, Peter Linsley, Betsy J. Barnes

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Figure 5

Risk neutrophils express elevated IRF5 transcript expression and are enriched for IRF7 and IFN-γ gene signatures.

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Risk neutrophils express elevated IRF5 transcript expression and are enr...
(A) RNA-Seq analysis of IRF5 transcript expression in neutrophils from risk (n = 5) and nonrisk (n = 6) donors. Median log2 expression of IRF5 between groups is shown by box plot (Wilcoxon’s test). The box plot depicts the minimum and maximum values (whiskers), the upper and lower quartiles, and the median. The length of the box represents the interquartile range. (B) Independent confirmation of IRF5 transcript expression in neutrophils from n = 8 risk and nonrisk donors by qPCR analysis. Data are represented as fold change in mRNA expression in risk compared with nonrisk (unpaired 2-tailed t test). (C) Heatmaps generated from RNA-Seq of risk and nonrisk neutrophils show the top 3 most enriched gene sets (IRF7/type I IFN, IFN-γ, and ROS). Relative gene expression was calculated as per-gene Z scores across all samples, and the mean Z score calculated for each gene per group is shown. (D) Neutrophil expression signatures of genes differentially expressed within each module/hallmark between risk and nonrisk donors are shown (limma’s roast function). Error bars show mean ± SEM. **P ≤ 0.01.

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