Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients

Highlights

• The DNA methylome of naïve CD4+ T cells in lupus patients has been characterized.

• We identified and replicated 86 CG sites that are differentially methylated in naïve CD4+ T cells from lupus patients.

• Interferon-regulated genes are significantly hypomethylated in naïve CD4+ T cells from lupus patients.

• Naïve CD4+ T cells are epigenetically poised to respond to type-1 interferon in lupus patients.

Abstract

Systemic lupus erythematosus is an autoimmune disease characterized by multi-system involvement and autoantibody production. Abnormal T cell DNA methylation and type-I interferon play an important role in the pathogenesis of lupus. We performed a genome-wide DNA methylation study in two independent sets of lupus patients and matched healthy controls to characterize the DNA methylome in naïve CD4+ T cells in lupus. DNA methylation was quantified for over 485,000 methylation sites across the genome, and differentially methylated sites between lupus patients and controls were identified and then independently replicated. Gene expression analysis was also performed from the same cells to investigate the relationship between the DNA methylation changes observed and mRNA expression levels. We identified and replicated 86 differentially methylated CG sites between patients and controls in 47 genes, with the majority being hypomethylated. We observed significant hypomethylation in interferon-regulated genes in naïve CD4+ T cells from lupus patients, including IFIT1, IFIT3, MX1, STAT1, IFI44L, USP18, TRIM22 and BST2, suggesting epigenetic transcriptional accessibility in these genetic loci. Indeed, the majority of the hypomethylated genes (21 out of 35 hypomethylated genes) are regulated by type I interferon. The hypomethylation in interferon-regulated genes was not related to lupus disease activity. Gene expression analysis showed overexpression of these genes in total but not naïve CD4+ T cells from lupus patients. Our data suggest epigenetic “poising” of interferon-regulated genes in lupus naïve CD4+ T cells, argue for a novel pathogenic implication for abnormal T cell DNA methylation in lupus, and suggest a mechanism for type-I interferon hyper-responsiveness in lupus T cells.

Introduction

Systemic lupus erythematosus is a chronic autoimmune disease characterized by the production of antinuclear antibody and multiple organ involvement. The etiology of lupus is incompletely understood, but clear evidence suggests an important role for abnormal T cell DNA methylation in the pathogenesis of the disease [1]. Indeed, demethylated T cells are sufficient to cause a lupus-like disease in mouse models [2].

DNA methylation is an epigenetic mechanism that regulates gene expression by altering transcriptional accessibility of regulatory regions within gene sequences. This chemical modification of cytosine residues most commonly occurs in CG dinucleotides, and is mediated by DNA methyltransferase enzymes [3]. In general, methylation of CG dinucleotides in regulatory sequences induces gene silencing, while hypomethylation allows for transcriptional chromatin accessibility, and active gene expression when appropriate transcription factors are available [3]. DNA methylation induces chromatin inaccessibility by several mechanisms, including recruitment of histone deacetylases that remove acetyl groups from histone tails thereby increasing the charge attraction between DNA and histone proteins to generate more compact chromatin configuration that prevents access by the transcriptional machinery [4].

DNA methylation plays an important role in T cell differentiation. Indeed, the interferon gamma locus demethylates upon T_H1 differentiation, and the interleukin (IL)-4, IL-5, and IL-13 common locus control region demethylates upon T_H2 differentiation, allowing for interferon gamma, and IL-4, IL-5, and IL-13 production in differentiated T_H1 and T_H2 cells, respectively [5]. In contrast, both loci are heavily methylated in naïve CD4+ T cells [5].

We have previously characterized DNA methylation changes in total CD4+ T cells from lupus patients and revealed wide-spread DNA methylation changes in patients compared to healthy controls [6]. Herein, we performed an extensive genome-wide DNA methylation study in naïve CD4+ T cells from lupus patients and controls, coupled with gene expression profiling from the same cells. We identified DNA methylation changes prior to T cell differentiation and activation in lupus and determined the effect of these methylation changes on gene expression.