Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus

Abstract

Systemic lupus erythematosus is a chronic-relapsing autoimmune disease of incompletely understood etiology. Recent evidence strongly supports an epigenetic contribution to the pathogenesis of lupus. To understand the extent and nature of dysregulated DNA methylation in lupus T cells, we performed a genome-wide DNA methylation study in CD4 (+) T cells in lupus patients compared to normal healthy controls. Cytosine methylation was quantified in 27,578 CG sites located within the promoter regions of 14,495 genes. We identified 236 hypomethylated and 105 hypermethylated CG sites in lupus CD4 (+) T cells compared to normal controls, consistent with widespread DNA methylation changes in lupus T cells. Of interest, hypomethylated genes in lupus T cells include CD9, which is known to provide potent T-cell co-stimulation signals. Other genes with known involvement in autoimmunity such as MMP9 and PDGFRA were also hypomethylated. The BST2 gene, an interferon-inducible membrane-bound protein that helps restrict the release of retroviral particles was also hypomethylated in lupus patients. Genes involved in folate biosynthesis, which plays a role in DNA methylation, were overrepresented among hypermethylated genes. In addition, the transcription factor RUNX3 was hypermethylated in patients, suggesting an impact on T-cell maturation. Protein-protein interaction maps identified a transcription factor, HNF4a, as a regulatory hub affecting a number of differentially methylated genes. Apoptosis was also an overrepresented ontology in these interaction maps. Further, our data suggest that the methylation status of RAB22A, STX1B2, LGALS3BP, DNASE1L1 and PREX1 correlates with disease activity in lupus patients.

Figure 1

Heatmap of differentially methylated genes between lupus patients and controls. Methylation values were standardized across rows and clustered with Euclidean distance metric and average linkage. Yellow/blue gradient represents standardized level of hypermethylation/hypomethylation in lupus patients compared to controls. The order of clustered genes is preserved in Supplemental Tables 1 and 2.

Figure 2

Interaction map between hypermethylated and hypomethylated genes in lupus CD4⁺ T cells and transcription factors affecting/affected by them. Green and red colors indicate hypomethylated and hypermethylated genes in lupus patients, respectively. White color indicates genes that are not user specified but incorporated into the network through relationships with other genes.