Whole-genome transcription and DNA methylation analysis of peripheral blood mononuclear cells identified aberrant gene regulation pathways in systemic lupus erythematosus

Abstract

BackgroundRecent achievement in genetics and epigenetics has led to the exploration of the pathogenesis of systemic lupus erythematosus (SLE). Identification of differentially expressed genes and their regulatory mechanism(s) at whole-genome level will provide a comprehensive understanding of the development of SLE and its devastating complications, lupus nephritis (LN).MethodsWe performed whole-genome transcription and DNA methylation analysis in PBMC of 30 SLE patients, including 15 with LN (SLE LN+) and 15 without LN (SLE LN−), and 25 normal controls (NC) using HumanHT-12 Beadchips and Illumina Human Methy450 chips. The serum proinflammatory cytokines were quantified using Bio-plex Human Cytokine 27-plex assay. Differentially expressed genes and differentially methylated CpG were analyzed with GenomeStudio, R, and SAM software. The association between DNA methylation and gene expression were tested. Gene interaction pathways of the differentially expressed genes were analyzed by IPA software.ResultsWe identified 552 upregulated genes and 550 downregulated genes in PBMC of SLE. Integration of DNA methylation and gene expression profiling showed that 334 upregulated genes were hypomethylated, and 479 downregulated genes were hypermethylated. Pathway analysis on the differential genes in SLE revealed significant enrichment in interferon (IFN) signaling and toll-like receptor (TLR) signaling pathways. Nine IFN- and seven TLR-related genes were identified and displayed step-wise increase in SLE LN− and SLE LN+. Hypomethylated CpG sites were detected on these genes. The gene expressions for MX1, GPR84, and E2F2 were increased in SLE LN+ as compared to SLE LN− patients. The serum levels of inflammatory cytokines, including IL17A, IP-10, bFGF, TNF-α, IL-6, IL-15, GM-CSF, IL-1RA, IL-5, and IL-12p70, were significantly elevated in SLE compared with NC. The levels of IL-15 and IL1RA correlated with their mRNA expression. The upregulation of IL-15 may be regulated by hypomethylated CpG sites in the promotor region of the gene.ConclusionsOur study has demonstrated that significant number of differential genes in SLE were involved in IFN, TLR signaling pathways, and inflammatory cytokines. The enrichment of differential genes has been associated with aberrant DNA methylation, which may be relevant to the pathogenesis of SLE. Our observations have laid the groundwork for further diagnostic and mechanistic studies of SLE and LN.Electronic supplementary materialThe online version of this article (doi:10.1186/s13075-016-1050-x) contains supplementary material, which is available to authorized users.

Activating and inhibitory receptors on natural killer cells in patients with systemic lupus erythematosis-regulation with interleukin-15

“…Patients with active SLE disease have higher IL-15 levels than those with inactive disease. Our finding is consistent with Zhu et al who recently showed that the serum level of IL-15 was significantly elevated in SLE patients and correlated with their mRNA expression [30]. The upregulation of IL-15 may be regulated by hypomethylated CpG in the promoter region of the gene.…”

“…We found that NKG2D, another NK-activating receptors in SLE activated by NKG2D ligands, was under-expressed on circulating NK cells from SLE, consistent with previous reports [30,32]. We further found that NKG2D on CD56 dim NK cells is lower in SLE with active disease compared to inactive disease.…”

Clinical and Immunologic Profiles in Incomplete Lupus Erythematosus and Improvement with Hydroxychloroquine Treatment

“…Levels of cytokines were measured in serum samples using the Bio-Rad Human 27-Plex array (Bio-Rad, Hercules, CA, USA) which uses a magnetic bead-based technique [10]. Results are expressed as the mean of two replicates in pg/mL using standard curves provided by the manufacturer for each cytokine.…”

DNA methylation alterations in the pathogenesis of lupus

“…Currently, Zhu et al . even identified that 334 up‐regulated genes are hypomethylated, and 479 down‐regulated genes are hypermethylated in PBMC of SLE by performing whole‐genome transcription and DNA methylation analysis .…”