The SLE Transcriptome Exhibits Evidence of Chronic Endotoxin Exposure and Has Widespread Dysregulation of Non-Coding and Coding RNAs

Abstract

BackgroundGene expression studies of peripheral blood mononuclear cells from patients with systemic lupus erythematosus (SLE) have demonstrated a type I interferon signature and increased expression of inflammatory cytokine genes. Studies of patients with Aicardi Goutières syndrome, commonly cited as a single gene model for SLE, have suggested that accumulation of non-coding RNAs may drive some of the pathologic gene expression, however, no RNA sequencing studies of SLE patients have been performed. This study was designed to define altered expression of coding and non-coding RNAs and to detect globally altered RNA processing in SLE.MethodsPurified monocytes from eight healthy age/gender matched controls and nine SLE patients (with low-moderate disease activity and lack of biologic drug use or immune suppressive treatment) were studied using RNA-seq. Quantitative RT-PCR was used to validate findings. Serum levels of endotoxin were measured by ELISA.ResultsWe found that SLE patients had diminished expression of most endogenous retroviruses and small nucleolar RNAs, but exhibited increased expression of pri-miRNAs. Splicing patterns and polyadenylation were significantly altered. In addition, SLE monocytes expressed novel transcripts, an effect that was replicated by LPS treatment of control monocytes. We further identified increased circulating endotoxin in SLE patients.ConclusionsMonocytes from SLE patients exhibit globally dysregulated gene expression. The transcriptome is not simply altered by the transcriptional activation of a set of genes, but is qualitatively different in SLE. The identification of novel loci, inducible by LPS, suggests that chronic microbial translocation could contribute to the immunologic dysregulation in SLE, a new potential disease mechanism.

Monocyte Enhancers are Highly Altered in Systemic Lupus Erythematosus

“…These data suggest that SLE is associated with activation of genes with monocyte intrinsic functions. Indeed, our transcriptome analysis found increased expression of genes involved in cytokine production and immune responses [24]. Enhancer status gives powerful insights into both the history of the cell and its specific pattern of gene expression [15][16][56][57].…”

“…This study is unique because it utilized matched samples from the same patients and controls and because these same samples had previously been examined by RNA-seq and IRF1 ChIP-seq [24,39]. This allowed us great power to define associations.…”

“…The controls and the SLE samples were comparable in the average of non-CD14 + cells in the preparations. Clinical characteristics of the patients used for ChIPseq have been previously reported and are summarized in Supplementary Table 1 [24]. Patients were selected for low disease activity and minimal medications to limit confounders related to medications.…”

“…Immunoprecipitation with anti-GST (Invitrogen, Camarillo, CA, USA) and input were used to define background. The same samples had parallel RNA-seq performed, which has been previously reported [24]. The library preparation utilized the SOLiD ChIP-seq kit and was performed according to the manufacturer's instructions.…”

“…The binding of transcription factor IRF1 and the transcriptome of the same samples have been previously measured by ChIP-seq and RNA-seq, respectively [24,27]. The ChIP-seq reads of both histone modifications were mapped to human reference genome (hg19), after which the sequencing depth around 27,588 uniquely located TSSs annotated by RefSeq was summarized to obtain a measurement for each TSS and sample.…”