Integrated analysis of lncRNA, miRNA and mRNA expression profiling in patients with systemic lupus erythematosus

Abstract

Introduction A great deal of research has reported dysregulated expression of genes in systemic lupus erythematosus (SLE). This study aimed to analyze the lncRNA, miRNA and mRNA expression profile in SLE. Material and methods RNA sequencing (RNA-seq) was used to detect the dysregulated RNAs in SLE. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis were used to explore the function of these differentially expressed RNAs. Results 2,353 lncRNAs, 827 mRNAs and 24 miRNAs were shown to be differentially expressed. GO analyses demonstrated that differentially expressed RNAs were enriched in a variety of molecular functions and biological processes including ribonucleotide, protein serine/threonine kinase activity function, regulation of B cell differentiation and others. KEGG pathway analyses revealed that differentially expressed mRNAs and lncRNAs were both enriched in FcγR-mediated phagocytosis, glycosaminoglycan biosynthesis-chondroitin sulfate/dermatan sulfate and glyoxylate and dicarboxylate metabolism pathways. The up-regulated miRNAs target genes were mainly enriched in the nuclear factor-κB (NF-κB) signaling pathway. The down-regulated miRNAs target genes were significantly enriched in metabolism of xenobiotics by cytochrome P450, bile secretion and terpenoid backbone biosynthesis pathways. Conclusions The current study reveals a comprehensive expression profile of lncRNAs, miRNAs and mRNAs and implies potential regulatory functions of these RNAs which are involved in the pathogenesis of SLE.

Systemic Lupus Erythematosus Dysregulates the Expression of Long Noncoding RNAs in Placentas

“…Our RNA-seq analysis revealed 81 dysregulated lncRNAs in SLE placentas with more upregulated genes than down-regulated, which agrees with the pattern in monocyte-derived dendritic cells [33] but differs from the patterns reported in PBMCs and whole blood from SLE patients [15,34]. Among these dysregulated lncRNAs, NONHSAT192272.1 and NONHSAT192274.1 have been reported in whole blood [34], while NONHSAT022132.2 has been found in PBMCs from SLE patients [32]. Interestingly, all the above 3 genes in SLE placentas show different expression patterns compared with blood samples.…”

“…Our RNA-seq analysis also identi ed 211 dysregulated mRNAs in SLE placentas with more up-regulated genes than the down-regulated, showing different patterns from PBMCs and whole blood from SLE patients [15,16,34]. The distribution of SLE-dysregulated mRNAs and lncRNAs on different chromosomes was also analyzed.…”

“…In this study, we de ned, for the rst time, the lncRNA expression pro les of human placentas from SLE pregnancies, though lncRNA expression pro les of human SLE have been reported in peripheral blood mononuclear cells (PBMCs) [15, 16, 18-20, 31, 32], monocyte-derived dendritic cells [33] and whole blood [34]. Our RNA-seq analysis revealed 81 dysregulated lncRNAs in SLE placentas with more upregulated genes than down-regulated, which agrees with the pattern in monocyte-derived dendritic cells [33] but differs from the patterns reported in PBMCs and whole blood from SLE patients [15,34]. Among these dysregulated lncRNAs, NONHSAT192272.1 and NONHSAT192274.1 have been reported in whole blood [34], while NONHSAT022132.2 has been found in PBMCs from SLE patients [32].…”

Circulating exosomal lncRNAs in patients with chronic coronary syndromes

“…LncRNAs are noncoding RNAs longer than 200 nucleotides, which regulate gene expression at the transcriptional, post-transcriptional, and translational levels. Previous studies have proved that lncRNAs were involved in regulating pathophysiological conditions, such as cancer [22][23][24], autoimmune diseases [25], and others [26]. In CAD, lncRNAs were found to be differently expressed in atherosclerotic coronary artery plaques [27], and were proved to serve as biomarkers to diagnose CAD [11][12][13][14].…”

Involvement of long noncoding RNAs in the pathogenesis of autoimmune diseases

“…Accumulating evidence indicates that lncRNAs might contribute to the pathogenesis of SLE. Comprehensive analyses using microarray or RNA sequencing revealed greatly altered lncRNA expression profiles in the whole blood [ 93 ], PBMCs [ 94 ], T cells [ 95 ], monocyte-derived dendritic cells (moDCs) [ 96 ] and plasma [ 97 ] of SLE patients compared to those of healthy controls, and the expression of some of these differentially expressed lncRNAs might correlate with the disease activity of SLE patients.…”