Expression Profile of Long Noncoding RNAs in Peripheral Blood Mononuclear Cells from Multiple Sclerosis Patients

Abstract

Aims: Long noncoding RNAs (lncRNAs) play a key role in regulating immunological functions. Their impact on the chronic inflammatory disease multiple sclerosis (MS), however, remains unknown. We investigated the expression of lncRNAs in peripheral blood mononuclear cells (PBMCs) of patients with MS and attempt to explain their possible role in the process of MS.

Methods: For this study, we recruited 26 patients with MS according to the revised McDonald criteria. Then, we randomly chose 6 patients for microarray analysis. Microarray assays identified outstanding differences in lncRNA expression, which were verified through real-time PCR. LncRNA functions were annotated for target genes using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, and regulatory relationships between lncRNAs and target genes were analyzed using the "cis" and "trans" model.

Results: There were 2353 upregulated lncRNAs, 389 downregulated lncRNAs, 1037 upregulated mRNAs, and 279 downregulated mRNAs in patients with MS compared to healthy control subjects (fold change >2.0). Real-time PCR results of six aberrant lncRNAs were consistent with the microarray data. The coexpression network comprised 864 lncRNAs and 628 mRNAs. Among differentially expressed lncRNAs, 10 lncRNAs were predicted to have 10 cis-regulated target genes, and 33 lncRNAs might regulate their trans target genes.

Conclusions: We identified a subset of dysregulated lncRNAs and mRNAs. The differentially expressed lncRNAs may be important in the process of MS. However, the specific molecular mechanisms and biological functions of these lncRNAs in the pathogenesis of MS need further study.

Keywords: Long noncoding RNAs; Microarray; Multiple sclerosis.

Figure 1

LncRNA and mRNA profiles of microarray data. (A, D). Log–log scatter plots of lncRNA and mRNA expression. The red and green points in the plot indicate more than 2‐fold change of lncRNAs and mRNAs between multiple sclerosis (MS) and healthy control samples. (B, E). Volcano plots of the differentially expressed lncRNAs and mRNAs. The red and green points in the plot represent the differentially expressed lncRNAs and mRNA having statistical significance. (C, F). Hierarchical clustering shows a distinguishable lncRNA and mRNA expression profile between the two groups. Plots here represent analysis of RNA extracted from peripheral blood mononuclear cells (PBMCs) obtained from 6 patients with MS and 5 healthy control subjects.

Figure 2

Comparison of lncRNA expression levels as determined by microarray and real‐time PCR analyses. Three upregulated and three downregulated differentially expressed lncRNAs were validated by real‐time PCR of RNA extracted from PBMCs from 20 patients with MS and 20 healthy control subjects. Each sample was analyzed in triplicate. Column heights represent mean fold changes in expression of the MS group. Real‐time PCR results are consistent with microarray data. ***P < 0.001: MS group versus healthy control group in real‐time PCR validation.

Figure 3

(A) Top 30 gene ontology (GO) terms for the difference in lncRNA coexpressed genes between patients with MS and healthy control subjects. (B) KEGG pathways analysis. Top 30 pathways for the difference in lncRNA coexpressed genes between the patients with MS and healthy control subjects.

Figure 4

(A) “TF–lncRNA” network comparison between the patients with MS and healthy control subjects. (B) “TF–lncRNA–target gene” core network of disrupted lncRNA expression in patients with MS versus healthy control subjects.