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. 2019 Jul;15(4):872-879.
doi: 10.5114/aoms.2018.79145. Epub 2018 Oct 19.

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

Qin Zhang  1   2 , Yan Liang  3 , Hui Yuan  4 , Si Li  1   2 , Jie-Bing Wang  1   2 , Xiao-Mei Li  5 , Jin-Hui Tao  5 , Hai-Feng Pan  1   2 , Dong-Qing Ye  1   2
Affiliations

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

Qin Zhang et al. Arch Med Sci. 2019 Jul.

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.

Keywords: RNA-seq; lncRNA; mRNA; miRNA; systemic lupus erythematosus.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Differentially expressed known RNAs between SLE and HC. Hierarchical analysis of known RNAs that were differentially expressed between two groups
Figure 2
Figure 2
Differentially expressed novel RNAs between SLE and HC. Hierarchical analysis of novel RNAs that were differentially expressed between two groups
See this image and copyright information in PMC

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References

    1. Grammatikos AP, Kyttaris VC, Kis-Toth K, et al. A T cell gene expression panel for the diagnosis and monitoring of disease activity in patients with systemic lupus erythematosus. Clin Immunol. 2014;150:192–200. - PMC - PubMed
    1. Kang SC, Hwang SJ, Chang YS, Chou CT, Tsai CY. Characteristics of comorbidities and costs among patients who died from systemic lupus erythematosus in Taiwan. Arch Med Sci. 2012;8:690–6. - PMC - PubMed
    1. Alexander JJ, Saxena AK, Bao L, Jacob A, Haas M, Quigg RJ. Prominent renal expression of a murine leukemia retrovirus in experimental systemic lupus erythematosus. J Am Soc Nephrol. 2002;13:2869–77. - PubMed
    1. Pignatelli M, Vilella AJ, Muffato M, et al. ncRNA orthologies in the vertebrate lineage. Database (Oxford) 2016;2016 - PMC - PubMed
    1. Shvedova AA, Yanamala N, Kisin ER, Khailullin TO, Birch ME, Fatkhutdinova LM. Integrated analysis of dysregulated ncRNA and mRNA expression profiles in humans exposed to carbon nanotubes. PLoS One. 2016;11:e0150628. - PMC - PubMed