Long Non-Coding RNA- Associated Competing Endogenous RNA Axes in T-Cells in Multiple Sclerosis

• Published in: Frontiers in immunology 2021-12, Vol.12, p.770679-770679
• Main Authors: Sabaie, Hani, Salkhordeh, Zoha, Asadi, Mohammad Reza, Ghafouri-Fard, Soudeh, Amirinejad, Nazanin, Askarinejad Behzadi, Mahla, Hussen, Bashdar Mahmud, Taheri, Mohammad, Rezazadeh, Maryam
• Format: Article
• Language: English
• Subjects: bioinformatics analysis; competing endogenous RNA; Computational Biology - methods; Databases, Genetic; Endopeptidases - genetics; Gene Regulatory Networks; Humans; Immunology; Kruppel-Like Transcription Factors - genetics; long non-coding RNA; microarray; MicroRNAs - genetics; multiple sclerosis; Multiple Sclerosis - genetics; RNA, Long Noncoding - genetics; RNA, Messenger - genetics; Signal Transduction - genetics; T-Lymphocytes - metabolism; Thiolester Hydrolases - genetics; Transcriptome - genetics
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2021.770679

Multiple sclerosis (MS) is an immune-mediated demyelinating and degenerative disease with unknown etiology. Inappropriate response of T-cells to myelin antigens has an essential role in the pathophysiology of MS. The clinical and pathophysiological complications of MS necessitate identification of potential molecular targets to understand the pathogenic events of MS. Since the functions and regulatory mechanisms of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in MS are yet uncertain, we conducted a bioinformatics analysis to explain the lncRNA-associated ceRNA axes to clarify molecular regulatory mechanisms involved in T-cells responses in MS. Two microarray datasets of peripheral blood T-cell from subjects with relapsing-remitting MS and matched controls containing data about miRNAs (GSE43590), mRNAs and lncRNAs (GSE43591) were downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs (DEmiRNAs), mRNAs (DEmRNAs), and lncRNAs (DElncRNAs) were identified by the limma package of the R software. Protein-protein interaction (PPI) network and module were developed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the Molecular Complex Detection (MCODE) Cytoscape plugin, respectively. Using DIANA-LncBase and miRTarBase, the lncRNA-associated ceRNA axes was constructed. We conducted a Pearson correlation analysis and selected the positive correlations among the lncRNAs and mRNAs in the ceRNA axes. Lastly, DEmRNAs pathway enrichment was conducted by the Enrichr tool. A ceRNA regulatory relationship among Small nucleolar RNA host gene 1 ( ), , YOD1 deubiquitinase ( ) and zinc finger protein 101 ( ) and downstream connected genes was identified. Pathway enrichment analysis showed that DEmRNAs were enriched in "Protein processing in endoplasmic reticulum" and "Herpes simplex virus 1 infection" pathways. To our knowledge, this would be the first report of a possible role of / / / axes in the pathogenesis of MS. This research remarks on the significance of ceRNAs and prepares new perceptions for discovering the molecular mechanism of MS.