Analysis of Long Noncoding RNA and mRNA Expression Profiles in IL-9-Activated Astrocytes and EAE Mice

Abstract

Background/Aims: Multiple sclerosis (MS) is an autoimmune disease in the central nervous system associated with demyelination and axonal injury. Astrocyte activation is involved in the pathogenesis of MS and experimental autoimmune encephalomyelitis (EAE), an animal model of MS. This study was designed to find potential lncRNAs in EAE mice and activated astrocytes. Methods: we performed microarray analysis of lncRNAs from the brain tissues of EAE mice and primary mouse astrocytes treated with IL-9(50 ng/ml). 12 lncRNAs were validated through real-time PCR. Gene ontology and KEGG pathway analysis were applied to explore the potential functions of lncRNAs. Results: Differentially expressed 3300 lncRNAs and 3250 mRNAs were in the brain tissues of EAE mice, and 3748 lncRNAs and 3332 mRNAs were in activated astrocytes. Notably, there were 2 co-up-regulated lncRNAs and 3 co-down-regulated lncRNAs both in the brain tissues of EAE mice and in activated astrocytes, including Gm14005, Gm12478, mouselincRNA1117, AK080435, and mouselincRNA0681, which regulate the ER calcium flux kinetics, zinc finger protein and cell apoptosis. Similarly, there were 7 mRNAs co-up-regulated and 2 mRNAs co-down-regulated both in vivo and in vitro. Gene ontology and KEGG pathway analysis showed that the biological functions of differentially expressed mRNAs were associated with metabolism, development and inflammation. The results of realtime PCR validation were consistent with the data from the microarrays. Conclusions: Our data uncovered the expression profiles of lncRNAs and mRNAs in vivo and in vitro, which may help delineate the mechanisms of astrocyte activation during MS/EAE process.

HIV-1 Tat enhances purinergic P2Y4 receptor signaling to mediate inflammatory cytokine production and neuronal damage via PI3K/Akt and ERK MAPK pathways

“…Total RNA was extracted from astrocytes and hippocampal tissues according to manufactures instructions. Reverse transcription and real-time PCR (qPCR) assay was performed as previously described [47]. The sequences of primers are listed in Additional file 1: Table S1.…”

HIV-1 Nef-induced lncRNA AK006025 regulates CXCL9/10/11 cluster gene expression in astrocytes through interaction with CBP/P300

“…The expression profiles of lncRNAs and mRNAs were detected as previously described [ 49 ]. Primary mouse astrocytes treated with 50 ng/ml Nef protein (Abcam, ab90462) were detected using Mouse LncRNA Microarray v2.0 (8 × 60 K, Arraystar) by Kangchen Bio-tech (Shanghai, China) that designed for the global profiling of mouse LncRNAs and protein-coding transcripts.…”

“…Real-time PCR (real-time PCR) assay was detected as previously described [ 49 ]. In brief, the total RNA from cultured astrocytes was extracted with TRIzol reagent (Invitrogen).…”

“…Gene ontology (GO) and KEGG analysis were applied to determine the functions of differentially expressed mRNAs in biological pathways using the standard enrichment computation method [ 49 ]. The P value (hypergeometric P value) denotes the significance of the pathway correlated to the conditions.…”

Long noncoding RNAs associated with phenotypic severity in multiple sclerosis

“…Though the study was unable to identify differential expression of either the lncRNA candidate or its associated gene, significant correlation between lnc-IL-7R and IL-7Ra were seen in both MS and healthy groups. These studies suggest a potential functional role of lncRNA transcripts in regulation of gene targets in MS. Several studies using animal models have also considered the role of lncRNAs in MS pathogenesis (Duan et al, 2018;Guo et al, 2017;Li et al, 2018;Liu et al, 2018;Sun et al, 2017), or combinations of human participants and animal model studies (Masoumi et al, 2019;Pahlevan Kakhki et al, 2018). These studies have demonstrated the role of multiple lncRNA transcripts in differentiation of CD4 + T cell linages.…”