Analysis of differentially expressed long non-coding RNAs in LPS-induced human HMC3 microglial cells

Long non-coding RNAs (lncRNAs) are emerging as key modulators of inflammatory gene expression, but their roles in neuroinflammation are poorly understood. Here, we identified the inflammation-related lncRNAs and correlated mRNAs of the lipopolysaccharide (LPS)-treated human microglial cell line HMC3...

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Bibliographic Details
Published in:BMC genomics 2022-12, Vol.23 (1), p.853-853, Article 853
Main Authors: Baek, Mina, Chai, Jin Choul, Choi, Hae In, Yoo, Eunyoung, Binas, Bert, Lee, Young Seek, Jung, Kyoung Hwa, Chai, Young Gyu
Format: Article
Language:English
Subjects:
Analysis
BET inhibitor
Cell Cycle Proteins - genetics
Gene Regulatory Networks
Health aspects
Human microglia
Humans
Inflammation - genetics
JQ1
Lipopolysaccharides
Lipopolysaccharides - pharmacology
Long non-coding RNA (LncRNA)
Microglia - metabolism
Neuroinflammation
Neuroinflammatory Diseases
Nuclear Proteins - genetics
RNA
RNA sequencing (RNA-seq)
RNA, Long Noncoding - genetics
RNA, Long Noncoding - metabolism
Transcription Factors - genetics
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Summary:Long non-coding RNAs (lncRNAs) are emerging as key modulators of inflammatory gene expression, but their roles in neuroinflammation are poorly understood. Here, we identified the inflammation-related lncRNAs and correlated mRNAs of the lipopolysaccharide (LPS)-treated human microglial cell line HMC3. We explored their potential roles and interactions using bioinformatics tools such as gene ontology (GO), kyoto encyclopedia of genes and genomes (KEGG), and weighted gene co-expression network analysis (WGCNA). We identified 5 differentially expressed (DE) lncRNAs, 4 of which (AC083837.1, IRF1-AS1, LINC02605, and MIR3142HG) are novel for microglia. The DElncRNAs with their correlated DEmRNAs (99 total) fell into two network modules that both were enriched with inflammation-related RNAs. However, treatment with the anti-inflammatory agent JQ1, an inhibitor of the bromodomain and extra-terminal (BET) protein BRD4, neutralized the LPS effect in only one module, showing little or even enhancing effect on the other. These results provide insight into, and a resource for studying, the regulation of microglia-mediated neuroinflammation and its potential therapy by small-molecule BET inhibitors.
ISSN:1471-2164
1471-2164
DOI:10.1186/s12864-022-09083-6