Background: The human microglial HMC3 cell line assumes an inflammatory phenotype when challenged with lipopolysaccharide (LPS). Long noncoding RNAs (lncRNAs) are emerging as key modulators of immune system by regulating the expression of inflammatory genes. Here, we identified the differentially expressed long non-coding RNAs (DElncRNAs) and correlated DEmRNAs and 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).
Results: We identified 5 DElncRNAs and 99 DEmRNAs including 4 novel DElncRNAs (AC083837.1, IRF1-AS1, LINC02605, and MIR3142HG) in microglia. The DElncRNAs with their correlated DEmRNAs 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.
Conclusions: These results provide insight into, and a resource for studying, the regulation of microglia-mediated neuro-inflammation and its potential therapy by small-molecule BET inhibitors.