Bioinformatics Identification of Candidate Biomarkers Associated with Periodontitis in Cytokine-Treated Periodontal Ligament Stem Cells

The primary objective of the current study was to investigate the potential molecular mechanism underlying cytokine-induced periodontal ligament stem cells (PDLSCs). Microarray data from the GSE260558 dataset were retrieved from the gene expression omnibus (GEO) database. After normalization, the dysregulated genes were identified. Then, the different expressed mRNAs (DE-mRNAs) were subjected to gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) enrichment analyses. Subsequently, hub genes were screened out based on protein-protein interaction (PPI) network. Finally, the competitive endogenous RNA (ceRNA) regulatory networks containing hub genes were established by using ENCORI website. A total of 739 different expressed lncRNAs (DE-lncRNAs) and 809 different expressed mRNAs (DE-mRNAs) were identified by using the limma package in the R programming language. Then, the GO and KEGG analyses demonstrated that the DE-mRNAs were closely associated with inflammation and extracellular matrix formation in cytokine-treated PDLSCs. A protein-protein interaction (PPI) network was constructed for DE-mRNAs, and hub genes were obtained by evaluating the degree. A total of 12 upregulated hub genes and 12 downregulated hub genes were screened. These upregulated and downregulated hub genes were then used to construct a ceRNA regulatory network, respectively. In these networks, upregulated ERC2-IT1 and downregulated EPB41L4A-AS1 were considered as key lncRNAs in periodontitis. In conclusion, the bioinformatics analysis revealed several key genes and a ceRNA regulatory network that participated in the progression of cytokine-induced PDLSCs. Although this study identified several candidate biomarkers related to periodontitis, further experimental validation in animal models or clinical samples is necessary.