Development of Ferroptosis-Associated ceRNA Network in Periodontitis

Abstract

Objectives: Periodontitis is a chronic inflammatory illness that may lead to tooth loosening and even loss, and its pathogenesis is not fully understood. Ferroptosis is an iron-dependent, regulated cell death. The present study aims to find the key ferroptosis-related genes (FRGs) in periodontitis and develop an mRNA-miRNA-lncRNA network to deeply explore the pathogenesis of periodontitis.

Methods: Data from the Gene Expression Omnibus (GEO) database and FerrDb database were downloaded to discover the differentially expressed mRNA, miRNA, and FRGs. Functional enrichment analysis was conducted for the differentially expressed FRGs (DE-FRGs), including gene ontology, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and protein-protein interaction (PPI) network analysis. Targetscan and miRtarbase were used to estimate the miRNAs that DE-FRGs may interact with, whilst StarBase v3.0 was used for lncRNA-miRNA interaction.

Results: Seven DE-FRGs were identified through differential expression analysis. Interleukin 1 beta (IL1B) interacted with XBP1 and MMP13 in the PPI network. After taking the intersection between DE-miRNAs and predicted miRNAs, a ceRNA network containing IL1B, has-miR-185, has-miR-204, has-miR-211, has-miR-4306, and 28 lncRNAs was established.

Conclusions: Seven FRGs in periodontitis were identified, which might promote deeper understanding of ferroptosis in periodontitis.

Keywords: Ferroptosis; Noncoding RNA; Periodontitis; ceRNA network.

Fig. 1

Experimental flowchart.

Fig. 2

Differential expression analysis of GSE10334 and GSE54710. A, Volcano plot of mRNA expression level in GSE10334, mRNAs with adjusted P value <.01 and log2(FC) >1.0 are shown by the red dot, whereas mRNAs with adjusted P value <.01 and log2(FC) <−1 are shown by the blue dot. B, Volcano plot of miRNAs expression level in GSE54710, miRNAs, with P value <.05 and log2(FC) >0.5 are shown by the red dot, whereas miRNAs with P value <.05 and log2(FC) <−0.5, are shown by the blue dot. C, The heatmap shows the expression of the top 20 up-regulated mRNAs and down-regulated mRNAs. D, The heatmap shows the expression of the top 20 up-regulated miRNAs and down-regulated miRNAs. E, The Venn diagram shows the overlapping parts of the differentially expressed genes (DEGs) and ferroptosis-related genes (FRGs), identifying 7 differentially expressed ferroptosis-related genes (DE-FRGs). F, Spearman correlation analysis of the 7 DE-FRGs.

Fig. 3

ceRNA network of IL1B, has-miR-185, has-miR-204, has-miR-211, has-miR-4306, and 28 lncRNAs. A, The pink square represents mRNA, the green square represents miRNA, and the blue square represents lncRNA. B, The top 8 hub nodes were identified through the CytoHubba.

Fig. 4

Expression levels and receiver operating characteristic (ROC) analysis of the 7 differentially expressed ferroptosis-related genes (DE-FRGs) in GSE10334. A–G, Expression levels of IL1B, XBP1, MMP13, ALOX15B, ENPP2, SLC2A3, and RGS4. H, ROC results of IL1B, XBP1, MMP13, ALOX15B, ENPP2, SLC2A3, and RGS4.

Fig. 5

Functional enrichment analysis of differentially expressed ferroptosis-related genes (DE-FRGs). A, The gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of the 7 DE-FRGs. B, The protein–protein interaction (PPI) network of the DE-FRGs. DE-FRGs that did not interact with other proteins are not displayed.