Identification of pain-related biomarkers and the associated potential molecular regulation mechanism in pulpitis by bioinformatics method
J Endod. 2026 Jun 29:S0099-2399(26)00321-3. doi: 10.1016/j.joen.2026.06.006. Online ahead of print.
ABSTRACT
INTRODUCTION: This study aims to screen pain-related genes through bioinformatics analysis and to explore their potential molecular regulatory mechanisms in pulpitis.
METHODS: Differentially expressed miRNAs were identified using datasets GSE77459 and HRA007469. Pain-related genes were obtained from the GeneCards database. Cytoscape was used for the ceRNA network visualization and analysis. MCODE was used to extract the subnetwork from the ceRNA network. A miRNA-mRNA-TF structure was constructed, and GO and KEGG analyses were performed. The LASSO regression model was constructed to predict pulpitis and CytoHubba analysis with the maximal clique centrality method was used to identify the hub RNAs. Finally, immunofluorescence was used to validate the expression of the screened biomarkers. Statistical analysis was conducted using the unpaired Student's t-test. p < 0.05 was considered statistically significant.
RESULTS: A total of 36 miRNAs exhibited consistent and statistically significant differential expression across GSE77459 and HRA007469. Meanwhile, 16,470 pain-related genes and 189 pulpitis pain-related genes were retrieved from GeneCards. A pain-associated ceRNA network was constructed, which integrated 26 miRNAs, 479 mRNAs, and 1 lncRNA. A subsequent MCODE-based module was identified, containing 11 miRNAs, 106 mRNAs, and 14 transcription factors. Among these, miR-223, miR-155, and miR-21 emerged as top candidate regulatory miRNAs, with NAMPT and ERBB4 as their common target genes. LASSO regression analysis identified SCD, FGL2, TET1, and PCDH10 as diagnostic biomarkers for pulpitis, with SCD exhibiting the highest interaction centrality score. Immunofluorescence analysis revealed that the expression levels of SCD, NAMPT and FGL2 were significantly higher in pulpitis.
CONCLUSIONS: MiR-21/155/223 and their target genes SCD, FGL2, TET1, PCDH10, NAMPT, ERBB4 may serve as key molecules which regulate the inflammatory response and pain sensitization in pulpitis.
PMID:42373071 | DOI:10.1016/j.joen.2026.06.006