Identification of Immune-Related Long Non-Coding RNAs for Pulpitis Prediction Based on Competing Endogenous RNAs

Pulpitis is a chronic inflammatory disease affecting oral health. We aim to identify immune-related lncRNAs via bioinformatics analyses and explore their functions through ceRNA networks.

The expression profiles of 6 patients with pulpitis and 8 normal dental pulp have been obtained from Genome Sequence Archive. The differentially expressed long non-coding RNAs (lncRNAs) between pulpitis and healthy samples were identified and the classification model was established by LASSO regression. We conducted single-sample gene-set enrichment analysis (ssGSEA) to determine the immune-related lncRNAs and screened their hallmark pathways. Further, weighted correlation network analysis (WGCNA) was performed to verify the function of immune lncRNAs. Finally, we constructed the lncRNA-miRNA-mRNA ceRNA network considering miRNA-target relationship from miRanda, negative miRNA-target expression correlation, and positive lncRNA-mRNA expression correlation.

A classification model of 5 lncRNAs was constructed. The lncRNAs CARD8-AS1 and LINC00924 were significantly related with immunity by ssGSEA. Further hallmark pathway analysis revealed that screened lncRNAs were significantly correlated with immune. WGCNA results implied CARD8-AS1 was in the Grey module and LINC00924 in the Brown module. Both Grey and Brown modules are significantly enriched in immune-related biological functions based on enrichment analysis. The immune-related ceRNA network was constructed for the lncRNAs CARD8-AS1 and LINC00924. Three miRNAs hsa-miR-3065-5p, hsa-miR-3910, and hsa-miR-514a-3p regulated both CARD8-AS1 and LINC00924. Particularly, CARD8-AS1 was confirmed to interact with immune-related genes through miRDB and TargetScan analyses. CARD8-AS1-associated mRNAs (PTGS2, NLRP3, and CXCL3) were identified through both functional enrichment analysis and a ceRNA network involving lncRNA-miRNA-mRNA interactions. These mRNAs showed significant enrichment in immune-related pathways such as the JAK-STAT signaling pathway, complement system, and TLR signaling.

The study found that lncRNA CARD8-AS1 and CARD8-AS1-based ceRNA network play an important role in regulating the immune response in pulpitis, and immune lncRNAs such as CARD8-AS1 can serve as new markers for non-invasive diagnosis.