Whole-transcriptome analysis of periodontal tissue and construction of immune-related competitive endogenous RNA network

Abstract

Background In periodontitis, noncoding RNAs may play a regulatory role in the immune microenvironment through competitive endogenous RNA. We aimed to profile noncoding RNA expression and construct immune-related ceRNA network in periodontitis. Methods Five inflamed periodontal tissue and five healthy gingivae were collected for whole-transcriptome sequencing. Differential gene, functional enrichment, and protein–protein interaction network analysis were performed to explore the function of differentially expressed genes. CIBERSORTx was used to analyze level of immune cell infiltration in the periodontal tissue. An immune-related competitive endogenous RNA network was constructed and expression of key regulators in the network was validated. Results Compared with healthy gingiva, 200 mRNAs, 90 long noncoding RNAs, 65 microRNAs, and 518 circular RNAs were differentially expressed, and cell chemotaxis was significantly enhanced in inflamed periodontal tissue. Immune cell infiltration analysis showed that neutrophils, macrophages M1, T follicular helper cells, and naive B cells were significantly increased in periodontitis. Key regulators including JUN, FOS, THBS1, KLF2, WIF1, were identified and their expression was then validated. Conclusion We constructed an immune-related competitive endogenous RNA network in periodontal tissue, which provided new insights into immune homeostasis in periodontitis and laid a foundation for further study of noncoding RNAs. Key regulators in this network may be promising targets for future periodontitis treatment.

The expression levels of chemotaxis-related molecules CXC chemokine receptor 1, interleukin-8, and pro-platelet basic protein in gingival tissues

“…The results show neutrophil chemotaxis, chemokine activity, and CXCR binding were elevated in inflammatory gingival tissues according to the enrichment analysis of the C5 GO genomic dataset. 18 In addition, we identified 10 hub genes from the protein-protein interaction network using topological analysis. And most of the hub genes were associated with chemokines and chemokine receptors.…”

“…We found that CXCR1 and PPBP were also included. 18 As CXCR1 and PPBP are important members of chemotaxis-related molecules, and play an important role in the induction and activation of neutrophils together with IL-8, it is of interest how their expression in gingival tissues.…”