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Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis.
PeerJ. 2019; 7:e7135.P

Abstract

Background

Pulpitis is a common inflammatory disease that affects dental pulp. It is important to understand the molecular signals of inflammation and repair associated with this process. Increasing evidence has revealed that long noncoding RNAs (lncRNAs), via competitively sponging microRNAs (miRNAs), can act as competing endogenous RNAs (ceRNAs) to regulate inflammation and reparative responses. The aim of this study was to elucidate the potential roles of lncRNA, miRNA and messenger RNA (mRNA) ceRNA networks in pulpitis tissues compared to normal control tissues.

Methods

The oligo and limma packages were used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively) based on expression profiles in two datasets, GSE92681 and GSE77459, from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were further analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Protein-protein interaction (PPI) networks and modules were established to screen hub genes using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the Molecular Complex Detection (MCODE) plugin for Cytoscape, respectively. Furthermore, an lncRNA-miRNA-mRNA-hub genes regulatory network was constructed to investigate mechanisms related to the progression and prognosis of pulpitis. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify critical lncRNAs that may significantly affect the pathogenesis in inflamed and normal human dental pulp.

Results

A total of 644 upregulated and 264 downregulated differentially expressed genes (DEGs) in pulpitis samples were identified from the GSE77459 dataset, while 8 up- and 19 downregulated probes associated with lncRNA were identified from the GSE92681 dataset. Protein-protein interaction (PPI) based on STRING analysis revealed a network of DEGs containing 4,929 edges and 623 nodes. Upon combined analysis of the constructed PPI network and the MCODE results, 10 hub genes, including IL6, IL8, PTPRC, IL1B, TLR2, ITGAM, CCL2, PIK3CG, ICAM1, and PIK3CD, were detected in the network. Next, a ceRNA regulatory relationship consisting of one lncRNA (PVT1), one miRNA (hsa-miR-455-5p) and two mRNAs (SOCS3 and PLXNC1) was established. Then, we constructed the network in which the regulatory relationship between ceRNA and hub genes was summarized. Finally, our qRT-PCR results confirmed significantly higher levels of PVT1 transcript in inflamed pulp than in normal pulp tissues (p = 0.03).

Conclusion

Our study identified a novel lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of pulpitis.

Authors+Show Affiliations

Department of Operative Dentistry and Endodontics, School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, People's Republic of China.Institute of Reproductive & Stem Cell Engineering, School of Basic Medical Science, Central South University, Changsha, Hunan, People's Republic of China.Department of Operative Dentistry and Endodontics, School of Stomatology, Xiangya Stomatological Hospital, Central South University, Changsha, Hunan, People's Republic of China.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31304055

Citation

Lei, Fangcao, et al. "Comprehensive Analysis of an lncRNA-miRNA-mRNA Competing Endogenous RNA Network in Pulpitis." PeerJ, vol. 7, 2019, pp. e7135.
Lei F, Zhang H, Xie X. Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis. PeerJ. 2019;7:e7135.
Lei, F., Zhang, H., & Xie, X. (2019). Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis. PeerJ, 7, e7135. https://doi.org/10.7717/peerj.7135
Lei F, Zhang H, Xie X. Comprehensive Analysis of an lncRNA-miRNA-mRNA Competing Endogenous RNA Network in Pulpitis. PeerJ. 2019;7:e7135. PubMed PMID: 31304055.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Comprehensive analysis of an lncRNA-miRNA-mRNA competing endogenous RNA network in pulpitis. AU - Lei,Fangcao, AU - Zhang,Han, AU - Xie,Xiaoli, Y1 - 2019/06/17/ PY - 2019/02/20/received PY - 2019/05/16/accepted PY - 2019/7/16/entrez PY - 2019/7/16/pubmed PY - 2019/7/16/medline KW - Bioinformatics analysis KW - Competing endogenous RNA network KW - Long noncoding RNA KW - Pulpitis SP - e7135 EP - e7135 JF - PeerJ JO - PeerJ VL - 7 N2 - Background: Pulpitis is a common inflammatory disease that affects dental pulp. It is important to understand the molecular signals of inflammation and repair associated with this process. Increasing evidence has revealed that long noncoding RNAs (lncRNAs), via competitively sponging microRNAs (miRNAs), can act as competing endogenous RNAs (ceRNAs) to regulate inflammation and reparative responses. The aim of this study was to elucidate the potential roles of lncRNA, miRNA and messenger RNA (mRNA) ceRNA networks in pulpitis tissues compared to normal control tissues. Methods: The oligo and limma packages were used to identify differentially expressed lncRNAs and mRNAs (DElncRNAs and DEmRNAs, respectively) based on expression profiles in two datasets, GSE92681 and GSE77459, from the Gene Expression Omnibus (GEO) database. Differentially expressed genes (DEGs) were further analyzed by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. Protein-protein interaction (PPI) networks and modules were established to screen hub genes using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the Molecular Complex Detection (MCODE) plugin for Cytoscape, respectively. Furthermore, an lncRNA-miRNA-mRNA-hub genes regulatory network was constructed to investigate mechanisms related to the progression and prognosis of pulpitis. Then, quantitative real-time polymerase chain reaction (qRT-PCR) was applied to verify critical lncRNAs that may significantly affect the pathogenesis in inflamed and normal human dental pulp. Results: A total of 644 upregulated and 264 downregulated differentially expressed genes (DEGs) in pulpitis samples were identified from the GSE77459 dataset, while 8 up- and 19 downregulated probes associated with lncRNA were identified from the GSE92681 dataset. Protein-protein interaction (PPI) based on STRING analysis revealed a network of DEGs containing 4,929 edges and 623 nodes. Upon combined analysis of the constructed PPI network and the MCODE results, 10 hub genes, including IL6, IL8, PTPRC, IL1B, TLR2, ITGAM, CCL2, PIK3CG, ICAM1, and PIK3CD, were detected in the network. Next, a ceRNA regulatory relationship consisting of one lncRNA (PVT1), one miRNA (hsa-miR-455-5p) and two mRNAs (SOCS3 and PLXNC1) was established. Then, we constructed the network in which the regulatory relationship between ceRNA and hub genes was summarized. Finally, our qRT-PCR results confirmed significantly higher levels of PVT1 transcript in inflamed pulp than in normal pulp tissues (p = 0.03). Conclusion: Our study identified a novel lncRNA-mediated ceRNA regulatory mechanisms in the pathogenesis of pulpitis. SN - 2167-8359 UR - https://www.unboundmedicine.com/medline/citation/31304055/Comprehensive_analysis_of_an_lncRNA_miRNA_mRNA_competing_endogenous_RNA_network_in_pulpitis_ L2 - https://doi.org/10.7717/peerj.7135 DB - PRIME DP - Unbound Medicine ER -
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