A combinative analysis of gene expression profiles and microRNA expression profiles identifies critical genes and microRNAs in oral lichen planus.
OBJECTIVE
Oral lichen planus (OLP) is a chronic inflammatory disease but aetiology and pathogenesis has not fully elucidated. To gain insight into the mechanism of OLP, bioinformatic analysis was performed in this study.


METHODS
GSE38616 and GSE38615 were downloaded from GEO, including 7 cases of OLP and 7 healthy controls. Differentially expressed genes (DEGs) and miRNAs (DEMs) between OLP and control were screened with package Limma of R. Potential regulatory miRNAs were screened via gene set enrichment analysis. A protein-protein interaction network was constructed for the DEGs. KEGG pathways for DEGs were revealed using Gene Set Analysis Toolkit V2.


RESULTS
After DEGs and DEMs were obtained, potential regulatory miRNAs of the DEGs were revealed and only miR-362 was differentially expressed in OLP compared with DEMs. Four targets of miR-362 were SLIT-ROBO Rho GTPase activating protein 2 (SRGAP2), vesicle-associated membrane protein 4 (VAMP4), leucine rich repeat transmembrane neuronal 4 (LRRTM4) and lysine (K)-specific demethylase5C (KDM5C). Identified DEGs were significantly enriched in olfactory transduction and ribosome pathways.


CONCLUSIONS
miR-362, targeting SRGAP2 and VAMP4, may be a potential risk miRNA to regulate OLP. The findings may provide potential biomarkers for diagnosis or treatment of the disease.
State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, Fourth Military Medical University, No. 145, Changle West Road, Xi'an, Shaanxi 710032, PR China. Electronic address: liuqing@fmmu.edu.cn.
Qing
Q
Liu
State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, Fourth Military Medical University, No. 145, Changle West Road, Xi'an, Shaanxi 710032, PR China.
Xinwen
X
Wang
State Key Laboratory of Military Stomatology, Department of Oral Pathology, School of Stomatology, Fourth Military Medical University, No. 145, Changle West Road, Xi'an, Shaanxi 710032, PR China.
Yuan
Y
Liu
State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, Fourth Military Medical University, No. 145, Changle West Road, Xi'an, Shaanxi 710032, PR China.
Minghui
M
Wei
State Key Laboratory of Military Stomatology, Department of Immunology, Fourth Military Medical University, No. 169, Changle West Road, Xi'an, Shaanxi 710032, PR China. Electronic address: chenlh@fmmu.edu.cn.
Lihua
L
Chen
D020690:GTPase-Activating Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D005819:Genetic Markers / Q000235:genetics; D056466:Histone Demethylases / Q000235:genetics; D006801:Humans; D017676:Lichen Planus, Oral / Q000235:genetics* / Q000378:metabolism; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics*; D058977:Molecular Sequence Annotation; D050683:R-SNARE Proteins / Q000235:genetics; D012333:RNA, Messenger / Q000096:biosynthesis; D059467:Transcriptome
D020690:GTPase-Activating Proteins; D005819:Genetic Markers; D035683:MicroRNAs; D050683:R-SNARE Proteins; D012333:RNA, Messenger; C501995:SRGAP2 protein, human; C476456:VAMP4 protein, human; D056466:Histone Demethylases; C086877:KDM5C protein, human
Differentially expressed genes; Differentially expressed microRNAs; KEGG pathway enrichment analysis; Oral lichen planus; Protein–protein interaction network