Whole-transcriptome sequencing and ceRNA interaction network of temporomandibular joint osteoarthritis

Fan Wu; Yanxin An; Libo Zhou; Yuqing Zhao; Lei Chen; Jing Wang; Gaoyi Wu

doi:10.3389/fgene.2022.962574

Whole-transcriptome sequencing and ceRNA interaction network of temporomandibular joint osteoarthritis

Front Genet. 2022 Oct 5:13:962574. doi: 10.3389/fgene.2022.962574. eCollection 2022.

Authors

Fan Wu^{1

2}, Yanxin An³, Libo Zhou¹, Yuqing Zhao⁴, Lei Chen⁵, Jing Wang², Gaoyi Wu¹

Affiliations

¹ School of Basic Medicine, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China.
² Department of Implantology, School of Stomatology, National Clinical Research Center for Oral Diseases & State Key Laboratory of Military Stomatology & Shaanxi Key Laboratory of Stomatology, Fourth Military Medical University, Xi'an, China.
³ Department of General Surgery, The First Affiliated Hospital of Xi'an Medical University, Xi'an, China.
⁴ School of Stomatology, Heilongjiang Key Lab of Oral Biomedicine Materials and Clinical Application, Experimental Center for Stomatology Engineering, Jiamusi University, Jiamusi, China.
⁵ Department of Orthodontics, School and Hospital of Stomatology, Cheeloo College of Medicine, Shandong University & Shandong Key Laboratory of Oral Tissue Regeneration & Shandong Engineering Laboratory for Dental Materials and Oral Tissue Regeneration, Shandong University, Jinan, China.

Abstract

Purpose: The aim of this study was to conduct a comprehensive transcriptomic analysis to explore the potential biological functions of noncoding RNA (ncRNAs) in temporomandibular joint osteoarthritis (TMJOA). Methods: Whole transcriptome sequencing was performed to identify differentially expressed genes (DEGs) profiles between the TMJOA and normal groups. The functions and pathways of the DEGs were analyzed using Metascape, and a competitive endogenous RNA (ceRNA) network was constructed using Cytoscape software. Results: A total of 137 DEmRNAs, 65 DEmiRNAs, 132 DElncRNAs, and 29 DEcircRNAs were identified between the TMJOA and normal groups. Functional annotation of the DEmRNAs revealed that immune response and apoptosis are closely related to TMJOA and also suggested key signaling pathways related to TMJOA, including chronic depression and PPAR signaling pathways. We identified vital mRNAs, including Klrk1, Adipoq, Cryab, and Hspa1b. Notably, Adipoq expression in cartilage was significantly upregulated in TMJOA compared with normal groups (10-fold, p < 0.001). According to the functional analysis of DEmRNAs regulated by the ceRNA network, we found that ncRNAs are involved in the regulation of autophagy and apoptosis. In addition, significantly DEncRNAs (lncRNA-COX7A1, lncRNA-CHTOP, lncRNA-UFM1, ciRNA166 and circRNA1531) were verified, and among these, circRNA1531 (14.5-fold, p < 0.001) and lncRNA-CHTOP (14.8-fold, p < 0.001) were the most significantly downregulated ncRNAs. Conclusion: This study showed the potential of lncRNAs, circRNAs, miRNAs, and mRNAs may as clinical biomarkers and provides transcriptomic insights into their functional roles in TMJOA. This study identified the transcriptomic signatures of mRNAs associated with immunity and apoptosis and the signatures of ncRNAs associated with autophagy and apoptosis and provides insight into ncRNAs in TMJOA.

Keywords: competitive endogenous RNA; high-throughput sequencing; interaction network; noncoding RNA; temporomandibular joint osteoarthritis.