Identification of abnormally methylated differentially expressed genes in chronic periodontitis by integrated bioinformatics analysis

Article type: Research Article

Authors: Tian, Xiufen^{a; b; 1} | Zheng, Juan^{c; 1} | Luo, Yuanyuan^a | Wei, Chengshi^a | Ma, Jing^d | Wang, Dawei^{e; *} | Li, Keyi^{a; *}

Affiliations: [a] Department of Stomatology, Liaocheng People’s Hospital, Liaocheng, Shandong, China | [b] Department of Orthopaedics, School of Medicine, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China | [c] Department of Joint Laboratory for Translational Medicine Research, Liaocheng People’s Hospital, Liaocheng, Shandong, China | [d] Department of Scientific Research, Liaocheng People’s Hospital, Liaocheng, Shandong, China | [e] Department of Orthopaedics, Liaocheng People’s Hospital, Liaocheng, Shandong, China

Correspondence: [*] Corresponding authors: Dawei Wang, Department of Orthopaedics, Liaocheng People’s Hospital, Liaocheng, Shandong, China. E-mail: wdw62@sohu.com. Keyi Li, Department of Stomatology, Liaocheng People’s Hospital, Liaocheng, 252000 Shandong, China. Tel.: +86 0635 8277803 ; E-mail: lkyxyw@163.com.

Note: [1] These authors have contributed equally to this work.

Abstract: BACKGROUND: DNA methylation plays a vital role as an epigenetic change that contributes to chronic periodontitis. OBJECTIVE: This study aimed to integrate two methylation datasets (GSE173081 and GSE59962) and two gene expression datasets (GSE10334 and GES16134) to identify abnormally methylated differentially expressed genes related to chronic periodontitis. METHODS: Differentially methylated genes were obtained. Functional enrichment analysis of DMGs was performed. The protein-protein interaction (PPI) network was constructed using STRING and Cytoscape software. Finally, the hub genes were selected from the PPI network by using CytoHubba. RESULTS: In total, 122 hypomethylated and highly expressed genes were enriched in the biological mechanisms that are involved in the differentiation of extracellular matrix organization, extracellular structure organization, and cell chemotaxis. The three selected hub genes of the PPI network were IL1B, KDR, and MMP9. A total of 122 hypermethylated and lowly expressed genes were identified, and biological processes, such as cornification, epidermis development, skin development, and keratinocyte differentiation were enriched. CDSN DSG1, and KRT2 were identified as the top 3 hub genes of the PPI network. CONCLUSION: Based on the comprehensive bioinformatics analysis, six hub genes (IL1B, KDR, MMP9, CDSN DSG1, and KRT2) were associated with chronic periodontitis. Our findings provide novel insights into the mechanisms underlying epigenetic changes in chronic periodontitis.

Keywords: Periodontitis, methylation, transcription, bioinformatic analysis, protein-protein interaction, hub genes

DOI: 10.3233/THC-220137

Journal: Technology and Health Care, vol. 31, no. 3, pp. 809-819, 2023