Background: This bioinformatics study aimed to reveal potential cross-talk genes,
related pathways, and transcription factors between periimplantitis and rheumatoid
arthritis (RA).
Methods: The datasets GSE33774 (seven periimplantitis and eight control samples) and
GSE106090 (six periimplantitis and six control samples) were included from the National
Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO). A
differential expression analysis (p < 0.05 and |logFC (fold change)| ≥ 1) and a functional
enrichment analysis (p < 0.05) were performed. Based on this, a protein–protein
interaction (PPI) network was constructed by Cytoscape. RA-related genes were
extracted from DisGeNET database, and an overlap between periimplantitis-related
genes and these RA-related genes was examined to identify potential cross-talk genes.
Gene expression was merged between two datasets, and feature selection was
performed by Recursive Feature Elimination (RFE) algorithm. For the feature selection
cross-talk genes, support vector machine (SVM) models were constructed. The
expression of these feature genes was determined from GSE93272 for RA. Finally, a
network including cross-talk genes, related pathways, and transcription factors
was constructed.
Results: Periimplantitis datasets included 138 common differentially expressed genes
(DEGs) including 101 up- and 37 downregulated DEGs. The PPI interwork of
periimplantitis comprised 1,818 nodes and 2,517 edges. The RFE method selected six
features, i.e., MERTK, CD14, MAPT, CCR1, C3AR1, and FCGR2B, which had the highest
prediction. Out of these feature genes, CD14 and FCGR2B were most highly expressed in
periimplantitis and RA. The final activated pathway–gene network contained 181 nodes
and 360 edges. Nuclear factor (NF) kappa B signaling pathway and osteoclast
differentiation were identified as potentially relevant pathways.
Conclusions: This current study revealed FCGR2B and CD14 as the most relevant
potential cross-talk genes between RA and periimplantitis, which suggests a similarity
between RA and periimplantitis and can serve as a theoretical basis for future research.
| Identifer | oai:union.ndltd.org:DRESDEN/oai:qucosa:de:qucosa:84303 |
| Date | 24 March 2023 |
| Creators | Li, Shiyi, Zhou, Changqing, Xu, Yongqian, Wang, Yujia, Li, Lijiao, Pelekos, George, Ziebolz, Dirk, Schmalz, Gerhard, Qin, Zeman |
| Publisher | Frontiers Research Foundation |
| Source Sets | Hochschulschriftenserver (HSSS) der SLUB Dresden |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/publishedVersion, doc-type:article, info:eu-repo/semantics/article, doc-type:Text |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | 1664-3224, 702661 |
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